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commit: 7d62034735e700ca67e977470d79f5571b15b221 |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Mon Oct 26 07:29:56 2015 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Mon Oct 26 07:32:25 2015 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7d620347 |
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|
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Drop "CCP4: Software for Macromolecular Crystallography" |
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obsoletes: |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196 |
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Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780 |
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|
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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app-office/sc/sc-7.16-r1.ebuild | 5 +- |
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dev-libs/libjwc_c/Manifest | 1 - |
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dev-libs/libjwc_c/files/612-gentoo.patch | 20 - |
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dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild | 31 -- |
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dev-libs/libjwc_c/metadata.xml | 8 - |
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dev-libs/libjwc_f/Manifest | 1 - |
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dev-libs/libjwc_f/files/612-gentoo.patch | 100 ---- |
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dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild | 38 -- |
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dev-libs/libjwc_f/metadata.xml | 8 - |
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profiles/arch/powerpc/package.use.force | 1 - |
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profiles/arch/powerpc/package.use.mask | 6 - |
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profiles/package.mask | 35 -- |
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sci-chemistry/arp-warp-bin/Manifest | 1 - |
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sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild | 81 --- |
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sci-chemistry/arp-warp-bin/files/7.3-setup.patch | 30 -- |
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sci-chemistry/arp-warp-bin/metadata.xml | 5 - |
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sci-chemistry/balbes/Manifest | 2 - |
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.../balbes/balbes-1.0.0_p100317-r2.ebuild | 79 --- |
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.../balbes/files/1.0.0_p100317-makefile.patch | 107 ---- |
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.../balbes/files/pyxml-0.8.4-python-2.6.patch | 28 - |
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sci-chemistry/balbes/metadata.xml | 18 - |
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sci-chemistry/ccp4-apps/Manifest | 2 - |
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sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild | 395 -------------- |
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.../ccp4-apps/files/6.1.3-clipper-template.patch | 70 --- |
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.../ccp4-apps/files/6.1.3-dont-build-balbes.patch | 14 - |
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.../6.1.3-dont-build-double-and-make-bindir.patch | 24 - |
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.../ccp4-apps/files/6.1.3-dont-build-imosflm.patch | 11 - |
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.../ccp4-apps/files/6.1.3-dont-build-libs.patch | 35 -- |
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.../ccp4-apps/files/6.1.3-dont-build-molref.patch | 19 - |
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.../ccp4-apps/files/6.1.3-dont-build-scala.patch | 42 -- |
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.../ccp4-apps/files/6.1.3-dont-build-xia.patch | 14 - |
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.../ccp4-apps/files/6.1.3-dont-configure.patch | 111 ---- |
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.../files/6.1.3-dont-make-dirs-in-configure.patch | 87 --- |
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sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch | 152 ------ |
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sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch | 597 --------------------- |
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sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch | 23 - |
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.../ccp4-apps/files/6.1.3-pythonpath.patch | 65 --- |
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.../ccp4-apps/files/6.1.3-rename-rapper-ng.patch | 60 --- |
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sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch | 131 ----- |
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.../ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch | 130 ----- |
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sci-chemistry/ccp4-apps/metadata.xml | 5 - |
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sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild | 38 -- |
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.../files/6.0.1-dont-make-dirs-in-configure.patch | 87 --- |
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.../files/6.0.1-ppc-double-define-gerror.patch | 11 - |
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.../files/6.0.2-dont-make-dirs-in-configure.patch | 87 --- |
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.../ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch | 14 - |
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.../files/6.0.2-ppc-double-define-gerror.patch | 11 - |
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.../ccp4/files/ccp4i-default-to-firefox.patch | 13 - |
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.../ccp4/files/check-blas-lapack-pthread.patch | 103 ---- |
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.../ccp4/files/clipper-find-mccp4-includes.patch | 11 - |
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.../ccp4/files/create-mosflm-bindir.patch | 10 - |
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sci-chemistry/ccp4/files/dont-build-rasmol.patch | 19 - |
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sci-chemistry/ccp4/files/make-ipmosflm-dir.patch | 10 - |
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.../ccp4/files/make-mosflm-cbf-libdir.patch | 11 - |
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.../ccp4/files/make-mosflm-index-libdir.patch | 10 - |
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sci-chemistry/ccp4/files/make-mosflm-libdir.patch | 10 - |
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.../ccp4/files/pass-clipper-enablevals.patch | 11 - |
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sci-chemistry/ccp4/metadata.xml | 9 - |
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sci-chemistry/ccp4i/Manifest | 3 - |
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sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild | 99 ---- |
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sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch | 22 - |
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.../ccp4i/files/6.1.3-rename-rapper.patch | 61 --- |
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.../ccp4i/files/6.1.3-rename-superpose.patch | 26 - |
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.../ccp4i/files/6.1.3-rename-truncate.patch | 91 ---- |
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sci-chemistry/ccp4i/metadata.xml | 5 - |
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sci-chemistry/coot/coot-0.7.1-r1.ebuild | 167 ------ |
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sci-chemistry/coot/coot-0.7.2.ebuild | 165 ------ |
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sci-chemistry/coot/coot-0.7.ebuild | 159 ------ |
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sci-chemistry/imosflm/Manifest | 1 - |
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sci-chemistry/imosflm/files/1.0.4-impl-dec.patch | 12 - |
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sci-chemistry/imosflm/files/1.0.4-tk.patch | 50 -- |
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sci-chemistry/imosflm/files/1.0.7-libpng16.patch | 13 - |
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sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild | 54 -- |
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sci-chemistry/imosflm/metadata.xml | 5 - |
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sci-chemistry/makecif/Manifest | 1 - |
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sci-chemistry/makecif/files/5.6.6-makefile.patch | 49 -- |
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sci-chemistry/makecif/makecif-5.6.6-r1.ebuild | 40 -- |
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sci-chemistry/makecif/makecif-5.6.6.ebuild | 39 -- |
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sci-chemistry/makecif/metadata.xml | 18 - |
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sci-chemistry/molrep/Manifest | 2 - |
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.../molrep/files/10.2.35-respect-FLAGS.patch | 61 --- |
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.../molrep/files/11.0.00-respect-FLAGS.patch | 12 - |
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sci-chemistry/molrep/files/11.0.00-test.patch | 191 ------- |
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sci-chemistry/molrep/files/11.0.03-EOR.patch | 16 - |
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sci-chemistry/molrep/metadata.xml | 8 - |
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sci-chemistry/molrep/molrep-11.0.02.ebuild | 57 -- |
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sci-chemistry/molrep/molrep-11.0.03-r1.ebuild | 59 -- |
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sci-chemistry/mosflm/Manifest | 1 - |
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sci-chemistry/mosflm/files/7.0.6-Makefile.patch | 13 - |
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sci-chemistry/mosflm/files/7.0.6-impl-dec.patch | 36 -- |
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sci-chemistry/mosflm/files/7.0.6-parallel.patch | 28 - |
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sci-chemistry/mosflm/files/7.0.7-parallel.patch | 92 ---- |
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sci-chemistry/mosflm/files/7.0.9-parallel.patch | 92 ---- |
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.../files/mosflm-7.0.7-buffer-overflow.patch | 16 - |
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.../mosflm/files/mosflm-7.0.7-impl-dec.patch | 29 - |
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.../files/mosflm-7.0.9-buffer-overflow.patch | 16 - |
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sci-chemistry/mosflm/metadata.xml | 8 - |
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sci-chemistry/mosflm/mosflm-7.0.9.ebuild | 74 --- |
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sci-chemistry/mrbump/Manifest | 1 - |
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sci-chemistry/mrbump/files/0.4.4-superpose.patch | 11 - |
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sci-chemistry/mrbump/metadata.xml | 10 - |
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sci-chemistry/mrbump/mrbump-0.4.4.ebuild | 57 -- |
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sci-chemistry/oasis/Manifest | 1 - |
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sci-chemistry/oasis/files/4.0-makefile.patch | 15 - |
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sci-chemistry/oasis/metadata.xml | 8 - |
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sci-chemistry/oasis/oasis-4.0-r3.ebuild | 70 --- |
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sci-chemistry/pdb-extract/Manifest | 2 - |
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.../files/pdb-extract-3.004-Makefile.patch | 46 -- |
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.../files/pdb-extract-3.004-cflags-install.patch | 199 ------- |
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.../pdb-extract/files/pdb-extract-3.004-env.patch | 11 - |
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.../files/pdb-extract-3.004-gcc-4.3.patch | 20 - |
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.../files/pdb-extract-3.11-cflags-install.patch | 207 ------- |
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.../files/pdb-extract-3.11-gcc-4.7.patch | 64 --- |
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sci-chemistry/pdb-extract/metadata.xml | 5 - |
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.../pdb-extract/pdb-extract-3.004-r2.ebuild | 71 --- |
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sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild | 60 --- |
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sci-chemistry/phaser/Manifest | 1 - |
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.../phaser/files/phaser-2.1.4-chmod.patch | 13 - |
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sci-chemistry/phaser/metadata.xml | 9 - |
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sci-chemistry/phaser/phaser-2.1.4.ebuild | 115 ---- |
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sci-chemistry/pointless/Manifest | 2 - |
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sci-chemistry/pointless/files/1.5.1-gcc4.4.patch | 12 - |
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sci-chemistry/pointless/metadata.xml | 8 - |
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sci-chemistry/pointless/pointless-1.6.14-r1.ebuild | 56 -- |
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sci-chemistry/pointless/pointless-1.6.14.ebuild | 60 --- |
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sci-chemistry/pointless/pointless-1.6.2.ebuild | 60 --- |
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sci-chemistry/refmac/Manifest | 2 - |
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sci-chemistry/refmac/files/5.5-test.log.patch | 32 -- |
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.../files/5.5.0110-allow-dynamic-linking.patch | 84 --- |
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sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch | 17 - |
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.../files/5.6.0110-allow-dynamic-linking.patch | 341 ------------ |
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.../files/5.6.0116-allow-dynamic-linking.patch | 341 ------------ |
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sci-chemistry/refmac/metadata.xml | 9 - |
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sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild | 85 --- |
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sci-chemistry/scala/Manifest | 1 - |
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sci-chemistry/scala/files/3.3.18-gcc4.6.patch | 17 - |
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sci-chemistry/scala/files/Makefile.am | 7 - |
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sci-chemistry/scala/files/configure.ac | 14 - |
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sci-chemistry/scala/metadata.xml | 13 - |
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sci-chemistry/scala/scala-3.3.20.ebuild | 38 -- |
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sci-chemistry/sfcheck/Manifest | 1 - |
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sci-chemistry/sfcheck/files/7.03.17-ldflags.patch | 12 - |
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sci-chemistry/sfcheck/metadata.xml | 5 - |
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sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild | 42 -- |
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sci-chemistry/solve-resolve-bin/Manifest | 2 - |
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sci-chemistry/solve-resolve-bin/metadata.xml | 8 - |
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.../solve-resolve-bin-2.13.ebuild | 68 --- |
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sci-chemistry/xdsi/Manifest | 1 - |
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sci-chemistry/xdsi/files/0.92-gentoo.patch | 27 - |
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sci-chemistry/xdsi/metadata.xml | 17 - |
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sci-chemistry/xdsi/xdsi-0.92-r1.ebuild | 54 -- |
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sci-chemistry/xia2/Manifest | 6 - |
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sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch | 61 --- |
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sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch | 61 --- |
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sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch | 61 --- |
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sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch | 61 --- |
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sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch | 28 - |
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sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch | 28 - |
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sci-chemistry/xia2/metadata.xml | 5 - |
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sci-chemistry/xia2/xia2-0.3.1.0.ebuild | 59 -- |
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sci-chemistry/xia2/xia2-0.3.1.6.ebuild | 66 --- |
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sci-chemistry/xia2/xia2-0.3.1.7.ebuild | 66 --- |
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sci-chemistry/xia2/xia2-0.3.3.1.ebuild | 70 --- |
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sci-chemistry/xia2/xia2-0.3.3.3.ebuild | 70 --- |
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sci-chemistry/xia2/xia2-0.3.4.0.ebuild | 70 --- |
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sci-libs/balbes-db/Manifest | 1 - |
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sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild | 47 -- |
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sci-libs/balbes-db/metadata.xml | 5 - |
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sci-libs/ccp4-libs/Manifest | 1 - |
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sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild | 359 ------------- |
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.../files/6.0.2-ppc-double-define-gerror.patch | 11 - |
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sci-libs/ccp4-libs/files/6.1.3-cbf.patch | 16 - |
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sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch | 33 -- |
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.../ccp4-libs/files/6.1.3-dont-build-mmdb.patch | 24 - |
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.../files/6.1.3-dont-make-dirs-in-configure.patch | 87 --- |
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sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch | 22 - |
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sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch | 140 ----- |
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sci-libs/ccp4-libs/files/6.1.3-lapack.patch | 597 --------------------- |
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sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch | 230 -------- |
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sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch | 87 --- |
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sci-libs/ccp4-libs/files/6.1.3-noinstall.patch | 142 ----- |
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sci-libs/ccp4-libs/files/6.1.3-overflows.patch | 35 -- |
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.../ccp4-libs/files/6.1.3-unbundle-libs-ng.patch | 367 ------------- |
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.../ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch | 395 -------------- |
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sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch | 203 ------- |
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.../ccp4-libs/files/ccp4-libs-6.1.3-force.patch | 16 - |
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.../files/ccp4-libs-6.1.3-format-security.patch | 16 - |
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sci-libs/ccp4-libs/metadata.xml | 9 - |
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sci-libs/clipper/clipper-2.1_p100511-r1.ebuild | 58 -- |
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sci-libs/coot-data/coot-data-2-r1.ebuild | 33 -- |
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sci-libs/coot-data/coot-data-2.ebuild | 33 -- |
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sci-libs/mmdb/mmdb-1.24.ebuild | 45 -- |
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sci-libs/mmdb/mmdb-1.25.5-r1.ebuild | 3 - |
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sci-libs/mmdb/mmdb-1.25.5.ebuild | 19 - |
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sci-libs/monomer-db/monomer-db-0.090729.ebuild | 31 -- |
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sci-libs/ssm/ssm-1.1.ebuild | 31 -- |
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sys-apps/coreutils/coreutils-8.20.ebuild | 2 +- |
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sys-apps/coreutils/coreutils-8.21.ebuild | 2 +- |
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sys-apps/coreutils/coreutils-8.22-r1.ebuild | 2 +- |
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sys-apps/coreutils/coreutils-8.22.ebuild | 2 +- |
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sys-apps/coreutils/coreutils-8.23.ebuild | 2 +- |
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sys-apps/coreutils/coreutils-8.24.ebuild | 2 +- |
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x11-libs/libxdl_view/Manifest | 1 - |
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x11-libs/libxdl_view/files/4.2-as-needed.patch | 16 - |
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x11-libs/libxdl_view/files/4.2-impl-dec.patch | 13 - |
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x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild | 32 -- |
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x11-libs/libxdl_view/metadata.xml | 8 - |
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207 files changed, 8 insertions(+), 11262 deletions(-) |
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|
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diff --git a/app-office/sc/sc-7.16-r1.ebuild b/app-office/sc/sc-7.16-r1.ebuild |
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index d9e0962..3c3083e 100644 |
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--- a/app-office/sc/sc-7.16-r1.ebuild |
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+++ b/app-office/sc/sc-7.16-r1.ebuild |
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@@ -3,6 +3,7 @@ |
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# $Id$ |
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|
257 |
EAPI=5 |
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+ |
259 |
inherit eutils multilib toolchain-funcs |
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|
261 |
DESCRIPTION="sc is a free curses-based spreadsheet program that uses key bindings similar to vi and less" |
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@@ -17,9 +18,7 @@ COMMON_DEPEND=">=sys-libs/ncurses-5.2" |
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DEPEND="virtual/pkgconfig" |
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RDEPEND=" |
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${COMMON_DEPEND} |
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- !dev-lang/stratego |
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- !<sci-chemistry/ccp4-apps-6.1.3-r4 |
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-" |
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+ !dev-lang/stratego" |
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|
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src_prepare() { |
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epatch \ |
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|
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diff --git a/dev-libs/libjwc_c/Manifest b/dev-libs/libjwc_c/Manifest |
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deleted file mode 100644 |
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index 91e153d..0000000 |
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--- a/dev-libs/libjwc_c/Manifest |
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+++ /dev/null |
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@@ -1 +0,0 @@ |
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-DIST libjwc_c-1.1.tar.gz 253637 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9 SHA512 5a095fdbf4f70d012f718d2bcd2a9689bf788801df3f3f97bead70861d08d5f6b5a9ac879e02c260974b755906d35de168646947900bcb18dad40839846d87ad WHIRLPOOL bca0bb19e2898c18f29a275c1997bf55058f5efbbc1147cb7e7a967f2eafb346c0d74975208dc6dd749ba60b256dca3c1548d9a58bd938fb19d77946a1aaa85a |
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|
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diff --git a/dev-libs/libjwc_c/files/612-gentoo.patch b/dev-libs/libjwc_c/files/612-gentoo.patch |
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deleted file mode 100644 |
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index af4a691..0000000 |
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--- a/dev-libs/libjwc_c/files/612-gentoo.patch |
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+++ /dev/null |
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@@ -1,20 +0,0 @@ |
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-diff -Nu libjwc_c-1.1/imglib.c libjwc_c/imglib.c |
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---- libjwc_c-1.1/imglib.c 1999-08-17 15:58:11.000000000 +0200 |
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-+++ libjwc_c/imglib.c 2004-06-03 14:24:05.000000000 +0200 |
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-@@ -4259,7 +4259,7 @@ |
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- { |
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- |
294 |
- /* Note: In this routine the first local axis is called 'x' and the |
295 |
-- second logal axi is called 'y' */ |
296 |
-+ second local axis is called 'y' */ |
297 |
- |
298 |
- int mxcent; /* Current max no. of elements in active |
299 |
- spots array */ |
300 |
-@@ -4469,6 +4469,7 @@ |
301 |
- |
302 |
- /* skipping condition */ |
303 |
- |
304 |
-+ iymid = (actspots[j].iyend+actspots[j].iybeg)/2; |
305 |
- itmp = abs(iymid-actspots[j].iycent); |
306 |
- if (abs((actspots[j].iyend+actspots[j].iybeg) -(iel+ibl))> |
307 |
- abs((actspots[j].iyend-actspots[j].iybeg) +(iel-ibl))&& |
308 |
|
309 |
diff --git a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild b/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild |
310 |
deleted file mode 100644 |
311 |
index cc9feb0..0000000 |
312 |
--- a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild |
313 |
+++ /dev/null |
314 |
@@ -1,31 +0,0 @@ |
315 |
-# Copyright 1999-2012 Gentoo Foundation |
316 |
-# Distributed under the terms of the GNU General Public License v2 |
317 |
-# $Id$ |
318 |
- |
319 |
-EAPI=4 |
320 |
- |
321 |
-AUTOTOOLS_AUTORECONF=yes |
322 |
- |
323 |
-inherit autotools-utils |
324 |
- |
325 |
-PATCH="612" |
326 |
- |
327 |
-DESCRIPTION="additional c library for ccp4" |
328 |
-HOMEPAGE="http://www.ccp4.ac.uk/main.html" |
329 |
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" |
330 |
- |
331 |
-SLOT="0" |
332 |
-LICENSE="GPL-2" |
333 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos" |
334 |
-IUSE="static-libs" |
335 |
- |
336 |
-DEPEND="sci-libs/ccp4-libs" |
337 |
-RDEPEND="${DEPEND}" |
338 |
- |
339 |
-PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch ) |
340 |
- |
341 |
-src_prepare() { |
342 |
- rm missing || die |
343 |
- echo "libjwc_c_la_LIBADD = -lm -lccp4f" >> Makefile.am || die |
344 |
- autotools-utils_src_prepare |
345 |
-} |
346 |
|
347 |
diff --git a/dev-libs/libjwc_c/metadata.xml b/dev-libs/libjwc_c/metadata.xml |
348 |
deleted file mode 100644 |
349 |
index d747d72..0000000 |
350 |
--- a/dev-libs/libjwc_c/metadata.xml |
351 |
+++ /dev/null |
352 |
@@ -1,8 +0,0 @@ |
353 |
-<?xml version="1.0" encoding="UTF-8"?> |
354 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
355 |
-<pkgmetadata> |
356 |
- <herd>sci</herd> |
357 |
- <maintainer> |
358 |
- <email>sci@g.o</email> |
359 |
- </maintainer> |
360 |
-</pkgmetadata> |
361 |
|
362 |
diff --git a/dev-libs/libjwc_f/Manifest b/dev-libs/libjwc_f/Manifest |
363 |
deleted file mode 100644 |
364 |
index 65e6fb7..0000000 |
365 |
--- a/dev-libs/libjwc_f/Manifest |
366 |
+++ /dev/null |
367 |
@@ -1 +0,0 @@ |
368 |
-DIST libjwc_f-1.1.tar.gz 170973 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199 SHA512 6d947e1513c137a23a4b6c2525e2a2f71c31a41f37455b9b3c97bd4c82128d5b3f4a7bfdd14aba57fbc258dcdcb8fa55e420a8573576992d0ae164bfe394f8d1 WHIRLPOOL 2652f3f43451cfb378d931ccff22a20131f2f44c40c2fe4c51ea45ef08f2e08306c1362f256c0c13014b9db3418ccbce437e4ccea41faae066c800a2ece02551 |
369 |
|
370 |
diff --git a/dev-libs/libjwc_f/files/612-gentoo.patch b/dev-libs/libjwc_f/files/612-gentoo.patch |
371 |
deleted file mode 100644 |
372 |
index e687d8b..0000000 |
373 |
--- a/dev-libs/libjwc_f/files/612-gentoo.patch |
374 |
+++ /dev/null |
375 |
@@ -1,100 +0,0 @@ |
376 |
-diff -Nu libjwc_f-1.1/configure.in ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in |
377 |
---- libjwc_f-1.1/configure.in 1999-10-21 16:07:14.000000000 +0200 |
378 |
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in 2004-03-11 17:31:45.000000000 +0100 |
379 |
-@@ -8,6 +8,7 @@ |
380 |
- AC_CANONICAL_SYSTEM |
381 |
- |
382 |
- AM_INIT_AUTOMAKE(libjwc_f, 1.1) |
383 |
-+AM_MAINTAINER_MODE |
384 |
- |
385 |
- case ${with_g77} in |
386 |
- "yes" ) CC="gcc" GCC=yes F77=g77 ;; |
387 |
-@@ -17,7 +18,7 @@ |
388 |
- AC_PROG_F77 |
389 |
- |
390 |
- AC_PROG_INSTALL |
391 |
--AC_PROG_RANLIB |
392 |
-+AC_PROG_LIBTOOL |
393 |
- |
394 |
- case "$target" in |
395 |
- *irix6* ) |
396 |
-@@ -26,8 +27,9 @@ |
397 |
- case "$FFLAGS" in |
398 |
- *-64* ) ;; # assume they meant it |
399 |
- *-o32* | *-32* ) ;; # presumably OK |
400 |
-- * ) FFLAGS="$FFLAGS -o32 -O -g3" |
401 |
-- CFLAGS=-32 |
402 |
-+ *-n32* ) ;; |
403 |
-+ * ) FFLAGS="$FFLAGS -n32 -O -g3" |
404 |
-+ CFLAGS=-n32 |
405 |
- AC_MSG_WARN([ |
406 |
- |
407 |
- *** Using compiler flag -o32 for probable compatibility with |
408 |
-@@ -47,8 +49,33 @@ |
409 |
- *** See the INSTALL file for more info. |
410 |
- ]) |
411 |
- fi ;; |
412 |
-+ *linux* ) |
413 |
-+ case $F77 in |
414 |
-+ g77*) |
415 |
-+ case "$FFLAGS" in |
416 |
-+ *no-second-underscore* ) ;; # presumably OK |
417 |
-+ * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;; |
418 |
-+ esac |
419 |
-+ esac ;; |
420 |
-+ *darwin* ) |
421 |
-+ case $F77 in |
422 |
-+ g77*) |
423 |
-+ case "$FFLAGS" in |
424 |
-+ *no-second-underscore* ) ;; # presumably OK |
425 |
-+ * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;; |
426 |
-+ esac |
427 |
-+#mac g77 currently goes not handle -fno-common |
428 |
-+ enable_shared=no; |
429 |
-+ esac ;; |
430 |
- * ) |
431 |
- esac |
432 |
-+# efc, version 7.1 at least does not support soname, so use CC |
433 |
-+case "$F77" in |
434 |
-+ *efc ) F77LD=${F77LD:-'${CC}'} ;; |
435 |
-+ * ) F77LD=${F77LD:-'${F77}'} |
436 |
-+esac |
437 |
-+ |
438 |
-+AC_SUBST(F77LD) |
439 |
- |
440 |
- AM_PROG_LIBTOOL |
441 |
- |
442 |
-Common subdirectories: libjwc_f-1.1/doc and ccp4-6.1.2/x-windows/libjwc/libjwc_f/doc |
443 |
-diff -Nu libjwc_f-1.1/opn_scr.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f |
444 |
---- libjwc_f-1.1/opn_scr.f 1999-09-07 12:50:13.000000000 +0200 |
445 |
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f 2000-10-25 13:03:09.000000000 +0200 |
446 |
-@@ -16,6 +16,6 @@ |
447 |
- C |
448 |
- C====== Open the file |
449 |
- C |
450 |
-- OPEN (IUN_SCR, STATUS='SCRATCH') |
451 |
-- RETURN |
452 |
-+C OPEN (IUN_SCR, STATUS='SCRATCH') |
453 |
-+ CALL CCPDPN(IUN_SCR,'JWCSCR','SCRATCH','U',0, IFAIL) |
454 |
- END |
455 |
-diff -Nu libjwc_f-1.1/rpf_dstar.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f |
456 |
---- libjwc_f-1.1/rpf_dstar.f 1999-07-09 13:39:38.000000000 +0200 |
457 |
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f 2004-06-04 12:10:59.000000000 +0200 |
458 |
-@@ -376,7 +376,8 @@ |
459 |
- INR_FLAG = 2 |
460 |
- PHIW = 0.0 |
461 |
- END IF |
462 |
-- ELSE |
463 |
-+ RETURN |
464 |
-+ ENDIF |
465 |
- C |
466 |
- C---- Calculate distance of edge of spot from sphere at end of rotation |
467 |
- Crotgen.for |
468 |
-@@ -418,7 +419,6 @@ |
469 |
- INR_FLAG = 4 |
470 |
- 40 RETURN |
471 |
- END IF |
472 |
-- END IF |
473 |
- END IF |
474 |
- RETURN |
475 |
- END |
476 |
|
477 |
diff --git a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild b/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild |
478 |
deleted file mode 100644 |
479 |
index 69a97bf..0000000 |
480 |
--- a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild |
481 |
+++ /dev/null |
482 |
@@ -1,38 +0,0 @@ |
483 |
-# Copyright 1999-2012 Gentoo Foundation |
484 |
-# Distributed under the terms of the GNU General Public License v2 |
485 |
-# $Id$ |
486 |
- |
487 |
-EAPI=4 |
488 |
- |
489 |
-AUTOTOOLS_AUTORECONF=yes |
490 |
- |
491 |
-inherit autotools-utils fortran-2 |
492 |
- |
493 |
-PATCH="612" |
494 |
- |
495 |
-DESCRIPTION="Additional fortran library for ccp4" |
496 |
-HOMEPAGE="http://www.ccp4.ac.uk/main.html" |
497 |
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" |
498 |
- |
499 |
-SLOT="0" |
500 |
-LICENSE="GPL-2" |
501 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos" |
502 |
-IUSE="static-libs" |
503 |
- |
504 |
-RDEPEND=" |
505 |
- dev-libs/libjwc_c |
506 |
- sci-libs/ccp4-libs" |
507 |
-DEPEND="${RDEPEND}" |
508 |
- |
509 |
-PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch ) |
510 |
- |
511 |
-src_prepare() { |
512 |
- rm missing || die |
513 |
- echo "libjwc_f_la_LIBADD = -ljwc_c -lccp4f" >> Makefile.am || die |
514 |
- autotools-utils_src_prepare |
515 |
-} |
516 |
- |
517 |
-src_install() { |
518 |
- autotools-utils_src_install |
519 |
- dohtml doc/* |
520 |
-} |
521 |
|
522 |
diff --git a/dev-libs/libjwc_f/metadata.xml b/dev-libs/libjwc_f/metadata.xml |
523 |
deleted file mode 100644 |
524 |
index d747d72..0000000 |
525 |
--- a/dev-libs/libjwc_f/metadata.xml |
526 |
+++ /dev/null |
527 |
@@ -1,8 +0,0 @@ |
528 |
-<?xml version="1.0" encoding="UTF-8"?> |
529 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
530 |
-<pkgmetadata> |
531 |
- <herd>sci</herd> |
532 |
- <maintainer> |
533 |
- <email>sci@g.o</email> |
534 |
- </maintainer> |
535 |
-</pkgmetadata> |
536 |
|
537 |
diff --git a/profiles/arch/powerpc/package.use.force b/profiles/arch/powerpc/package.use.force |
538 |
index d011e8f..846a4b6 100644 |
539 |
--- a/profiles/arch/powerpc/package.use.force |
540 |
+++ b/profiles/arch/powerpc/package.use.force |
541 |
@@ -15,5 +15,4 @@ net-p2p/sancho-bin java |
542 |
# sci-chemistry/arp-warp-bin is not available for ppc |
543 |
# sci-chemistry/solve-resolve-bin is not available for ppc |
544 |
# sci-chemistry/cns is not available for ppc |
545 |
-sci-chemistry/oasis minimal |
546 |
sci-libs/cctbx minimal |
547 |
|
548 |
diff --git a/profiles/arch/powerpc/package.use.mask b/profiles/arch/powerpc/package.use.mask |
549 |
index 4a791e4..cf9c154 100644 |
550 |
--- a/profiles/arch/powerpc/package.use.mask |
551 |
+++ b/profiles/arch/powerpc/package.use.mask |
552 |
@@ -291,12 +291,6 @@ mail-client/claws-mail pda |
553 |
# No media-sound/lilypond here, yet (bug #356069) |
554 |
app-text/asciidoc test |
555 |
|
556 |
-# Kacper Kowalik <xarthisius@g.o> (16 Jan 2011) |
557 |
-# bug 303931 |
558 |
-# dev-lang/icc is not available for ppc |
559 |
-# sci-chemistry/arp-warp-bin is not available for ppc |
560 |
-sci-chemistry/ccp4 arpwarp |
561 |
- |
562 |
# Justin Lecher <jlec@g.o> (01 Nov 2010) |
563 |
# Deps not Keyworded |
564 |
sci-chemistry/apbs fetk |
565 |
|
566 |
diff --git a/profiles/package.mask b/profiles/package.mask |
567 |
index ace3976..cdbcb01 100644 |
568 |
--- a/profiles/package.mask |
569 |
+++ b/profiles/package.mask |
570 |
@@ -241,41 +241,6 @@ net-firewall/shorewall6-lite |
571 |
=app-emulation/vmware-workstation-9* |
572 |
=app-emulation/vmware-modules-271* |
573 |
|
574 |
-# Justin Lecher <jlec@g.o> (15 Sep 2015) |
575 |
-# Outdated and multiple bugs |
576 |
-# Use upstream installer for up to version |
577 |
-dev-libs/libjwc_c |
578 |
-dev-libs/libjwc_f |
579 |
-sci-chemistry/arp-warp-bin |
580 |
-sci-chemistry/balbes |
581 |
-sci-chemistry/ccp4 |
582 |
-sci-chemistry/ccp4-apps |
583 |
-sci-chemistry/ccp4i |
584 |
-<sci-chemistry/coot-0.8 |
585 |
-sci-chemistry/imosflm |
586 |
-sci-chemistry/makecif |
587 |
-sci-chemistry/molrep |
588 |
-sci-chemistry/mosflm |
589 |
-sci-chemistry/mrbump |
590 |
-sci-chemistry/oasis |
591 |
-sci-chemistry/pdb-extract |
592 |
-sci-chemistry/pointless |
593 |
-sci-chemistry/refmac |
594 |
-sci-chemistry/scala |
595 |
-sci-chemistry/sfcheck |
596 |
-sci-chemistry/solve-resolve-bin |
597 |
-sci-chemistry/xdsi |
598 |
-sci-chemistry/xia2 |
599 |
-sci-libs/balbes-db |
600 |
-sci-libs/cctbx |
601 |
-<sci-libs/coot-data-3 |
602 |
-sci-libs/ccp4-libs |
603 |
-<=sci-libs/clipper-2.1_p100511-r1 |
604 |
-<sci-libs/mmdb-1.25.5-r1:0 |
605 |
-<sci-libs/monomer-db-5.41 |
606 |
-<sci-libs/ssm-1.4 |
607 |
-x11-libs/libxdl_view |
608 |
- |
609 |
# Michał Górny <mgorny@g.o> (09 Sep 2015) |
610 |
# Package to be used with gentoo-x86 CVS, so pretty much defunct now. |
611 |
# Removal in 30 days. Bug #560056. |
612 |
|
613 |
diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest |
614 |
deleted file mode 100644 |
615 |
index 739b86d..0000000 |
616 |
--- a/sci-chemistry/arp-warp-bin/Manifest |
617 |
+++ /dev/null |
618 |
@@ -1 +0,0 @@ |
619 |
-DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532 |
620 |
|
621 |
diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild |
622 |
deleted file mode 100644 |
623 |
index ef10d0a..0000000 |
624 |
--- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild |
625 |
+++ /dev/null |
626 |
@@ -1,81 +0,0 @@ |
627 |
-# Copyright 1999-2015 Gentoo Foundation |
628 |
-# Distributed under the terms of the GNU General Public License v2 |
629 |
-# $Id$ |
630 |
- |
631 |
-EAPI=5 |
632 |
- |
633 |
-inherit eutils prefix |
634 |
- |
635 |
-MY_P="arp_warp_${PV}" |
636 |
- |
637 |
-DESCRIPTION="Improvement and interpretation of crystallographic electron density maps" |
638 |
-SRC_URI="${MY_P}.tar.gz" |
639 |
-HOMEPAGE="http://www.embl-hamburg.de/ARP/" |
640 |
- |
641 |
-LICENSE="ArpWarp" |
642 |
-SLOT="0" |
643 |
-KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux" |
644 |
-IUSE="cpu_flags_x86_sse2" |
645 |
- |
646 |
-REQUIRED_USE="cpu_flags_x86_sse2" |
647 |
- |
648 |
-RDEPEND=" |
649 |
- app-shells/tcsh |
650 |
- sci-chemistry/refmac |
651 |
- virtual/awk |
652 |
- virtual/jre |
653 |
- virtual/opengl |
654 |
- x11-libs/libX11" |
655 |
-DEPEND="" |
656 |
- |
657 |
-RESTRICT="fetch" |
658 |
- |
659 |
-S="${WORKDIR}/${MY_P}" |
660 |
- |
661 |
-QA_PREBUILT="opt/arp-warp-bin/bin/*" |
662 |
- |
663 |
-pkg_nofetch(){ |
664 |
- elog "Fill out the form at http://www.embl-hamburg.de/ARP/" |
665 |
- elog "and place ${A} in ${DISTDIR}" |
666 |
-} |
667 |
- |
668 |
-src_prepare() { |
669 |
- epatch "${FILESDIR}"/7.3-setup.patch |
670 |
- eprefixify "${S}"/share/arpwarp_setup_base.* |
671 |
- |
672 |
- sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die |
673 |
-} |
674 |
- |
675 |
-src_install(){ |
676 |
- m_type=$(uname -m) |
677 |
- os_type=$(uname) |
678 |
- |
679 |
- exeinto /opt/${PN}/bin/bin-${m_type}-${os_type} |
680 |
- doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh} |
681 |
- |
682 |
- insinto /opt/${PN}/bin/bin-${m_type}-${os_type} |
683 |
- doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm} |
684 |
- |
685 |
- insinto /etc/profile.d/ |
686 |
- newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh |
687 |
- newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh |
688 |
- |
689 |
- dodoc "${S}"/README manual/UserGuide${PV}.pdf |
690 |
- dohtml -r "${S}"/manual/html/* |
691 |
-} |
692 |
- |
693 |
-pkg_postinst(){ |
694 |
- testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}') |
695 |
- if [ $testcommand == "1,5" ];then |
696 |
- ewarn "*** ERROR ***" |
697 |
- ewarn " 3/2=" $testcommand |
698 |
- ewarn "Invalid decimal separator (must be ".")" |
699 |
- ewarn "You need to set this correctly!!!" |
700 |
- echo |
701 |
- ewarn "One way of setting the decimal separator is:" |
702 |
- ewarn "setenv LC_NUMERIC C' in your .cshrc file" |
703 |
- ewarn "\tor" |
704 |
- ewarn "export LC_NUMERIC=C' in your .bashrc file" |
705 |
- ewarn "Otherwise please consult your system manager" |
706 |
- fi |
707 |
-} |
708 |
|
709 |
diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch |
710 |
deleted file mode 100644 |
711 |
index faed9c1..0000000 |
712 |
--- a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch |
713 |
+++ /dev/null |
714 |
@@ -1,30 +0,0 @@ |
715 |
-diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash |
716 |
-index 29e769c..0b8a51e 100644 |
717 |
---- a/share/arpwarp_setup_base.bash |
718 |
-+++ b/share/arpwarp_setup_base.bash |
719 |
-@@ -13,10 +13,10 @@ else |
720 |
- identifier=${nameprocessor}'-'${namesystem} |
721 |
- fi |
722 |
- # |
723 |
--arpwarphome="$1X" |
724 |
-+arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin" |
725 |
- # |
726 |
- export warpbin=${arpwarphome}/bin/bin-${identifier} |
727 |
--export warpdoc=${arpwarphome}/manual |
728 |
-+export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/ |
729 |
- export PATH=${warpbin}:${PATH} |
730 |
- # |
731 |
- # Checks for existence of $warpbin directory |
732 |
-diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh |
733 |
-index 41b11e9..a4edcff 100644 |
734 |
---- a/share/arpwarp_setup_base.csh |
735 |
-+++ b/share/arpwarp_setup_base.csh |
736 |
-@@ -13,7 +13,7 @@ else |
737 |
- set identifier = ${nameprocessor}'-'${namesystem} |
738 |
- endif |
739 |
- # |
740 |
--set arpwarphome = '$1X' |
741 |
-+set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin' |
742 |
- # |
743 |
- setenv warpbin ${arpwarphome}/bin/bin-${identifier} |
744 |
- # |
745 |
|
746 |
diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml |
747 |
deleted file mode 100644 |
748 |
index 51fdeda..0000000 |
749 |
--- a/sci-chemistry/arp-warp-bin/metadata.xml |
750 |
+++ /dev/null |
751 |
@@ -1,5 +0,0 @@ |
752 |
-<?xml version="1.0" encoding="UTF-8"?> |
753 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
754 |
-<pkgmetadata> |
755 |
- <herd>sci-chemistry</herd> |
756 |
-</pkgmetadata> |
757 |
|
758 |
diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest |
759 |
deleted file mode 100644 |
760 |
index c5f8b27..0000000 |
761 |
--- a/sci-chemistry/balbes/Manifest |
762 |
+++ /dev/null |
763 |
@@ -1,2 +0,0 @@ |
764 |
-DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c SHA512 0029e459877113de212574daec8532f0d225e96772c6a777d34af94e5f11c1253ca941266e68da79e0a5c5a96416a824f76c6f1d8652d9a60a34756989cae41e WHIRLPOOL 9024490eea43ef526f00aff9f2045e2689dd6d9e7575c9fd3de2a23fc4af3ad784660df4c78c9aa6380df1dac9fbf46c8b6be105a3094761ebdd43c5cb541beb |
765 |
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c |
766 |
|
767 |
diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild |
768 |
deleted file mode 100644 |
769 |
index 5334207..0000000 |
770 |
--- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild |
771 |
+++ /dev/null |
772 |
@@ -1,79 +0,0 @@ |
773 |
-# Copyright 1999-2012 Gentoo Foundation |
774 |
-# Distributed under the terms of the GNU General Public License v2 |
775 |
-# $Id$ |
776 |
- |
777 |
-EAPI=3 |
778 |
- |
779 |
-CCP4VER="6.1.3" |
780 |
-PYTHON_DEPEND="2" |
781 |
- |
782 |
-inherit eutils fortran-2 python toolchain-funcs |
783 |
- |
784 |
-DESCRIPTION="Automated molecular replacement (MR) pipeline" |
785 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html" |
786 |
-SRC_URI=" |
787 |
- mirror://gentoo/${P}.tar.gz |
788 |
- ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz" |
789 |
- |
790 |
-SLOT="0" |
791 |
-LICENSE="ccp4" |
792 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
793 |
-IUSE="" |
794 |
- |
795 |
-# bundled PyXML is modified and cannot be replaced |
796 |
- |
797 |
-COMMON_DEPEND="sci-libs/ccp4-libs" |
798 |
-RDEPEND="${COMMON_DEPEND} |
799 |
- ~sci-libs/balbes-db-${CCP4VER} |
800 |
- !<=sci-chemistry/ccp4-apps-6.1.3-r1" |
801 |
-DEPEND="${COMMON_DEPEND}" |
802 |
- |
803 |
-S="${WORKDIR}"/src |
804 |
- |
805 |
-pkg_setup() { |
806 |
- fortran-2_pkg_setup |
807 |
- python_set_active_version 2 |
808 |
-} |
809 |
- |
810 |
-src_unpack() { |
811 |
- unpack ${P}.tar.gz |
812 |
- tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \ |
813 |
- ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ |
814 |
- ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 |
815 |
- python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes |
816 |
-} |
817 |
- |
818 |
-src_prepare() { |
819 |
- mkdir "${WORKDIR}"/bin || die |
820 |
- epatch "${FILESDIR}"/${PV}-makefile.patch |
821 |
- cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/ |
822 |
- epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch |
823 |
-} |
824 |
- |
825 |
-src_compile() { |
826 |
- emake \ |
827 |
- BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die |
828 |
- cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 |
829 |
- find build -delete |
830 |
- $(PYTHON) setup.py build |
831 |
- find xml/xslt test -delete |
832 |
-} |
833 |
- |
834 |
-src_install() { |
835 |
- insinto /usr/share/balbes/BALBES_0.0.1/ |
836 |
- doins -r \ |
837 |
- "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ |
838 |
- "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die |
839 |
- dobin \ |
840 |
- "${WORKDIR}"/bin/* \ |
841 |
- "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \ |
842 |
- || die |
843 |
-} |
844 |
- |
845 |
-pkg_postinst() { |
846 |
- python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} |
847 |
-} |
848 |
- |
849 |
-pkg_postrm() { |
850 |
- python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} |
851 |
-} |
852 |
|
853 |
diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch |
854 |
deleted file mode 100644 |
855 |
index da17240..0000000 |
856 |
--- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch |
857 |
+++ /dev/null |
858 |
@@ -1,107 +0,0 @@ |
859 |
-diff --git a/makefile b/makefile |
860 |
-index baaceb5..85a7baf 100755 |
861 |
---- a/makefile |
862 |
-+++ b/makefile |
863 |
-@@ -70,6 +70,15 @@ OBJDB_G = get_pdb_list.o |
864 |
- |
865 |
- #OBJDB_Z = blanc2mtz.o libutils.o |
866 |
- |
867 |
-+# incomplete targets: |
868 |
-+# dimer_search_db domain_search_db domain align3 |
869 |
-+all: search_db get_structure_db manage_db search_dm dom2ch \ |
870 |
-+ save_si get_pdb_list_db update_db \ |
871 |
-+ update_dom_db bl2mtz check_file_db fobs2cif sol_check \ |
872 |
-+ get_trns p2s check_cell alt_sg \ |
873 |
-+ align cell_list create_bins \ |
874 |
-+ get_pdb_list_db get_ch get_nm get_mod |
875 |
-+ |
876 |
- search_db: sdb_l |
877 |
- |
878 |
- get_structure_db: tdb_l |
879 |
-@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f |
880 |
- $(BLANC_FORT) -c save_seg_id.f |
881 |
- |
882 |
- sdb_l: $(OBJDB_S) |
883 |
-- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) |
884 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) |
885 |
- tdb_l: $(OBJDB_T) |
886 |
-- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) |
887 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) |
888 |
- mdb_l: $(OBJDB_M) |
889 |
-- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) |
890 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) |
891 |
- mdm_l: $(OBJDB_MD) |
892 |
-- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) |
893 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) |
894 |
- d2c_l: $(OBJDB_A) |
895 |
-- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) |
896 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) |
897 |
- upd_l: $(OBJDB_U) |
898 |
-- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) |
899 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) |
900 |
- dom_l: $(OBJDB_V) |
901 |
-- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) |
902 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) |
903 |
- ddb_l: $(OBJDB_D) |
904 |
-- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) |
905 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) |
906 |
- dmdb_l: $(OBJDB_N) |
907 |
-- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) |
908 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) |
909 |
- gdb_l: $(OBJDB_G) |
910 |
-- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) |
911 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) |
912 |
- b2m_l: blanc2mtz.o libutils.o |
913 |
-- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a |
914 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c |
915 |
- f2c_l: f2cif.o libutils.o |
916 |
-- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o |
917 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o |
918 |
- chf_l: check_file_DB.o libutils.o |
919 |
-- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o |
920 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o |
921 |
- chc_l: check_cell_sg.o libutils.o |
922 |
-- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o |
923 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o |
924 |
- asl_l: alt_sg_list.o libutils.o |
925 |
-- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o |
926 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o |
927 |
- sc_l: $(OBJDB_C) |
928 |
-- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) |
929 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) |
930 |
- gt_l: $(OBJDB_R) |
931 |
-- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) |
932 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) |
933 |
- dmn_l: domain.o libutils.o |
934 |
-- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o |
935 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o |
936 |
- pack: pdb_pack.o libutils.o |
937 |
-- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o |
938 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o |
939 |
- p2s_l: $(OBJDB_P) |
940 |
-- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) |
941 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) |
942 |
- aln_l: align_DB.o DB_subr.o libutils.o |
943 |
-- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o |
944 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o |
945 |
- aln3_l: align_DB_new.o DB_subr.o libutils.o |
946 |
-- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o |
947 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o |
948 |
- cell_l: create_cell_list.o DB_subr.o libutils.o |
949 |
-- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o |
950 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o |
951 |
- getch_l: get_chain.o DB_subr.o libutils.o |
952 |
-- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o |
953 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o |
954 |
- getnmr_l: get_nmr.o DB_subr.o libutils.o |
955 |
-- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o |
956 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o |
957 |
- getmod_l: get_model.o libutils.o |
958 |
-- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o |
959 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o |
960 |
- crb_l: create_binaries.o DB_subr.o libutils.o |
961 |
-- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o |
962 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o |
963 |
- save_si_l: save_seg_id.o DB_subr.o libutils.o |
964 |
-- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o |
965 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o |
966 |
|
967 |
diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch |
968 |
deleted file mode 100644 |
969 |
index d29b0b6..0000000 |
970 |
--- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch |
971 |
+++ /dev/null |
972 |
@@ -1,28 +0,0 @@ |
973 |
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py |
974 |
---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900 |
975 |
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:57:02.000000000 +0900 |
976 |
-@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP |
977 |
- self._rel = rel |
978 |
- nt = ParsedNodeTest.ParsedNodeTest('node', '') |
979 |
- ppl = ParsedPredicateList.ParsedPredicateList([]) |
980 |
-- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') |
981 |
-- self._step = ParsedStep.ParsedStep(as, nt, ppl) |
982 |
-+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') |
983 |
-+ self._step = ParsedStep.ParsedStep(as_, nt, ppl) |
984 |
- return |
985 |
- |
986 |
- def evaluate(self, context): |
987 |
-diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py |
988 |
---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900 |
989 |
-+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:58:58.000000000 +0900 |
990 |
-@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP |
991 |
- self._right = right |
992 |
- nt = ParsedNodeTest.ParsedNodeTest('node','') |
993 |
- ppl = ParsedPredicateList.ParsedPredicateList([]) |
994 |
-- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') |
995 |
-- self._middle = ParsedStep.ParsedStep(as, nt, ppl) |
996 |
-+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') |
997 |
-+ self._middle = ParsedStep.ParsedStep(as_, nt, ppl) |
998 |
- |
999 |
- def evaluate(self, context): |
1000 |
- res = [] |
1001 |
|
1002 |
diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml |
1003 |
deleted file mode 100644 |
1004 |
index 4bb6be5..0000000 |
1005 |
--- a/sci-chemistry/balbes/metadata.xml |
1006 |
+++ /dev/null |
1007 |
@@ -1,18 +0,0 @@ |
1008 |
-<?xml version="1.0" encoding="UTF-8"?> |
1009 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
1010 |
-<pkgmetadata> |
1011 |
- <herd>sci-chemistry</herd> |
1012 |
- <maintainer> |
1013 |
- <email>jlec@g.o</email> |
1014 |
- </maintainer> |
1015 |
- <longdescription> |
1016 |
- BALBES is a system for solving protein structures using x-ray |
1017 |
- crystalographic data. Molecular Replacement(MR) is its core |
1018 |
- scientific method. BALBES aims to integrate all components, |
1019 |
- necessary for finding a solution structure by MR, into one system. |
1020 |
- It consists of a database, scientific programs and a python |
1021 |
- pipeline. The system is automated so that it needs no user's |
1022 |
- intervention when running complicated combination of jobs such |
1023 |
- as model searching, molecular replacement and refinement. |
1024 |
-</longdescription> |
1025 |
-</pkgmetadata> |
1026 |
|
1027 |
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest |
1028 |
deleted file mode 100644 |
1029 |
index e56aec5..0000000 |
1030 |
--- a/sci-chemistry/ccp4-apps/Manifest |
1031 |
+++ /dev/null |
1032 |
@@ -1,2 +0,0 @@ |
1033 |
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 |
1034 |
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c |
1035 |
|
1036 |
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild |
1037 |
deleted file mode 100644 |
1038 |
index 5e10321..0000000 |
1039 |
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild |
1040 |
+++ /dev/null |
1041 |
@@ -1,395 +0,0 @@ |
1042 |
-# Copyright 1999-2015 Gentoo Foundation |
1043 |
-# Distributed under the terms of the GNU General Public License v2 |
1044 |
-# $Id$ |
1045 |
- |
1046 |
-EAPI=5 |
1047 |
- |
1048 |
-PYTHON_COMPAT=( python2_7 ) |
1049 |
- |
1050 |
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs |
1051 |
- |
1052 |
-MY_P="${PN/-apps}-${PV}" |
1053 |
- |
1054 |
-#UPDATE="04_03_09" |
1055 |
-#PATCHDATE="090511" |
1056 |
- |
1057 |
-PATCH_TOT="0" |
1058 |
- |
1059 |
-DESCRIPTION="Protein X-ray crystallography toolkit" |
1060 |
-HOMEPAGE="http://www.ccp4.ac.uk/" |
1061 |
-SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
1062 |
-SRC_URI=" |
1063 |
- ${SRC}/${PV}/${MY_P}-core-src.tar.gz |
1064 |
- https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" |
1065 |
-# patch tarball from upstream |
1066 |
- [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
1067 |
-# patches created by us |
1068 |
- [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
1069 |
- |
1070 |
-for i in $(seq $PATCH_TOT); do |
1071 |
- NAME="PATCH${i}[1]" |
1072 |
- SRC_URI="${SRC_URI} |
1073 |
- ${SRC}/${PV}/patches/${!NAME}" |
1074 |
-done |
1075 |
- |
1076 |
-LICENSE="ccp4" |
1077 |
-SLOT="0" |
1078 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
1079 |
-IUSE="examples X" |
1080 |
- |
1081 |
-X11DEPS=" |
1082 |
- x11-libs/libX11 |
1083 |
- x11-libs/libXaw |
1084 |
- x11-libs/libXt |
1085 |
- x11-libs/libxdl_view" |
1086 |
- |
1087 |
-TKDEPS=" |
1088 |
- >=dev-lang/tk-8.3:0= |
1089 |
- >=dev-tcltk/blt-2.4 |
1090 |
- dev-tcltk/iwidgets |
1091 |
- dev-tcltk/itcl |
1092 |
- dev-tcltk/itk |
1093 |
- >=dev-tcltk/tdom-0.8 |
1094 |
- dev-tcltk/tktreectrl" |
1095 |
- |
1096 |
-SCILIBS=" |
1097 |
- ~sci-libs/ccp4-libs-${PV} |
1098 |
- >=sci-libs/ccp4-libs-${PV}-r7 |
1099 |
- sci-libs/clipper |
1100 |
- sci-libs/fftw:2.1 |
1101 |
- sci-libs/mmdb:0 |
1102 |
- sci-libs/ssm |
1103 |
- virtual/blas |
1104 |
- virtual/lapack" |
1105 |
- |
1106 |
-SCIAPPS=" |
1107 |
- sci-chemistry/pdb-extract |
1108 |
- sci-chemistry/pymol |
1109 |
- sci-chemistry/rasmol |
1110 |
- >=sci-chemistry/oasis-4.0-r1" |
1111 |
- |
1112 |
-RDEPEND=" |
1113 |
- ${TKDEPS} |
1114 |
- ${SCILIBS} |
1115 |
- app-shells/tcsh |
1116 |
- dev-python/pyxml |
1117 |
- dev-libs/libxml2:2 |
1118 |
- dev-libs/libjwc_c |
1119 |
- dev-libs/libjwc_f |
1120 |
- dev-libs/boehm-gc |
1121 |
- !app-office/sc |
1122 |
- !<sci-chemistry/ccp4-6.1.3 |
1123 |
- X? ( ${X11DEPS} )" |
1124 |
-DEPEND="${RDEPEND} |
1125 |
- X? ( |
1126 |
- x11-misc/imake |
1127 |
- x11-proto/inputproto |
1128 |
- x11-proto/xextproto |
1129 |
- )" |
1130 |
-PDEPEND="${SCIAPPS}" |
1131 |
- |
1132 |
-RESTRICT="mirror" |
1133 |
- |
1134 |
-S="${WORKDIR}/${MY_P}" |
1135 |
- |
1136 |
-pkg_setup() { |
1137 |
- fortran-2_pkg_setup |
1138 |
- python-single-r1_pkg_setup |
1139 |
-} |
1140 |
- |
1141 |
-src_prepare() { |
1142 |
- tc-export PKG_CONFIG |
1143 |
- einfo "Applying upstream patches ..." |
1144 |
- for patch in $(seq $PATCH_TOT); do |
1145 |
- base="PATCH${patch}" |
1146 |
- dir=$(eval echo \${${base}[0]}) |
1147 |
- p=$(eval echo \${${base}[1]}) |
1148 |
- pushd "${dir}" >& /dev/null |
1149 |
- ccp_patch "${DISTDIR}/${p}" |
1150 |
- popd >& /dev/null |
1151 |
- done |
1152 |
- einfo "Done." |
1153 |
- echo |
1154 |
- |
1155 |
- [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
1156 |
- |
1157 |
- einfo "Applying Gentoo patches ..." |
1158 |
- |
1159 |
- # it tries to create libdir, bindir etc on live system in configure |
1160 |
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
1161 |
- |
1162 |
- # We already have sci-chemistry/rasmol |
1163 |
- # Also remember to create the bindir. |
1164 |
- ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch |
1165 |
- |
1166 |
- # libraries come from sci-libs/ccp4-libs |
1167 |
- ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch |
1168 |
- |
1169 |
- # We have seperate ebuilds for those |
1170 |
- for bin in molref xia scala imosflm balbes; do |
1171 |
- ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch |
1172 |
- done |
1173 |
- |
1174 |
- # don't configure what is not build |
1175 |
- ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch |
1176 |
- |
1177 |
- # Set python paths correctly |
1178 |
- ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch |
1179 |
- |
1180 |
- # Set python paths correctly |
1181 |
- ccp_patch "${FILESDIR}"/${PV}-pisa.patch |
1182 |
- |
1183 |
- # Set python paths correctly |
1184 |
- ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch |
1185 |
- |
1186 |
- # Fix upstreams code |
1187 |
- ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch |
1188 |
- |
1189 |
- # Not renaming, but unbundling libs |
1190 |
- ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch |
1191 |
- |
1192 |
- # Use pkg-config to detect BLAS/LAPCK |
1193 |
- ccp_patch "${FILESDIR}"/${PV}-lapack.patch |
1194 |
- |
1195 |
- # unbundle libs |
1196 |
- ccp_patch "${FILESDIR}"/${PV}-unbundle.patch |
1197 |
- |
1198 |
- # tcl-8.6 |
1199 |
- ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch |
1200 |
- |
1201 |
- # Update things for oasis 4 usage |
1202 |
- epatch "${WORKDIR}"/${PV}-oasis4.0.patch |
1203 |
- sed 's: oasis : :g' -i src/Makefile.in || die |
1204 |
- |
1205 |
- einfo "Done." # done applying Gentoo patches |
1206 |
- echo |
1207 |
- |
1208 |
- find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete |
1209 |
- |
1210 |
- sed \ |
1211 |
- -e "s:/usr:${EPREFIX}/usr:g" \ |
1212 |
- -e 's:-Wl,-rpath,$CLIB::g' \ |
1213 |
- -e 's: -rpath $CLIB::g' \ |
1214 |
- -e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
1215 |
- -e 's:sleep 1:sleep .2:g' \ |
1216 |
- -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ |
1217 |
- -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ |
1218 |
- -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ |
1219 |
- -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ |
1220 |
- -i configure || die |
1221 |
- |
1222 |
- sed \ |
1223 |
- -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ |
1224 |
- -i src/Makefile* || die |
1225 |
- |
1226 |
- find "${S}" -name "Makefile.*" \ |
1227 |
- -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; |
1228 |
- |
1229 |
- # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version |
1230 |
- sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die |
1231 |
- |
1232 |
- # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. |
1233 |
- pushd src/rapper 2>/dev/null |
1234 |
- eautoreconf |
1235 |
- popd 2>/dev/null |
1236 |
- |
1237 |
- gnuconfig_update |
1238 |
- |
1239 |
- python_fix_shebang -f . |
1240 |
-} |
1241 |
- |
1242 |
-src_configure() { |
1243 |
- # Build system is broken if we set LDFLAGS |
1244 |
- export GENTOOLDFLAGS="${LDFLAGS}" |
1245 |
- unset LDFLAGS |
1246 |
- |
1247 |
- # These are broken with ./src/procheck/ps.f |
1248 |
- filter-flags "-floop-*" |
1249 |
- |
1250 |
- # GENTOO_OSNAME can be one of: |
1251 |
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
1252 |
- # linux_compaq_compilers linux_intel_compilers generic Darwin |
1253 |
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
1254 |
- if [[ "$(tc-getFC)" = "ifort" ]]; then |
1255 |
- if use ia64; then |
1256 |
- GENTOO_OSNAME="ia64_linux_intel" |
1257 |
- else |
1258 |
- # Should be valid for x86, maybe amd64 |
1259 |
- GENTOO_OSNAME="linux_intel_compilers" |
1260 |
- fi |
1261 |
- else |
1262 |
- # Should be valid for x86 and amd64, at least |
1263 |
- GENTOO_OSNAME="linux" |
1264 |
- fi |
1265 |
- |
1266 |
- # Sets up env |
1267 |
- ln -s \ |
1268 |
- ccp4.setup-bash \ |
1269 |
- "${S}"/include/ccp4.setup |
1270 |
- |
1271 |
- # We agree to the license by emerging this, set in LICENSE |
1272 |
- sed -i \ |
1273 |
- -e "s~^\(^agreed=\).*~\1yes~g" \ |
1274 |
- "${S}"/configure || die |
1275 |
- |
1276 |
- # Fix up variables -- need to reset CCP4_MASTER at install-time |
1277 |
- sed -i \ |
1278 |
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
1279 |
- -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
1280 |
- -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
1281 |
- -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
1282 |
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
1283 |
- "${S}"/include/ccp4.setup* || die |
1284 |
- |
1285 |
- # Set up variables for build |
1286 |
- source "${S}"/include/ccp4.setup-sh |
1287 |
- |
1288 |
- export CC=$(tc-getCC) |
1289 |
- export CXX=$(tc-getCXX) |
1290 |
- export COPTIM=${CFLAGS} |
1291 |
- export CXXOPTIM=${CXXFLAGS} |
1292 |
- # Default to -O2 if FFLAGS is unset |
1293 |
- export FC=$(tc-getFC) |
1294 |
- export FOPTIM=${FFLAGS:- -O2} |
1295 |
- export BINSORT_SCR="${T}" |
1296 |
- export CCP4_MASTER="${WORKDIR}" |
1297 |
- export CCP4I_TCLTK="${EPREFIX}/usr/bin" |
1298 |
- export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" |
1299 |
- |
1300 |
- # Can't use econf, configure rejects unknown options like --prefix |
1301 |
- ./configure \ |
1302 |
- $(use_enable X x) \ |
1303 |
- --with-shared-libs \ |
1304 |
- --with-fftw="${EPREFIX}/usr" \ |
1305 |
- --with-warnings \ |
1306 |
- --disable-pdb_extract \ |
1307 |
- --disable-cctbx \ |
1308 |
- --disable-phaser \ |
1309 |
- --disable-diffractionImg \ |
1310 |
- --disable-clipper \ |
1311 |
- --disable-ssm \ |
1312 |
- --disable-mosflm \ |
1313 |
- --disable-mrbump \ |
1314 |
- --tmpdir="${TMPDIR}" \ |
1315 |
- ${GENTOO_OSNAME} || die "configure failed" |
1316 |
- |
1317 |
- # We do this manually, since disabling the clipper libraries also |
1318 |
- # disables the clipper programs |
1319 |
- pushd src/clipper_progs 2>/dev/null |
1320 |
- econf \ |
1321 |
- --prefix="${S}" \ |
1322 |
- --bindir="${ED}"/usr/libexec/ccp4/bin \ |
1323 |
- --with-ccp4="${S}" \ |
1324 |
- --with-clipper="${EPREFIX}/usr" \ |
1325 |
- --with-fftw="${EPREFIX}/usr" \ |
1326 |
- --with-mmdb="${EPREFIX}/usr" \ |
1327 |
- CXX=$(tc-getCXX) |
1328 |
- popd 2>/dev/null |
1329 |
-} |
1330 |
- |
1331 |
-src_compile() { |
1332 |
- # fsplit is required for the programs |
1333 |
- pushd lib/src 2>/dev/null |
1334 |
- emake fsplit -j1 || die |
1335 |
- popd 2>/dev/null |
1336 |
- |
1337 |
- # We do this manually, since disabling the clipper libraries also |
1338 |
- # disables the clipper programs |
1339 |
- pushd src/clipper_progs 2>/dev/null |
1340 |
- emake || die |
1341 |
- popd 2>/dev/null |
1342 |
- |
1343 |
- emake -j1 || die "emake failed" |
1344 |
-} |
1345 |
- |
1346 |
-src_install() { |
1347 |
- # Set up variables for build |
1348 |
- source "${S}"/include/ccp4.setup-sh |
1349 |
- |
1350 |
- # if we don't make this, a ton of programs fail to install |
1351 |
- mkdir "${S}"/bin || die |
1352 |
- |
1353 |
- # We do this manually, since disabling the clipper libraries also |
1354 |
- # disables the clipper programs |
1355 |
- pushd "${S}"/src/clipper_progs 2>/dev/null |
1356 |
- emake install || die |
1357 |
- popd 2>/dev/null |
1358 |
- |
1359 |
- einstall || die "install failed" |
1360 |
- |
1361 |
- # Collision with sci-chemistry/mrbump |
1362 |
- rm -f "${S}"/bin/{mrbump,pydbviewer} || die |
1363 |
- |
1364 |
- # Bins |
1365 |
- exeinto /usr/libexec/ccp4/bin/ |
1366 |
- doexe "${S}"/bin/* || die |
1367 |
- |
1368 |
- # Libs |
1369 |
- for file in "${S}"/lib/*; do |
1370 |
- if [[ -d ${file} ]]; then |
1371 |
- continue |
1372 |
- elif [[ -x ${file} ]]; then |
1373 |
- dolib.so ${file} || die |
1374 |
- else |
1375 |
- insinto /usr/$(get_libdir) |
1376 |
- doins ${file} || die |
1377 |
- fi |
1378 |
- done |
1379 |
- |
1380 |
- rm -f "${S}"/include/ccp4.setup* |
1381 |
- |
1382 |
- # smartie -- log parsing |
1383 |
- insinto /usr/share/ccp4 |
1384 |
- doins -r "${S}"/share/smartie || die |
1385 |
- |
1386 |
- # Install docs and examples |
1387 |
- local _man |
1388 |
- pushd "${S}"/man/cat1 > /dev/null |
1389 |
- for _man in *; do |
1390 |
- newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} |
1391 |
- done |
1392 |
- popd > /dev/null |
1393 |
- |
1394 |
- mv "${S}"/manual/README "${S}"/manual/README-manual |
1395 |
- dodoc manual/* README CHANGES doc/* examples/README || die |
1396 |
- |
1397 |
- rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* |
1398 |
- rm "${ED}"/usr/share/doc/${PF}/COPYING.* |
1399 |
- |
1400 |
- dohtml -r "${S}"/html/* |
1401 |
- |
1402 |
- if use examples; then |
1403 |
- for i in data rnase toxd; do |
1404 |
- docinto examples/${i} |
1405 |
- dodoc "${S}"/examples/${i}/* |
1406 |
- done |
1407 |
- |
1408 |
- docinto examples/tutorial |
1409 |
- dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css |
1410 |
- for i in data results; do |
1411 |
- docinto examples/tutorial/${i} |
1412 |
- dodoc "${S}"/examples/tutorial/${i}/* |
1413 |
- done |
1414 |
- |
1415 |
- for i in non-runnable runnable; do |
1416 |
- docinto examples/unix/${i} |
1417 |
- dodoc "${S}"/examples/unix/${i}/* |
1418 |
- done |
1419 |
- fi |
1420 |
- # Needed for ccp4i docs to work |
1421 |
- dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die |
1422 |
- dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die |
1423 |
- |
1424 |
- cat >> "${T}"/baubles <<- EOF |
1425 |
- #!${EPREFIX}/bin/bash |
1426 |
- exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" |
1427 |
- EOF |
1428 |
- |
1429 |
- exeinto /usr/libexec/ccp4/bin/ |
1430 |
- doexe "${T}"/baubles || die |
1431 |
-} |
1432 |
- |
1433 |
-# Epatch wrapper for bulk patching |
1434 |
-ccp_patch() { |
1435 |
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
1436 |
-} |
1437 |
|
1438 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch |
1439 |
deleted file mode 100644 |
1440 |
index 433a78d..0000000 |
1441 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch |
1442 |
+++ /dev/null |
1443 |
@@ -1,70 +0,0 @@ |
1444 |
---- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 |
1445 |
-+++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 |
1446 |
-@@ -70,9 +70,31 @@ |
1447 |
- { |
1448 |
- public: |
1449 |
- //! constructor: takes the datalist against which to calc target |
1450 |
-- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); |
1451 |
-+ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) |
1452 |
-+ { |
1453 |
-+ hkl_data1 = &hkl_data1_; |
1454 |
-+ hkl_data2 = &hkl_data2_; |
1455 |
-+ } |
1456 |
- //! return the value and derivatives of the target function |
1457 |
-- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; |
1458 |
-+ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const |
1459 |
-+ { |
1460 |
-+ Rderiv result; |
1461 |
-+ result.r = result.dr = result.dr2 = 0.0; |
1462 |
-+ const T1& it1 = (*hkl_data1)[ih]; |
1463 |
-+ const T2& it2 = (*hkl_data2)[ih]; |
1464 |
-+ if ( !it1.missing() && !it2.missing() ) |
1465 |
-+ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { |
1466 |
-+ const ftype eps = ih.hkl_class().epsilon(); |
1467 |
-+ const ftype i1 = it1.I() / eps; |
1468 |
-+ const ftype i2 = it2.I() / eps; |
1469 |
-+ const ftype w = sqrt( i1 * i2 ); |
1470 |
-+ const ftype d = intensityh + log(i1) - log(i2); |
1471 |
-+ result.r = w * d * d; |
1472 |
-+ result.dr = 2.0 * w * d; |
1473 |
-+ result.dr2 = 2.0 * w; |
1474 |
-+ } |
1475 |
-+ return result; |
1476 |
-+ } |
1477 |
- //! the type of the function: optionally used to improve convergence |
1478 |
- FNtype type() const { return QUADRATIC; } |
1479 |
- private: |
1480 |
-@@ -109,33 +131,4 @@ |
1481 |
- return result; |
1482 |
- } |
1483 |
- |
1484 |
-- // Log I1-I2 scaling |
1485 |
-- |
1486 |
-- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) |
1487 |
-- { |
1488 |
-- hkl_data1 = &hkl_data1_; |
1489 |
-- hkl_data2 = &hkl_data2_; |
1490 |
-- } |
1491 |
-- |
1492 |
-- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const |
1493 |
-- { |
1494 |
-- Rderiv result; |
1495 |
-- result.r = result.dr = result.dr2 = 0.0; |
1496 |
-- const T1& it1 = (*hkl_data1)[ih]; |
1497 |
-- const T2& it2 = (*hkl_data2)[ih]; |
1498 |
-- if ( !it1.missing() && !it2.missing() ) |
1499 |
-- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { |
1500 |
-- const ftype eps = ih.hkl_class().epsilon(); |
1501 |
-- const ftype i1 = it1.I() / eps; |
1502 |
-- const ftype i2 = it2.I() / eps; |
1503 |
-- const ftype w = sqrt( i1 * i2 ); |
1504 |
-- const ftype d = intensityh + log(i1) - log(i2); |
1505 |
-- result.r = w * d * d; |
1506 |
-- result.dr = 2.0 * w * d; |
1507 |
-- result.dr2 = 2.0 * w; |
1508 |
-- } |
1509 |
-- return result; |
1510 |
-- } |
1511 |
-- |
1512 |
-- |
1513 |
- #endif |
1514 |
|
1515 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch |
1516 |
deleted file mode 100644 |
1517 |
index f1df3e5..0000000 |
1518 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch |
1519 |
+++ /dev/null |
1520 |
@@ -1,14 +0,0 @@ |
1521 |
-diff --git a/share/Makefile.in b/share/Makefile.in |
1522 |
-index 2d4f20b..4500993 100755 |
1523 |
---- a/share/Makefile.in |
1524 |
-+++ b/share/Makefile.in |
1525 |
-@@ -18,9 +18,6 @@ install : |
1526 |
- for i in $(MRBUMP_TARGETS); do \ |
1527 |
- test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ |
1528 |
- done |
1529 |
-- for i in $(BALBES_TARGETS); do \ |
1530 |
-- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ |
1531 |
-- done |
1532 |
- |
1533 |
- clean : ; -rm -f core *.o *~ a.out |
1534 |
- |
1535 |
|
1536 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch |
1537 |
deleted file mode 100644 |
1538 |
index e62ae12..0000000 |
1539 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch |
1540 |
+++ /dev/null |
1541 |
@@ -1,24 +0,0 @@ |
1542 |
---- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 |
1543 |
-+++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 |
1544 |
-@@ -35,7 +35,7 @@ |
1545 |
- # |
1546 |
- # all |
1547 |
- # |
1548 |
--all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm |
1549 |
-+all : rotgen_ hklview xjiffy |
1550 |
- # |
1551 |
- # xdl_view |
1552 |
- # |
1553 |
-@@ -157,11 +157,10 @@ |
1554 |
- # |
1555 |
- install_obj = hklview rotgen ipmosflm |
1556 |
- install: all |
1557 |
-+ mkdir -p $(bindir) |
1558 |
- $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) |
1559 |
- cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install |
1560 |
-- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) |
1561 |
- cd $(rotgen_dir); $(MAKE) install |
1562 |
-- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) |
1563 |
- # |
1564 |
- # clean |
1565 |
- # |
1566 |
|
1567 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch |
1568 |
deleted file mode 100644 |
1569 |
index f645643..0000000 |
1570 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch |
1571 |
+++ /dev/null |
1572 |
@@ -1,11 +0,0 @@ |
1573 |
---- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 |
1574 |
-+++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 |
1575 |
-@@ -9,7 +9,7 @@ |
1576 |
- SHELL = /bin/sh |
1577 |
- DESTDIR = $(prefix) |
1578 |
- CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin |
1579 |
--CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer |
1580 |
-+CCP4I_TARGETS = ccp4i loggraph crank mapslicer |
1581 |
- |
1582 |
- install : |
1583 |
- for i in $(CCP4I_TARGETS); do \ |
1584 |
|
1585 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch |
1586 |
deleted file mode 100644 |
1587 |
index 1d13230..0000000 |
1588 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch |
1589 |
+++ /dev/null |
1590 |
@@ -1,35 +0,0 @@ |
1591 |
---- Makefile.in 2009-06-19 15:13:29.000000000 +0200 |
1592 |
-+++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 |
1593 |
-@@ -2,7 +2,7 @@ |
1594 |
- # $Id$ |
1595 |
- |
1596 |
- SHELL = /bin/sh |
1597 |
--DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) |
1598 |
-+DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) |
1599 |
- # this is for the benefit of makes that don't pass variable values in |
1600 |
- # recursive invocations, so that you can override these values on the |
1601 |
- # command line at the top level |
1602 |
-@@ -69,19 +69,19 @@ |
1603 |
- $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ |
1604 |
- $(MAKE) install |
1605 |
- |
1606 |
--srcdir : FORCE libdir |
1607 |
-+srcdir : FORCE |
1608 |
- if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi |
1609 |
- |
1610 |
- supported : srcdir |
1611 |
- |
1612 |
--unsupported : FORCE libdir |
1613 |
-+unsupported : FORCE |
1614 |
- if test -d unsupported/src; then cd unsupported/src; \ |
1615 |
- $(MAKE) $(MFLAGS) $(MVARS); else true; fi |
1616 |
- |
1617 |
--datadir : FORCE libdir |
1618 |
-+datadir : FORCE |
1619 |
- cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) |
1620 |
- |
1621 |
--xwindir : FORCE libdir |
1622 |
-+xwindir : FORCE |
1623 |
- if test -f x-windows/Makefile; then cd x-windows; \ |
1624 |
- $(MAKE) -i $(MFLAGS) ; else true; fi |
1625 |
- |
1626 |
|
1627 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch |
1628 |
deleted file mode 100644 |
1629 |
index f16b0ec..0000000 |
1630 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch |
1631 |
+++ /dev/null |
1632 |
@@ -1,19 +0,0 @@ |
1633 |
---- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 |
1634 |
-+++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 |
1635 |
-@@ -1,4 +1,4 @@ |
1636 |
--SUBDIRS = molref pisastore sbase |
1637 |
-+SUBDIRS = pisastore sbase |
1638 |
- |
1639 |
- pkgdatadir = $(datadir)/pisa |
1640 |
- |
1641 |
---- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 |
1642 |
-+++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 |
1643 |
-@@ -82,7 +82,7 @@ |
1644 |
- am__quote = @am__quote@ |
1645 |
- install_sh = @install_sh@ |
1646 |
- pisa_LDFLAGS = @pisa_LDFLAGS@ |
1647 |
--SUBDIRS = molref pisastore sbase |
1648 |
-+SUBDIRS = pisastore sbase |
1649 |
- |
1650 |
- dist_pkgdata_DATA = pisa.cfg |
1651 |
- |
1652 |
|
1653 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch |
1654 |
deleted file mode 100644 |
1655 |
index af4fd82..0000000 |
1656 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch |
1657 |
+++ /dev/null |
1658 |
@@ -1,42 +0,0 @@ |
1659 |
---- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 |
1660 |
-+++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 |
1661 |
-@@ -50,7 +50,7 @@ |
1662 |
- |
1663 |
- # these live in subdirectories and have more than one dependency: |
1664 |
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ |
1665 |
-- scala dm dmmulti stereo mapmask maprot ncsmask \ |
1666 |
-+ dm dmmulti stereo mapmask maprot ncsmask \ |
1667 |
- sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ |
1668 |
- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat |
1669 |
- |
1670 |
-@@ -637,7 +637,7 @@ |
1671 |
- |
1672 |
- ### scala, mapmask, maprot, ncsmask, combat |
1673 |
- |
1674 |
--scala mapmask maprot ncsmask combat sc dyndom: # dependencies below |
1675 |
-+mapmask maprot ncsmask combat sc dyndom: # dependencies below |
1676 |
- @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ |
1677 |
- cd $(srcdir)/$@_; \ |
1678 |
- echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ |
1679 |
-@@ -1002,21 +1002,6 @@ |
1680 |
- proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par |
1681 |
- rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc |
1682 |
- |
1683 |
--scaladir = $(srcdir)/scala_ |
1684 |
--scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ |
1685 |
-- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ |
1686 |
-- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ |
1687 |
-- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ |
1688 |
-- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ |
1689 |
-- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ |
1690 |
-- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ |
1691 |
-- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ |
1692 |
-- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ |
1693 |
-- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ |
1694 |
-- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ |
1695 |
-- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ |
1696 |
-- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh |
1697 |
-- |
1698 |
- freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ |
1699 |
- $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ |
1700 |
- $(dmdir)/params.fh $(dmdir)/uvwdata.fh |
1701 |
|
1702 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch |
1703 |
deleted file mode 100644 |
1704 |
index 3af4af5..0000000 |
1705 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch |
1706 |
+++ /dev/null |
1707 |
@@ -1,14 +0,0 @@ |
1708 |
---- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 |
1709 |
-+++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 |
1710 |
-@@ -50,9 +50,9 @@ |
1711 |
- |
1712 |
- # these live in subdirectories and have more than one dependency: |
1713 |
- OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ |
1714 |
-- scala dm dmmulti stereo mapmask maprot ncsmask chef \ |
1715 |
-+ scala dm dmmulti stereo mapmask maprot ncsmask \ |
1716 |
- sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ |
1717 |
-- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat |
1718 |
-+ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf |
1719 |
- |
1720 |
- # targets built from .c sources: |
1721 |
- CSIMPLE = pltdev binsort |
1722 |
|
1723 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch |
1724 |
deleted file mode 100644 |
1725 |
index 1e59578..0000000 |
1726 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch |
1727 |
+++ /dev/null |
1728 |
@@ -1,111 +0,0 @@ |
1729 |
---- configure 2009-08-07 12:11:28.000000000 +0200 |
1730 |
-+++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 |
1731 |
-@@ -3113,41 +3113,6 @@ |
1732 |
- RX_L="$configdir/lib/rxdispencer/rx" |
1733 |
- export RX_H RX_L |
1734 |
- fi |
1735 |
-- echo |
1736 |
-- echo "Running separate configure for CCIF library." |
1737 |
-- echo |
1738 |
-- cd lib/ccif |
1739 |
-- echo "Updating modification times for configuration files" |
1740 |
-- echo "Please wait..." |
1741 |
-- for i in configure.in aclocal.m4 configure Makefile.in; do |
1742 |
-- touch $i && sleep 1 |
1743 |
-- done |
1744 |
-- echo "...done." |
1745 |
-- |
1746 |
-- if [ "X$LIBFOPTIM" != "X" ]; then |
1747 |
-- FOPTIM_save=$FOPTIM |
1748 |
-- FOPTIM=$LIBFOPTIM |
1749 |
-- FFLAGS="${FOPTIM} ${XFFLAGS}" |
1750 |
-- fi |
1751 |
-- if [ "X$LIBCOPTIM" != "X" ]; then |
1752 |
-- COPTIM_save=$COPTIM |
1753 |
-- COPTIM=$LIBCOPTIM |
1754 |
-- CFLAGS="${COPTIM} ${XCFLAGS}" |
1755 |
-- fi |
1756 |
-- ( touch /tmp/$$.cache_file 2>/dev/null && \ |
1757 |
-- cat /dev/null > /tmp/$$.cache_file && \ |
1758 |
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ |
1759 |
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif |
1760 |
-- rm -f /tmp/$$.cache_file |
1761 |
-- if [ "X$LIBFOPTIM" != "X" ]; then |
1762 |
-- FOPTIM=$FOPTIM_save |
1763 |
-- FFLAGS="${FOPTIM} ${XFFLAGS}" |
1764 |
-- fi |
1765 |
-- if [ "X$LIBCOPTIM" != "X" ]; then |
1766 |
-- COPTIM=$COPTIM_save |
1767 |
-- CFLAGS="${COPTIM} ${XCFLAGS}" |
1768 |
-- fi |
1769 |
-- cd ../.. |
1770 |
- echo |
1771 |
- echo "Returning to main configure." |
1772 |
- echo |
1773 |
-@@ -5094,53 +5059,6 @@ |
1774 |
- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" |
1775 |
- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} |
1776 |
- echo |
1777 |
-- echo "CCP4 configure: Running separate configure for libjwc_c library." |
1778 |
-- echo |
1779 |
-- cd ${srcdir}/${xwindir}/libjwc/libjwc_c |
1780 |
-- echo "Updating modification times for configuration files in libjwc_c" |
1781 |
-- echo "Please wait..." |
1782 |
-- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do |
1783 |
-- touch $i && sleep 1 |
1784 |
-- done |
1785 |
-- echo "...done." |
1786 |
-- echo |
1787 |
-- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" |
1788 |
-- ( touch /tmp/$$.cache_file 2>/dev/null && \ |
1789 |
-- cat /dev/null > /tmp/$$.cache_file && \ |
1790 |
-- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ |
1791 |
-- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} |
1792 |
-- rm -f /tmp/$$.cache_file |
1793 |
-- echo |
1794 |
-- echo "CCP4 configure: Running separate configure for libjwc_f library." |
1795 |
-- echo |
1796 |
-- cd ${srcdir}/${xwindir}/libjwc/libjwc_f |
1797 |
-- # for g77 3.1 some builds do not have no-common for system libs, |
1798 |
-- # so disable for now |
1799 |
-- echo "Updating modification times for configuration files in libjwc_f" |
1800 |
-- echo "Please wait..." |
1801 |
-- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do |
1802 |
-- touch $i && sleep 1 |
1803 |
-- done |
1804 |
-- echo "...done." |
1805 |
-- echo |
1806 |
-- # for g77 3.1 some builds do not have no-common for system libs, |
1807 |
-- # so disable for now |
1808 |
-- case $system in |
1809 |
-- Darwin* ) |
1810 |
-- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" |
1811 |
-- ( touch /tmp/$$.cache_file 2>/dev/null && \ |
1812 |
-- cat /dev/null > /tmp/$$.cache_file && \ |
1813 |
-- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ |
1814 |
-- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} |
1815 |
-- ;; |
1816 |
-- * ) |
1817 |
-- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" |
1818 |
-- ( touch /tmp/$$.cache_file 2>/dev/null && \ |
1819 |
-- cat /dev/null > /tmp/$$.cache_file && \ |
1820 |
-- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ |
1821 |
-- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} |
1822 |
-- esac |
1823 |
-- rm -f /tmp/$$.cache_file |
1824 |
- |
1825 |
- if test "$non_shared" = yes; then |
1826 |
- #this is a bit of a cheat/fudge but that's life! |
1827 |
-@@ -5210,12 +5128,6 @@ |
1828 |
- fi |
1829 |
- |
1830 |
- echo |
1831 |
-- echo "CCP4 configure: Running separate configure for Mosflm" |
1832 |
-- echo |
1833 |
-- cd ${srcdir}/${mosflmdir} |
1834 |
-- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" |
1835 |
-- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} |
1836 |
-- echo |
1837 |
- cd ../.. |
1838 |
- echo "Returning to main configure." |
1839 |
- echo |
1840 |
|
1841 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch |
1842 |
deleted file mode 100644 |
1843 |
index 583697c..0000000 |
1844 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch |
1845 |
+++ /dev/null |
1846 |
@@ -1,87 +0,0 @@ |
1847 |
---- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 |
1848 |
-+++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 |
1849 |
-@@ -643,45 +643,45 @@ |
1850 |
- # echo "! Beware -- the $system installation isn't properly tested." ; } |
1851 |
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' |
1852 |
- |
1853 |
--if test -z "$onlylibs" ; then |
1854 |
-- for i in CCP4_SCR BINSORT_SCR; do |
1855 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
1856 |
-- else |
1857 |
-- eval echo "! No directory \$$i and can\'t create it." |
1858 |
-- echo " Check the value of $i." |
1859 |
-- badvar=1 |
1860 |
-- fi |
1861 |
-- done |
1862 |
-- |
1863 |
-- for i in libdir bindir includedir; do |
1864 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
1865 |
-- else |
1866 |
-- eval echo "! No directory \$$i and can\'t create it." |
1867 |
-- echo " Check the argument of --$i." |
1868 |
-- badvar=1 |
1869 |
-- fi |
1870 |
-- done |
1871 |
-- |
1872 |
-- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
1873 |
-- if test -d $i || mkdir $i; then : |
1874 |
-- else |
1875 |
-- eval echo "! No directory $i and can\'t create it." |
1876 |
-- badvar=1 |
1877 |
-- fi |
1878 |
-- done |
1879 |
--else |
1880 |
-- # Kludge to fool the "Makefile" target in the top-level CCP4 |
1881 |
-- # Makefile into not trying to remake src/Makefile.in |
1882 |
-- for i in $srcdir/src $srcdir/lib/src ; do |
1883 |
-- if test -d $i || mkdir $i; then |
1884 |
-- if ! test -f $i/Makefile.in ; then |
1885 |
-- echo |
1886 |
-- echo "onlylibs: making dummy file $i/Makefile.in" |
1887 |
-- touch $i/Makefile.in |
1888 |
-- fi |
1889 |
-- fi |
1890 |
-- done |
1891 |
--fi |
1892 |
-+#if test -z "$onlylibs" ; then |
1893 |
-+# for i in CCP4_SCR BINSORT_SCR; do |
1894 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
1895 |
-+# else |
1896 |
-+# eval echo "! No directory \$$i and can\'t create it." |
1897 |
-+# echo " Check the value of $i." |
1898 |
-+# badvar=1 |
1899 |
-+# fi |
1900 |
-+# done |
1901 |
-+# |
1902 |
-+# for i in libdir bindir includedir; do |
1903 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
1904 |
-+# else |
1905 |
-+# eval echo "! No directory \$$i and can\'t create it." |
1906 |
-+# echo " Check the argument of --$i." |
1907 |
-+# badvar=1 |
1908 |
-+# fi |
1909 |
-+# done |
1910 |
-+# |
1911 |
-+# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
1912 |
-+# if test -d $i || mkdir $i; then : |
1913 |
-+# else |
1914 |
-+# eval echo "! No directory $i and can\'t create it." |
1915 |
-+# badvar=1 |
1916 |
-+# fi |
1917 |
-+# done |
1918 |
-+#else |
1919 |
-+# # Kludge to fool the "Makefile" target in the top-level CCP4 |
1920 |
-+# # Makefile into not trying to remake src/Makefile.in |
1921 |
-+# for i in $srcdir/src $srcdir/lib/src ; do |
1922 |
-+# if test -d $i || mkdir $i; then |
1923 |
-+# if ! test -f $i/Makefile.in ; then |
1924 |
-+# echo |
1925 |
-+# echo "onlylibs: making dummy file $i/Makefile.in" |
1926 |
-+# touch $i/Makefile.in |
1927 |
-+# fi |
1928 |
-+# fi |
1929 |
-+# done |
1930 |
-+#fi |
1931 |
- |
1932 |
- ### sanity checks |
1933 |
- |
1934 |
|
1935 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch |
1936 |
deleted file mode 100644 |
1937 |
index db82360..0000000 |
1938 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch |
1939 |
+++ /dev/null |
1940 |
@@ -1,152 +0,0 @@ |
1941 |
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c |
1942 |
-index bfda882..f821e04 100755 |
1943 |
---- a/lib/DiffractionImage/Bruker/FRM_LIB.c |
1944 |
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c |
1945 |
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. |
1946 |
- #include "sys/types.h" /* _open, etc. */ |
1947 |
- #include "sys/stat.h" /* _open, etc. */ |
1948 |
- |
1949 |
-+#include <unistd.h> |
1950 |
-+ |
1951 |
- #ifndef _MSC_VER |
1952 |
- int min(int a, int b) |
1953 |
- { |
1954 |
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c |
1955 |
-index 1a933de..1c40c32 100755 |
1956 |
---- a/lib/DiffractionImage/MAR/mar300_header.c |
1957 |
-+++ b/lib/DiffractionImage/MAR/mar300_header.c |
1958 |
-@@ -23,6 +23,9 @@ |
1959 |
- */ |
1960 |
- #include "mar300_header.h" |
1961 |
- |
1962 |
-+#include <sys/types.h> |
1963 |
-+#include <unistd.h> |
1964 |
-+ |
1965 |
- /* |
1966 |
- * Local functions |
1967 |
- */ |
1968 |
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c |
1969 |
-index a8351ea..16d0f7b 100755 |
1970 |
---- a/lib/DiffractionImage/MAR/mar345_header.c |
1971 |
-+++ b/lib/DiffractionImage/MAR/mar345_header.c |
1972 |
-@@ -32,6 +32,9 @@ |
1973 |
- */ |
1974 |
- #include "mar345_header.h" |
1975 |
- |
1976 |
-+#include <sys/types.h> |
1977 |
-+#include <unistd.h> |
1978 |
-+ |
1979 |
- /* |
1980 |
- * Definitions |
1981 |
- */ |
1982 |
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c |
1983 |
-index 07f2741..6364ca4 100755 |
1984 |
---- a/lib/DiffractionImage/MAR/nb_header.c |
1985 |
-+++ b/lib/DiffractionImage/MAR/nb_header.c |
1986 |
-@@ -20,6 +20,8 @@ |
1987 |
- #include <io.h> |
1988 |
- #endif |
1989 |
- |
1990 |
-+#include <sys/types.h> |
1991 |
-+#include <unistd.h> |
1992 |
- /* |
1993 |
- * mar software include files |
1994 |
- */ |
1995 |
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c |
1996 |
-index 443bb8c..0d96b3f 100755 |
1997 |
---- a/lib/DiffractionImage/MAR/swap.c |
1998 |
-+++ b/lib/DiffractionImage/MAR/swap.c |
1999 |
-@@ -10,6 +10,9 @@ |
2000 |
- * |
2001 |
- **********************************************************************/ |
2002 |
- |
2003 |
-+#define _XOPEN_SOURCE |
2004 |
-+#include <unistd.h> |
2005 |
-+ |
2006 |
- void swaplong(); |
2007 |
- void swapshort(); |
2008 |
- |
2009 |
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c |
2010 |
-index 0f6a6b7..a09dc48 100755 |
2011 |
---- a/lib/ccif/f_interface.c |
2012 |
-+++ b/lib/ccif/f_interface.c |
2013 |
-@@ -25,6 +25,7 @@ |
2014 |
- ********************************************************************/ |
2015 |
- |
2016 |
- #include "stdpccts.h" |
2017 |
-+#include <sys/mman.h> |
2018 |
- |
2019 |
- /* This file is terribly organised, and badly needs re-doing. There is probably |
2020 |
- * scope for splitting this into three modules: |
2021 |
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c |
2022 |
-index 8b5d04f..74ee3f7 100755 |
2023 |
---- a/lib/src/ccp4_general_f.c |
2024 |
-+++ b/lib/src/ccp4_general_f.c |
2025 |
-@@ -26,6 +26,7 @@ |
2026 |
- #include <string.h> |
2027 |
- #include <stdlib.h> |
2028 |
- #include <math.h> |
2029 |
-+#include <time.h> |
2030 |
- #include "ccp4_errno.h" |
2031 |
- #include "ccp4_fortran.h" |
2032 |
- #include "ccp4_parser.h" |
2033 |
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c |
2034 |
-index 3e83d4d..bb3e975 100755 |
2035 |
---- a/lib/src/ccp4_program.c |
2036 |
-+++ b/lib/src/ccp4_program.c |
2037 |
-@@ -25,6 +25,7 @@ |
2038 |
- #include <stdio.h> |
2039 |
- #include <stdlib.h> |
2040 |
- #include <string.h> |
2041 |
-+#include <time.h> |
2042 |
- #include "ccp4_program.h" |
2043 |
- #include "ccp4_parser.h" |
2044 |
- #include "ccp4_utils.h" |
2045 |
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c |
2046 |
-index ee8af24..c6fb3cd 100755 |
2047 |
---- a/lib/src/fsplit.c |
2048 |
-+++ b/lib/src/fsplit.c |
2049 |
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; |
2050 |
- #include <string.h> |
2051 |
- #include <sys/types.h> |
2052 |
- #include <sys/stat.h> |
2053 |
-+#include <unistd.h> |
2054 |
- |
2055 |
- /* |
2056 |
- * usage: fsplit [-e efile] ... [file] |
2057 |
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c |
2058 |
-index ea52e96..30dbd56 100755 |
2059 |
---- a/src/clipper_progs/src/pirate/compress42.c |
2060 |
-+++ b/src/clipper_progs/src/pirate/compress42.c |
2061 |
-@@ -142,6 +142,7 @@ |
2062 |
- #include <sys/types.h> |
2063 |
- #include <sys/stat.h> |
2064 |
- #include <errno.h> |
2065 |
-+#include <unistd.h> |
2066 |
- |
2067 |
- #ifdef DIRENT |
2068 |
- # include <dirent.h> |
2069 |
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c |
2070 |
-index e224430..c7b82f4 100755 |
2071 |
---- a/src/mtz2cif_/mtz2cif.c |
2072 |
-+++ b/src/mtz2cif_/mtz2cif.c |
2073 |
-@@ -28,6 +28,7 @@ |
2074 |
- #include "cmtzlib.h" |
2075 |
- #include "ccp4_parser.h" |
2076 |
- #include "ccp4_general.h" |
2077 |
-+#include "ccp4_program.h" |
2078 |
- #include "csymlib.h" |
2079 |
- #include "mtz2cif_lib.h" |
2080 |
- |
2081 |
-diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c |
2082 |
-index 67e0bf1..76526ab 100755 |
2083 |
---- a/x-windows/XCCPJIFFY/xplot84driver.c |
2084 |
-+++ b/x-windows/XCCPJIFFY/xplot84driver.c |
2085 |
-@@ -11,6 +11,7 @@ |
2086 |
- |
2087 |
- #include <stdio.h> |
2088 |
- #include <sys/types.h> |
2089 |
-+#include <stdlib.h> |
2090 |
- |
2091 |
- #include <X11/StringDefs.h> |
2092 |
- #include <X11/Intrinsic.h> |
2093 |
|
2094 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch |
2095 |
deleted file mode 100644 |
2096 |
index 62892db..0000000 |
2097 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch |
2098 |
+++ /dev/null |
2099 |
@@ -1,597 +0,0 @@ |
2100 |
-diff --git a/configure b/configure |
2101 |
-index 833f483..bcfa62d 100755 |
2102 |
---- a/configure |
2103 |
-+++ b/configure |
2104 |
-@@ -3226,574 +3226,14 @@ else |
2105 |
- echo |
2106 |
- echo "Warning: this option has not been extensively tested!" |
2107 |
- echo "Please report problems to ccp4@×××××××.uk" |
2108 |
-- # Search for vendor LAPACK/BLAS first |
2109 |
-- if test ! "$with_netlib_lapack" ; then |
2110 |
-- # Initialise variables to blank |
2111 |
-- lapackdir= |
2112 |
-- XLAPACK_LIB= |
2113 |
-- # Possible directories to check for vendor or pre-existing LAPACK or |
2114 |
-- # BLAS - add to these if you want to test others |
2115 |
-- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" |
2116 |
-- # Possible library names |
2117 |
-- # These are the names like xxxx where the library will be libxxxx.a |
2118 |
-- # or libxxxx.so |
2119 |
-- echo |
2120 |
-- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" |
2121 |
-- echo "on this system" |
2122 |
-- case $system in |
2123 |
-- linux | linux64 | linux32 ) |
2124 |
-- # linux users will usually have them in /usr/lib but don't call it |
2125 |
-- trylapack="lapack" |
2126 |
-- tryblas="blas" |
2127 |
-- # if code is non_shared then this can lead to problems. both blas and lapack |
2128 |
-- # need to be resolved even if they are not called! |
2129 |
-- if test "$non_shared" = yes; then |
2130 |
-- echo "You are compiling linux non_shared. This sometimes causes problems " |
2131 |
-- echo " so checking for requirements." |
2132 |
-- echo "Checking: try to link library against test program" |
2133 |
-- if test -f testlink.f || test -f testlink ; then |
2134 |
-- rm -f testlink* |
2135 |
-- fi |
2136 |
-- cat > testlink.f <<EOF |
2137 |
-- PROGRAM TESTLINK |
2138 |
--C A bit of scala code to test the linking |
2139 |
-- real bf(3), bnorm |
2140 |
--c |
2141 |
-- integer maxbmt |
2142 |
-- parameter (maxbmt = 2) |
2143 |
-- double precision B(maxbmt,maxbmt), eigval(maxbmt), |
2144 |
-- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) |
2145 |
-- integer m, ia, ix, istat |
2146 |
--c |
2147 |
-- B(1,1) = 1.00 |
2148 |
-- B(1,2) = 1.00 |
2149 |
-- B(2,1) = 1.00 |
2150 |
-- B(2,2) = 1.00 |
2151 |
--c |
2152 |
-- m = maxbmt |
2153 |
-- ia = maxbmt |
2154 |
-- ix = maxbmt |
2155 |
-- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) |
2156 |
-- end |
2157 |
--EOF |
2158 |
-- #firstly test without -lblas |
2159 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" |
2160 |
-- echo $test_compile |
2161 |
-- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then |
2162 |
-- # Compilation was okay |
2163 |
-- echo "... only -llapack needed" |
2164 |
-- XLAPACK_LIB="-llapack" |
2165 |
-- # Set the next two variables so that configure |
2166 |
-- # doesn't try to build netlib libraries |
2167 |
-- LAPACKLIB="lapack" |
2168 |
-- noblas=yes |
2169 |
-- trylapack= |
2170 |
-- tryblas= |
2171 |
-- else |
2172 |
-- echo "more than just -llapack needed...." |
2173 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" |
2174 |
-- echo $test_compile |
2175 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2176 |
-- # Compilation was okay |
2177 |
-- echo "...-llapack and -lblas were needed" |
2178 |
-- XLAPACK_LIB="-llapack -lblas" |
2179 |
-- # Set the next two variables so that configure |
2180 |
-- # doesn't try to build netlib libraries |
2181 |
-- LAPACKLIB="lapack blas" |
2182 |
-- noblas=no |
2183 |
-- trylapack= |
2184 |
-- tryblas= |
2185 |
-- else |
2186 |
-- echo "....could not find either lapack or blas." |
2187 |
-- fi |
2188 |
-- fi |
2189 |
-- fi |
2190 |
-- # add 64 bit libs |
2191 |
-- case $system in |
2192 |
-- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; |
2193 |
-- esac |
2194 |
-- |
2195 |
-- ;; |
2196 |
-- osf1) |
2197 |
-- # OSF1 has dxml (old version) and cxml |
2198 |
-- # which should have both lapack and blas |
2199 |
-- trylapack="dxml cxml" |
2200 |
-- tryblas= |
2201 |
-- trydirs="${trydirs} /usr/shlib" |
2202 |
-- ;; |
2203 |
-- irix) |
2204 |
-- # Additional search paths for IRIX |
2205 |
-- trydirs="${trydirs} /usr/lib32" |
2206 |
-- # SCSL should have both LAPACK and BLAS |
2207 |
-- trylapack="scs" |
2208 |
-- tryblas="blas" |
2209 |
-- ;; |
2210 |
-- irix64) |
2211 |
-- # Additional search paths for IRIX64 |
2212 |
-- trydirs="${trydirs} /usr/lib64" |
2213 |
-- # SCSL should have both LAPACK and BLAS |
2214 |
-- trylapack="scs" |
2215 |
-- tryblas="blas" |
2216 |
-- # Extra compiler flags? |
2217 |
-- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" |
2218 |
-- ;; |
2219 |
-- aix) |
2220 |
-- # Additional search paths for AIX |
2221 |
-- trydirs="${trydirs}" |
2222 |
-- # AIX might have ESSL library - blas only I think |
2223 |
-- trylapack= |
2224 |
-- tryblas="essl" |
2225 |
-- ;; |
2226 |
-- hpux) |
2227 |
-- # Additional search paths for HPUX |
2228 |
-- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" |
2229 |
-- # HPUX should have both LAPACK (part of mlib) and BLAS |
2230 |
-- trylapack="lapack" |
2231 |
-- tryblas="blas" |
2232 |
-- # Extra compiler flags? |
2233 |
-- # +U77 required for ETIME function - this is already in XFFLAGS |
2234 |
-- #XLAPACKFLAGS="+U77" |
2235 |
-- ;; |
2236 |
-- |
2237 |
-- sunos | sunos64) |
2238 |
-- # Sun has libraries with BLAS and LAPACK invoked using |
2239 |
-- # -xlic_lib=sunperf |
2240 |
-- trylapack= |
2241 |
-- tryblas= |
2242 |
-- echo "SunOs can use the Sun Performance Library (if installed)" |
2243 |
-- echo "which has both BLAS and LAPACK 3.0" |
2244 |
-- echo |
2245 |
-- echo "Looking for a valid library to use..." |
2246 |
-- echo |
2247 |
-- # Loop over the possible library names |
2248 |
-- try_libs="sunperf" |
2249 |
-- for testlib in $try_libs |
2250 |
-- do |
2251 |
-- if test ! "$XLAPACK_LIB" ; then |
2252 |
-- # Try running a test compile to see if this a valid library |
2253 |
-- if test -f testlink.f || test -f testlink ; then |
2254 |
-- rm -f testlink* |
2255 |
-- fi |
2256 |
-- cat > testlink.f <<EOF |
2257 |
--c Test fortran program to link against library |
2258 |
-- PROGRAM TESTLINK |
2259 |
-- IMPLICIT NONE |
2260 |
-- INTEGER A |
2261 |
-- A = 1 |
2262 |
-- STOP |
2263 |
-- END |
2264 |
--EOF |
2265 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" |
2266 |
-- echo $test_compile |
2267 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2268 |
-- # Compilation was okay |
2269 |
-- echo "... -xlic_lib=$testlib is okay" |
2270 |
-- XLAPACK_LIB="-dalign -xlic_lib=$testlib" |
2271 |
-- # Set the next two variables so that configure |
2272 |
-- # doesn't try to build netlib libraries |
2273 |
-- LAPACKLIB="$testlib" |
2274 |
-- noblas=yes |
2275 |
-- else |
2276 |
-- # Compilation failed |
2277 |
-- echo "... cannot use -xlic_lib=$testlib" |
2278 |
-- fi |
2279 |
-- # End of test for testlib |
2280 |
-- fi |
2281 |
-- # End of loop over possible lib names |
2282 |
-- done |
2283 |
-- # Report if no suitable library was found |
2284 |
-- if test ! "$XLAPACK_LIB" ; then |
2285 |
-- echo |
2286 |
-- echo "No suitable LAPACK library was found." |
2287 |
-- echo "This may be because the Sun Performance Library is not" |
2288 |
-- echo "installed on your system" |
2289 |
-- echo "Contact your system administrator or Sun vendor" |
2290 |
-- fi |
2291 |
-- ;; |
2292 |
-- Darwin | Darwin32 | Darwin64 ) |
2293 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
2294 |
-- # -framework vecLib |
2295 |
-- echo "Darwin can use the vecLib Library (if installed)" |
2296 |
-- echo "which has both BLAS and LAPACK 3.0" |
2297 |
-- echo |
2298 |
-- # This is a special case so try running a test compile |
2299 |
-- echo "Checking: try to link library against test program" |
2300 |
-- if test -f testlink.f || test -f testlink ; then |
2301 |
-- rm -f testlink* |
2302 |
-- fi |
2303 |
-- cat > testlink.f <<EOF |
2304 |
--c Test fortran program to link against library |
2305 |
-- PROGRAM TESTLINK |
2306 |
-- IMPLICIT NONE |
2307 |
-- INTEGER A |
2308 |
-- A = 1 |
2309 |
-- STOP |
2310 |
-- END |
2311 |
--EOF |
2312 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" |
2313 |
-- echo $test_compile |
2314 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2315 |
-- # Compilation was okay |
2316 |
-- echo "... -framework vecLib is okay" |
2317 |
-- XLAPACK_LIB="-framework vecLib" |
2318 |
-- # Set the next two variables so that configure |
2319 |
-- # doesn't try to build netlib libraries |
2320 |
-- LAPACKLIB="vecLib" |
2321 |
-- noblas=yes |
2322 |
-- else |
2323 |
--#alternative linking for vecLib libraries |
2324 |
-- case `uname -sr` in |
2325 |
-- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; |
2326 |
-- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; |
2327 |
-- esac |
2328 |
-- |
2329 |
-- echo $test_compile |
2330 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2331 |
-- # Compilation was okay |
2332 |
-- echo "... -framework vecLib is okay" |
2333 |
-- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" |
2334 |
-- # Set the next two variables so that configure |
2335 |
-- # doesn't try to build netlib libraries |
2336 |
-- LAPACKLIB="-Wl,-framework -Wl,vecLib" |
2337 |
-- noblas=yes |
2338 |
-- else |
2339 |
-- # Compilation failed |
2340 |
-- echo "... cannot use -framework vecLib" |
2341 |
-- echo |
2342 |
-- fi |
2343 |
-- fi |
2344 |
-- trylapack= |
2345 |
-- tryblas= |
2346 |
--# try the fink installation |
2347 |
-- trydirs="${trydirs} /sw" |
2348 |
-- ;; |
2349 |
-- Darwin_ibm_compilers ) |
2350 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
2351 |
-- # -framework vecLib |
2352 |
-- echo "Darwin can use the vecLib Library (if installed)" |
2353 |
-- echo "which has both BLAS and LAPACK 3.0" |
2354 |
-- echo |
2355 |
-- # This is a special case so try running a test compile |
2356 |
-- echo "Checking: try to link library against test program" |
2357 |
-- if test -f testlink.f || test -f testlink ; then |
2358 |
-- rm -f testlink* |
2359 |
-- fi |
2360 |
-- cat > testlink.f <<EOF |
2361 |
--c Test fortran program to link against library |
2362 |
-- PROGRAM TESTLINK |
2363 |
-- IMPLICIT NONE |
2364 |
-- INTEGER A |
2365 |
-- A = 1 |
2366 |
-- STOP |
2367 |
-- END |
2368 |
--EOF |
2369 |
-- case `uname -sr` in |
2370 |
-- Darwin\ 8* ) |
2371 |
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" |
2372 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" |
2373 |
-- ;; |
2374 |
-- Darwin\ 7* ) |
2375 |
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" |
2376 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" |
2377 |
-- ;; |
2378 |
-- *) |
2379 |
-- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" |
2380 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" |
2381 |
-- esac |
2382 |
-- echo $test_compile |
2383 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2384 |
-- # Compilation was okay |
2385 |
-- echo "... -framework vecLib is okay" |
2386 |
-- # Set the next two variables so that configure |
2387 |
-- # doesn't try to build netlib libraries |
2388 |
-- LAPACKLIB="vecLib" |
2389 |
-- noblas=yes |
2390 |
-- else |
2391 |
-- # Compilation failed |
2392 |
-- XLAPACK_LIB="" |
2393 |
-- echo "... cannot use -framework vecLib" |
2394 |
-- echo |
2395 |
-- fi |
2396 |
-- trylapack= |
2397 |
-- tryblas= |
2398 |
--# try the fink installation |
2399 |
-- trydirs="${trydirs} /sw" |
2400 |
-- ;; |
2401 |
-- |
2402 |
-- Darwin_intel_compilers) |
2403 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
2404 |
-- # -F vecLib |
2405 |
-- echo "Darwin can use the vecLib Library (if installed)" |
2406 |
-- echo "which has both BLAS and LAPACK 3.0" |
2407 |
-- echo |
2408 |
-- # This is a special case so try running a test compile |
2409 |
-- echo "Checking: try to link library against test program" |
2410 |
-- if test -f testlink.f || test -f testlink ; then |
2411 |
-- rm -f testlink* |
2412 |
-- fi |
2413 |
-- cat > testlink.f <<EOF |
2414 |
--c Test fortran program to link against library |
2415 |
-- PROGRAM TESTLINK |
2416 |
-- IMPLICIT NONE |
2417 |
-- INTEGER A |
2418 |
-- A = 1 |
2419 |
-- STOP |
2420 |
-- END |
2421 |
--EOF |
2422 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" |
2423 |
-- echo $test_compile |
2424 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2425 |
-- # Compilation was okay |
2426 |
-- # doesn't try to build netlib libraries |
2427 |
-- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" |
2428 |
-- LAPACKLIB="vecLib" |
2429 |
-- noblas=yes |
2430 |
-- else |
2431 |
-- # Compilation failed |
2432 |
-- echo "... cannot use -framework vecLib" |
2433 |
-- echo |
2434 |
-- fi |
2435 |
-- trylapack= |
2436 |
-- tryblas= |
2437 |
--# try the fink installation |
2438 |
-- trydirs="${trydirs} /sw" |
2439 |
-- ;; |
2440 |
-- |
2441 |
--# linux_ia64_sgi_altix) |
2442 |
--# SGI Japan |
2443 |
-- ia64_linux_intel) |
2444 |
-- # Additional search paths for Linux/IA64 |
2445 |
-- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" |
2446 |
-- # SCSL and MKL should have both LAPACK and BLAS |
2447 |
-- trylapack="mkl_lapack scs lapack" |
2448 |
-- tryblas="mkl scs blas" |
2449 |
-- ;; |
2450 |
-- linux_ibm_compilers ) |
2451 |
-- trylapack="lapack" |
2452 |
-- tryblas="blas" |
2453 |
-- ;; |
2454 |
-- linux64_ibm_compilers ) |
2455 |
-- trydirs="/usr/lib64 ${trydirs}" |
2456 |
-- trylapack="lapack" |
2457 |
-- tryblas="blas" |
2458 |
-- ;; |
2459 |
-- linux_intel_compilers ) |
2460 |
-- trydirs="/usr/lib64 ${trydirs}" |
2461 |
-- trylapack="mkl_lapack lapack" |
2462 |
-- tryblas="mkl blas" |
2463 |
-- ;; |
2464 |
-- *) |
2465 |
-- echo "The guesses for this system may not be correct - please" |
2466 |
-- echo "e-mail ccp4@×××××××.uk if you have any extra information" |
2467 |
-- echo |
2468 |
-- # Default guess is just libblas |
2469 |
-- trylapack="lapack" |
2470 |
-- tryblas="blas" |
2471 |
-- ;; |
2472 |
-- esac |
2473 |
-- # |
2474 |
-- # Search for LAPACK libraries |
2475 |
-- # |
2476 |
-- # Write out what the guesses are |
2477 |
-- if test "$trylapack" ; then |
2478 |
-- echo "Possible LAPACK library names for this system:" |
2479 |
-- for libname in $trylapack |
2480 |
-- do |
2481 |
-- echo " lib$libname" |
2482 |
-- done |
2483 |
-- # Possible library name extensions |
2484 |
-- tryexts="a so dylib" |
2485 |
-- # Now loop over all the possibilities and see if anything |
2486 |
-- # turns up |
2487 |
-- echo |
2488 |
-- echo "Searching for libraries with LAPACK and BLAS:" |
2489 |
-- for testdir in $trydirs |
2490 |
-- do |
2491 |
-- for testlib in $trylapack |
2492 |
-- do |
2493 |
-- for ext in $tryexts |
2494 |
-- do |
2495 |
-- if test ! "$LAPACKLIB"; then |
2496 |
-- if test -s "$testdir/lib$testlib.$ext" ; then |
2497 |
-- echo "...found LAPACK library: $testdir/lib$testlib.$ext" |
2498 |
-- # Now try and link to a test program |
2499 |
-- # This is really for IRIX where libraries can be |
2500 |
-- # o32 or n32 |
2501 |
-- echo " Testing: try to link library against test program" |
2502 |
-- if test -f testlink.f || test -f testlink ; then |
2503 |
-- rm -f testlink* |
2504 |
-- fi |
2505 |
-- cat > testlink.f <<EOF |
2506 |
--c Test fortran program to link against library |
2507 |
-- PROGRAM TESTLINK |
2508 |
-- IMPLICIT NONE |
2509 |
-- INTEGER A |
2510 |
-- A = 1 |
2511 |
-- STOP |
2512 |
-- END |
2513 |
--EOF |
2514 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
2515 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
2516 |
-- echo $test_compile |
2517 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
2518 |
-- have_lapack=yes |
2519 |
-- else |
2520 |
--# cover clapack option |
2521 |
-- echo $test_ccompile |
2522 |
-- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then |
2523 |
-- have_lapack=yes |
2524 |
-- fi |
2525 |
-- fi |
2526 |
-- if test x$have_lapack = xyes ; then |
2527 |
-- # This one is okay |
2528 |
-- LAPACKLIB="$testlib" |
2529 |
-- LAPACKDIR="$testdir" |
2530 |
-- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" |
2531 |
-- # |
2532 |
-- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" |
2533 |
-- # |
2534 |
-- # Test to see if we need BLAS too |
2535 |
-- # Do this by trying to compile a test program |
2536 |
-- # Use the LSAME test for now |
2537 |
-- echo |
2538 |
-- echo " * Checking whether we need a separate BLAS library *" |
2539 |
-- echo " Testing: try linking library against test program" |
2540 |
-- cd lib/lapack/test |
2541 |
-- if test -f testlsame ; then |
2542 |
-- rm -f testsame testlsame.o |
2543 |
-- fi |
2544 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" |
2545 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" |
2546 |
-- echo $test_compile |
2547 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then |
2548 |
-- have_blas=yes |
2549 |
-- else |
2550 |
--#cblas route |
2551 |
-- echo $test_ccompile |
2552 |
-- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then |
2553 |
-- have_blas=yes |
2554 |
-- fi |
2555 |
-- fi |
2556 |
-- if test x$have_blas = xyes ; then |
2557 |
-- echo "Test program okay - additional separate BLAS not required" |
2558 |
-- noblas=yes |
2559 |
-- else |
2560 |
-- echo "Test program failed - need a separate BLAS library" |
2561 |
-- fi |
2562 |
-- cd ../../.. |
2563 |
-- else |
2564 |
-- # Keep looking |
2565 |
-- echo " link failed - cannot use lib$testlib" |
2566 |
-- fi |
2567 |
-- fi |
2568 |
-- fi |
2569 |
-- done |
2570 |
-- done |
2571 |
-- if test ! "$LAPACKLIB"; then |
2572 |
-- echo "...nothing in $testdir" |
2573 |
-- fi |
2574 |
-- done |
2575 |
-- fi |
2576 |
-- |
2577 |
-- # If LAPACKLIB hasn't been set at this point then no LAPACK library |
2578 |
-- # was found |
2579 |
-- if test ! "$LAPACKLIB" ; then |
2580 |
-- echo |
2581 |
-- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" |
2582 |
-- make_lapack=lapacklib |
2583 |
-- fi |
2584 |
-- # Look for possible BLAS |
2585 |
-- if test ! "$noblas" ; then |
2586 |
-- if test "$tryblas" ; then |
2587 |
-- echo |
2588 |
-- echo "Possible BLAS library names for this system:" |
2589 |
-- for libname in $tryblas |
2590 |
-- do |
2591 |
-- echo " lib$libname" |
2592 |
-- done |
2593 |
-- # Possible library name extensions |
2594 |
-- tryexts="a so" |
2595 |
-- # Now loop over all the possibilities and see if anything |
2596 |
-- # turns up |
2597 |
-- echo |
2598 |
-- echo "Searching for libraries with BLAS:" |
2599 |
-- for testdir in $trydirs |
2600 |
-- do |
2601 |
-- for testlib in $tryblas |
2602 |
-- do |
2603 |
-- for ext in $tryexts |
2604 |
-- do |
2605 |
-- if test ! "$BLASLIB"; then |
2606 |
-- if test -s "$testdir/lib$testlib.$ext" ; then |
2607 |
-- echo "...found BLAS library: $testdir/lib$testlib.$ext" |
2608 |
-- # Now try and link to a test program |
2609 |
-- # This is really for IRIX where libraries can be |
2610 |
-- # o32 or n32 |
2611 |
-- echo " Testing: try to link library against test program" |
2612 |
-- if test -f testlink.f || test -f testlink ; then |
2613 |
-- rm -f testlink* |
2614 |
-- fi |
2615 |
-- cat > testlink.f <<EOF |
2616 |
--c Test fortran program to link against library |
2617 |
-- PROGRAM TESTLINK |
2618 |
-- IMPLICIT NONE |
2619 |
-- INTEGER A |
2620 |
-- A = 1 |
2621 |
-- STOP |
2622 |
-- END |
2623 |
--EOF |
2624 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
2625 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
2626 |
-- echo $test_compile |
2627 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then |
2628 |
-- have_blas=yes |
2629 |
-- else |
2630 |
-- echo $test_ccompile |
2631 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then |
2632 |
-- have_blas=yes |
2633 |
-- fi |
2634 |
-- fi |
2635 |
-- if test x$have_blas = xyes ; then |
2636 |
-- # This one is okay |
2637 |
-- BLASLIB="$testlib" |
2638 |
-- BLASDIR="$testdir" |
2639 |
-- BLASEXT="$ext" |
2640 |
-- echo "Link ok - using lib$BLASLIB from $BLASDIR" |
2641 |
-- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" |
2642 |
-- else |
2643 |
-- # Keep looking |
2644 |
-- echo " link failed - cannot use lib$testlib" |
2645 |
-- fi |
2646 |
-- fi |
2647 |
-- fi |
2648 |
-- done |
2649 |
-- done |
2650 |
-- if test ! "$BLASLIB"; then |
2651 |
-- echo "...nothing in $testdir" |
2652 |
-- fi |
2653 |
-- done |
2654 |
-- fi |
2655 |
-- # Do we need to build BLAS too? |
2656 |
-- if test ! "$BLASLIB" ; then |
2657 |
-- echo |
2658 |
-- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" |
2659 |
-- echo "This may result in poorer performance of the LAPACK routines" |
2660 |
-- make_blas=blaslib |
2661 |
-- BLASLIB=blas |
2662 |
-- BLASDIR="$srcdir/lib/lapack" |
2663 |
-- BLASEXT="a" |
2664 |
-- fi |
2665 |
-- fi |
2666 |
-+ # gentoo is clever |
2667 |
-+ make_blas= |
2668 |
-+ make_lapack= |
2669 |
-+ BLASLIB=$(${PKG_CONFIG} --libs blas) |
2670 |
-+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) |
2671 |
-+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" |
2672 |
-+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" |
2673 |
- # Otherwise force building of NetLib BLAS and LAPACK libs |
2674 |
-- else |
2675 |
-- echo |
2676 |
-- echo "! Force building of NetLib BLAS and LAPACK..." |
2677 |
-- make_blas=blaslib |
2678 |
-- make_lapack=lapacklib |
2679 |
-- BLASLIB=blas |
2680 |
-- BLASDIR="$srcdir/lib/lapack" |
2681 |
-- BLASEXT="a" |
2682 |
-- fi |
2683 |
- # need to know if we the lapack library was linked using the C or |
2684 |
- # fortran linker |
2685 |
- if test -f testlink.f || test -f testlink || test -f testlink.c ; then |
2686 |
-@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} |
2687 |
- INSTALL_DATA = ${INSTALL_DATA} |
2688 |
- libdir = $libdir |
2689 |
- # |
2690 |
--BLASLIB = lib${BLASLIB}.${BLASEXT} |
2691 |
--LAPACKLIB = liblapack.a |
2692 |
-+BLASLIB = ${BLASLIB} |
2693 |
-+LAPACKLIB = ${LAPACKLIB} |
2694 |
- # |
2695 |
- # These variables define targets in the main Makefile |
2696 |
- blaslib = ${make_blas} |
2697 |
|
2698 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch |
2699 |
deleted file mode 100644 |
2700 |
index 9d8fefe..0000000 |
2701 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch |
2702 |
+++ /dev/null |
2703 |
@@ -1,23 +0,0 @@ |
2704 |
-diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am |
2705 |
-index 053e83a..4ff3394 100755 |
2706 |
---- a/src/pisa/sbase/Makefile.am |
2707 |
-+++ b/src/pisa/sbase/Makefile.am |
2708 |
-@@ -1,4 +1,4 @@ |
2709 |
--pkgdatadir = $(datadir)/sbase |
2710 |
-+pkgdatadir = $(datadir)/pisa/sbase |
2711 |
- dist_pkgdata_DATA = \ |
2712 |
- graph.sbase index.sbase struct.sbase |
2713 |
- |
2714 |
-diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in |
2715 |
-index faa3f7f..8630bd7 100755 |
2716 |
---- a/src/pisa/sbase/Makefile.in |
2717 |
-+++ b/src/pisa/sbase/Makefile.in |
2718 |
-@@ -62,7 +62,7 @@ POST_UNINSTALL = : |
2719 |
- EXEEXT = @EXEEXT@ |
2720 |
- OBJEXT = @OBJEXT@ |
2721 |
- PATH_SEPARATOR = @PATH_SEPARATOR@ |
2722 |
--pkgdatadir = $(datadir)/sbase |
2723 |
-+pkgdatadir = $(datadir)/pisa/sbase |
2724 |
- AMTAR = @AMTAR@ |
2725 |
- AR_FLAGS = @AR_FLAGS@ |
2726 |
- AWK = @AWK@ |
2727 |
|
2728 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch |
2729 |
deleted file mode 100644 |
2730 |
index 7a012be..0000000 |
2731 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch |
2732 |
+++ /dev/null |
2733 |
@@ -1,65 +0,0 @@ |
2734 |
-diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash |
2735 |
-index 9848101..cea8ae6 100755 |
2736 |
---- a/ccp4-6.1.2/include/ccp4.setup-bash |
2737 |
-+++ b/ccp4-6.1.2/include/ccp4.setup-bash |
2738 |
-@@ -188,9 +188,9 @@ fi |
2739 |
- #Python path for the subprocess fixed module |
2740 |
- |
2741 |
- if [ $ccp4_first_in_path -eq 1 ]; then |
2742 |
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} |
2743 |
-+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} |
2744 |
- else |
2745 |
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python |
2746 |
-+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python |
2747 |
- fi |
2748 |
- |
2749 |
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### |
2750 |
-diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh |
2751 |
-index 42f0820..93c2cf3 100755 |
2752 |
---- a/ccp4-6.1.2/include/ccp4.setup-csh |
2753 |
-+++ b/ccp4-6.1.2/include/ccp4.setup-csh |
2754 |
-@@ -180,9 +180,9 @@ endif |
2755 |
- #Python path for the subprocess fixed module |
2756 |
- if (${?PYTHONPATH}) then |
2757 |
- if ($ccp4_first_in_path) then |
2758 |
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} |
2759 |
-+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} |
2760 |
- else |
2761 |
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python |
2762 |
-+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python |
2763 |
- endif |
2764 |
- else |
2765 |
- setenv PYTHONPATH ${CCP4}/share/python |
2766 |
-diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh |
2767 |
-index 4396ebf..a0455bd 100755 |
2768 |
---- a/ccp4-6.1.2/include/ccp4.setup-sh |
2769 |
-+++ b/ccp4-6.1.2/include/ccp4.setup-sh |
2770 |
-@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg |
2771 |
- #Python path for the subprocess fixed module |
2772 |
- |
2773 |
- if test $ccp4_first_in_path -eq 1; then |
2774 |
-- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} |
2775 |
-+ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} |
2776 |
- else |
2777 |
-- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python |
2778 |
-+ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python |
2779 |
- fi |
2780 |
- |
2781 |
- ################### THE REST SHOULDN'T NEED EDITING ##################### |
2782 |
-diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh |
2783 |
-index 0e5c2ce..53523f3 100755 |
2784 |
---- a/ccp4-6.1.2/include/ccp4.setup-zsh |
2785 |
-+++ b/ccp4-6.1.2/include/ccp4.setup-zsh |
2786 |
-@@ -157,10 +157,10 @@ export CLASSPATH |
2787 |
- #Python path for the subprocess fixed module |
2788 |
- |
2789 |
- if ($ccp4_first_in_path) then |
2790 |
-- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} |
2791 |
-+ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} |
2792 |
- export PYTHONPATH |
2793 |
- else |
2794 |
-- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python |
2795 |
-+ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python |
2796 |
- export PYTHONPATH |
2797 |
- fi |
2798 |
- |
2799 |
|
2800 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch |
2801 |
deleted file mode 100644 |
2802 |
index a5144cf..0000000 |
2803 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch |
2804 |
+++ /dev/null |
2805 |
@@ -1,60 +0,0 @@ |
2806 |
-diff --git a/src/Makefile.in b/src/Makefile.in |
2807 |
-index 70781f3..b2dcc25 100755 |
2808 |
---- a/src/Makefile.in |
2809 |
-+++ b/src/Makefile.in |
2810 |
-@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o |
2811 |
- pdbcur : $(pdbcurobjs) |
2812 |
- @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) |
2813 |
- ncont : $(ncontobjs) |
2814 |
-- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) |
2815 |
-+ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb |
2816 |
- coord_format : $(coord_formatobjs) |
2817 |
- @$(SETFLAGS) xxx=1 ; \ |
2818 |
- rm -f coord_format; \ |
2819 |
-diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am |
2820 |
-index 85f212e..2608c6d 100755 |
2821 |
---- a/src/rapper/LOOP/Makefile.am |
2822 |
-+++ b/src/rapper/LOOP/Makefile.am |
2823 |
-@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. |
2824 |
- hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ |
2825 |
- residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp |
2826 |
- |
2827 |
--rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la |
2828 |
-+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ |
2829 |
- |
2830 |
- pkgdatadir = $(datadir)/rapper |
2831 |
- dist_pkgdata_DATA = params.xml |
2832 |
- |
2833 |
--INCLUDES = -I. -I../gc7.0/include -I../libxml2/include |
2834 |
-+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ |
2835 |
- #SUBDIRS = \ |
2836 |
- #@PYTHON_USE_TRUE@ python |
2837 |
- |
2838 |
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am |
2839 |
-index e78b10d..486b931 100755 |
2840 |
---- a/src/rapper/Makefile.am |
2841 |
-+++ b/src/rapper/Makefile.am |
2842 |
-@@ -1,3 +1,3 @@ |
2843 |
--SUBDIRS = libxml2 gc7.0 LOOP data |
2844 |
-+SUBDIRS = LOOP data |
2845 |
- |
2846 |
- EXTRA_DIST = |
2847 |
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac |
2848 |
-index 5e4ef69..268a579 100755 |
2849 |
---- a/src/rapper/configure.ac |
2850 |
-+++ b/src/rapper/configure.ac |
2851 |
-@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) |
2852 |
- |
2853 |
- AC_SUBST(rapper_LDFLAGS) |
2854 |
- |
2855 |
--AC_CONFIG_SUBDIRS([gc7.0 libxml2]) |
2856 |
-+PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) |
2857 |
-+AC_SUBST([LIBXML_CFLAGS]) |
2858 |
-+AC_SUBST([LIBXML_LIBS]) |
2859 |
-+ |
2860 |
-+PKG_CHECK_MODULES([GC],[bdw-gc]) |
2861 |
-+AC_SUBST([GC_CFLAGS]) |
2862 |
-+AC_SUBST([GC_LIBS]) |
2863 |
-+ |
2864 |
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) |
2865 |
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) |
2866 |
|
2867 |
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch |
2868 |
deleted file mode 100644 |
2869 |
index 107cfd7..0000000 |
2870 |
--- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch |
2871 |
+++ /dev/null |
2872 |
@@ -1,131 +0,0 @@ |
2873 |
- src/Makefile.in | 14 +++++----- |
2874 |
- src/pisa/configure.ac | 67 +++++++++---------------------------------------- |
2875 |
- 2 files changed, 19 insertions(+), 62 deletions(-) |
2876 |
- |
2877 |
-diff --git a/src/Makefile.in b/src/Makefile.in |
2878 |
-index 70781f3..b11db04 100755 |
2879 |
---- a/src/Makefile.in |
2880 |
-+++ b/src/Makefile.in |
2881 |
-@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) |
2882 |
- eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) |
2883 |
- pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end |
2884 |
- @$(SETFLAGS) xxx=1 ; \ |
2885 |
-- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; |
2886 |
-- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp |
2887 |
-+ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; |
2888 |
-+ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp |
2889 |
- |
2890 |
- ### bp3, afro, gcx |
2891 |
- |
2892 |
-@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) |
2893 |
- |
2894 |
- $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end |
2895 |
- @$(SETFLAGS) xxx=1 ; \ |
2896 |
-- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ |
2897 |
-- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C |
2898 |
-+ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ |
2899 |
-+ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C |
2900 |
- |
2901 |
- ### crunch2 pmf |
2902 |
- |
2903 |
-@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) |
2904 |
- cross_validate : $(cross_validateobjs) |
2905 |
- @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) |
2906 |
- cif2xml.o cross_validate.o : # dependencies at end |
2907 |
-- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp |
2908 |
-+ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp |
2909 |
- |
2910 |
- pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract |
2911 |
- pdb_extract_suite : |
2912 |
-@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : |
2913 |
- $(dev_tools_cxxtargets) : |
2914 |
- @$(SETFLAGS) xxx=1; \ |
2915 |
- rm -f $@; \ |
2916 |
-- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ |
2917 |
-- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) |
2918 |
-+ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ |
2919 |
-+ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) |
2920 |
- |
2921 |
- ### mlphare |
2922 |
- mlphare: |
2923 |
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac |
2924 |
-index 81afdda..044b6f8 100755 |
2925 |
---- a/src/pisa/configure.ac |
2926 |
-+++ b/src/pisa/configure.ac |
2927 |
-@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) |
2928 |
- # test for function in m |
2929 |
- AC_CHECK_LIB([m], [sqrt]) |
2930 |
- |
2931 |
--dnl Optional: Check for MMDB. |
2932 |
--AM_PATH_MMDB(, |
2933 |
-- [ if test "x$mmdb_prefix" != x ; then |
2934 |
-- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then |
2935 |
-- case "$ac_MMDB_CXXFLAGS" in |
2936 |
-- *src/mmdb ) |
2937 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` |
2938 |
-- ;; |
2939 |
-- *include/mmdb ) |
2940 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` |
2941 |
-- ;; |
2942 |
-- *) |
2943 |
-- esac |
2944 |
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" |
2945 |
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` |
2946 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
2947 |
-- else |
2948 |
-- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" |
2949 |
-- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" |
2950 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
2951 |
-- fi |
2952 |
-- else |
2953 |
-- AC_MSG_ERROR([mmdb not found]) |
2954 |
-- fi |
2955 |
-- ] |
2956 |
--) |
2957 |
-+PKG_CHECK_MODULES([MMDB],[mmdb]) |
2958 |
-+PKG_CHECK_MODULES([SSM],[ssm]) |
2959 |
-+ |
2960 |
-+MMDB_CXXFLAGS=${MMDB_CFLAGS} |
2961 |
-+ |
2962 |
-+AC_SUBST([MMDB_CFLAGS]) |
2963 |
-+AC_SUBST([MMDB_CXXFLAGS]) |
2964 |
-+AC_SUBST([SSM_CFLAGS]) |
2965 |
-+ |
2966 |
-+AC_SUBST([MMDB_LIBS]) |
2967 |
-+AC_SUBST([SSM_LIBS]) |
2968 |
- |
2969 |
--ac_saved_CXXFLAGS=$CXXFLAGS |
2970 |
--ac_saved_LIBS=$LIBS |
2971 |
- CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" |
2972 |
- LIBS="$MMDB_LIBS $LIBS" |
2973 |
--AM_PATH_SSM(, |
2974 |
-- [ if test "x$ssm_prefix" != x ; then |
2975 |
-- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then |
2976 |
-- case "$ac_SSM_CXXFLAGS" in |
2977 |
-- *lib/ssm ) |
2978 |
-- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` |
2979 |
-- ;; |
2980 |
-- *include/ssm ) |
2981 |
-- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` |
2982 |
-- ;; |
2983 |
-- *) |
2984 |
-- esac |
2985 |
-- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" |
2986 |
-- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` |
2987 |
-- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) |
2988 |
-- else |
2989 |
-- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" |
2990 |
-- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" |
2991 |
-- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) |
2992 |
-- fi |
2993 |
-- else |
2994 |
-- AC_MSG_ERROR([ssm not found]) |
2995 |
-- fi |
2996 |
-- ] |
2997 |
--) |
2998 |
--CXXFLAGS=$ac_saved_CXXFLAGS |
2999 |
--LIBS=$ac_saved_LIBS |
3000 |
-+ |
3001 |
- |
3002 |
- # Checks for typedefs, structures, and compiler characteristics. |
3003 |
- # |
3004 |
|
3005 |
diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch |
3006 |
deleted file mode 100644 |
3007 |
index 4b98545..0000000 |
3008 |
--- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch |
3009 |
+++ /dev/null |
3010 |
@@ -1,130 +0,0 @@ |
3011 |
- src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++--------------- |
3012 |
- 1 file changed, 17 insertions(+), 17 deletions(-) |
3013 |
- |
3014 |
-diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c |
3015 |
-index 2c9f02f..98d814a 100755 |
3016 |
---- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c |
3017 |
-+++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c |
3018 |
-@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags, |
3019 |
- puts("canvas_draw_line: about to evaluate the command..."); |
3020 |
- } |
3021 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3022 |
-- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result); |
3023 |
-+ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); |
3024 |
- return 0; |
3025 |
- } |
3026 |
- if (CCP4MAPWISH_CANVAS_DIAG) |
3027 |
-@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y, |
3028 |
- puts("canvas_draw_rectangle: about to evaluate the command..."); |
3029 |
- } |
3030 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3031 |
-- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result); |
3032 |
-+ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); |
3033 |
- printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units); |
3034 |
- return 0; |
3035 |
- } |
3036 |
-@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y, |
3037 |
- /* Execute the command which draws the label */ |
3038 |
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command); |
3039 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3040 |
-- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result); |
3041 |
-+ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3042 |
- return 0; |
3043 |
- } |
3044 |
- |
3045 |
-@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale) |
3046 |
- /* Execute the command which scales the canvas */ |
3047 |
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command); |
3048 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3049 |
-- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); |
3050 |
-+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3051 |
- return 0; |
3052 |
- } |
3053 |
- |
3054 |
-@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas) |
3055 |
- /* Execute the command which resizes the canvas */ |
3056 |
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); |
3057 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3058 |
-- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result); |
3059 |
-+ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3060 |
- return 0; |
3061 |
- } |
3062 |
- |
3063 |
-@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty) |
3064 |
- /* Execute the command which resizes the canvas */ |
3065 |
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); |
3066 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3067 |
-- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result); |
3068 |
-+ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3069 |
- return 0; |
3070 |
- } |
3071 |
- |
3072 |
-@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag) |
3073 |
- /* Execute the command which deletes the tagged items */ |
3074 |
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command); |
3075 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3076 |
-- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); |
3077 |
-+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3078 |
- return 0; |
3079 |
- } |
3080 |
- |
3081 |
-@@ -892,15 +892,15 @@ int canvas_exists(char *canvas) |
3082 |
- |
3083 |
- sprintf(tmpstr,"winfo exists %s",canvas); |
3084 |
- if (Tcl_Eval(interp,tmpstr) != TCL_OK) { |
3085 |
-- printf("canvas_exists: error from Tcl_Eval: %s",interp->result); |
3086 |
-+ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); |
3087 |
- return 0; |
3088 |
- } |
3089 |
- /* Extract a long int using strtol |
3090 |
- If no conversion takes place then "endptr" will be equal |
3091 |
- to "result" */ |
3092 |
-- istatus = (int) strtol(interp->result,&endptr,10); |
3093 |
-- if (strcmp(interp->result,endptr) == 0) { |
3094 |
-- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result); |
3095 |
-+ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10); |
3096 |
-+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { |
3097 |
-+ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp)); |
3098 |
- return 0; |
3099 |
- } |
3100 |
- if (!istatus) { |
3101 |
-@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units) |
3102 |
- |
3103 |
- /* Execute the tk scaling command */ |
3104 |
- if (Tcl_Eval(interp,"tk scaling") != TCL_OK) { |
3105 |
-- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result); |
3106 |
-+ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); |
3107 |
- return (float) 0.0; |
3108 |
- } |
3109 |
- |
3110 |
- /* Extract a float from the result */ |
3111 |
-- tkscale = ((float) strtod(interp->result,&endptr)); |
3112 |
-- if (strcmp(interp->result,endptr) == 0) { |
3113 |
-+ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr)); |
3114 |
-+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { |
3115 |
- printf("canvas_get_tk_scaling: couldn't extract scale factor\n"); |
3116 |
- return (float) 0.0; |
3117 |
- } |
3118 |
-@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4]) |
3119 |
- |
3120 |
- /* Evaluate the command */ |
3121 |
- if (Tcl_Eval(interp,command) != TCL_OK) { |
3122 |
-- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result); |
3123 |
-+ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); |
3124 |
- return 0; |
3125 |
- } |
3126 |
- |
3127 |
- /* Process the result - it should consist of 4 integers */ |
3128 |
- /* Use strtok which can split the string based on tokens |
3129 |
- set by the programmer - in this case a space */ |
3130 |
-- if (!interp->result) { |
3131 |
-+ if (!Tcl_GetStringResult(interp)) { |
3132 |
- puts("canvas_get_limits: failed to fetch canvas limits"); |
3133 |
- return TCL_ERROR; |
3134 |
- } |
3135 |
- i = 0; |
3136 |
-- p = strtok(interp->result," "); |
3137 |
-+ p = strtok(Tcl_GetStringResult(interp)," "); |
3138 |
- if (p == NULL) { |
3139 |
- return 0; |
3140 |
- } |
3141 |
|
3142 |
diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml |
3143 |
deleted file mode 100644 |
3144 |
index 51fdeda..0000000 |
3145 |
--- a/sci-chemistry/ccp4-apps/metadata.xml |
3146 |
+++ /dev/null |
3147 |
@@ -1,5 +0,0 @@ |
3148 |
-<?xml version="1.0" encoding="UTF-8"?> |
3149 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
3150 |
-<pkgmetadata> |
3151 |
- <herd>sci-chemistry</herd> |
3152 |
-</pkgmetadata> |
3153 |
|
3154 |
diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild |
3155 |
deleted file mode 100644 |
3156 |
index eea4a40..0000000 |
3157 |
--- a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild |
3158 |
+++ /dev/null |
3159 |
@@ -1,38 +0,0 @@ |
3160 |
-# Copyright 1999-2012 Gentoo Foundation |
3161 |
-# Distributed under the terms of the GNU General Public License v2 |
3162 |
-# $Id$ |
3163 |
- |
3164 |
-EAPI=4 |
3165 |
- |
3166 |
-inherit fortran-2 |
3167 |
- |
3168 |
-DESCRIPTION="Protein X-ray crystallography toolkit -- meta package" |
3169 |
-HOMEPAGE="http://www.ccp4.ac.uk/" |
3170 |
-SRC_URI="" |
3171 |
- |
3172 |
-LICENSE="ccp4" |
3173 |
-SLOT="0" |
3174 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
3175 |
-IUSE="X arpwarp +balbes" |
3176 |
- |
3177 |
-RDEPEND=" |
3178 |
- ~sci-chemistry/ccp4-apps-${PV}[X?] |
3179 |
- !<=sci-chemistry/ccp4-apps-${PV}-r2 |
3180 |
- >=sci-chemistry/molrep-11.0.00-r1 |
3181 |
- >=sci-chemistry/mosflm-7.0.6-r2 |
3182 |
- sci-chemistry/mrbump[X?] |
3183 |
- >=sci-chemistry/oasis-4.0-r1 |
3184 |
- >=sci-chemistry/pdb-extract-3.004-r2 |
3185 |
- >=sci-chemistry/refmac-5.5.0110-r1 |
3186 |
- >=sci-chemistry/scala-3.3.18-r1 |
3187 |
- >=sci-chemistry/sfcheck-7.03.18-r1 |
3188 |
- sci-chemistry/xia2 |
3189 |
- arpwarp? ( sci-chemistry/arp-warp-bin ) |
3190 |
- balbes? ( sci-chemistry/balbes ) |
3191 |
- X? ( |
3192 |
- ~sci-chemistry/ccp4i-${PV} |
3193 |
- sci-chemistry/imosflm |
3194 |
- sci-chemistry/pymol |
3195 |
- sci-chemistry/rasmol |
3196 |
- )" |
3197 |
-DEPEND="" |
3198 |
|
3199 |
diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch |
3200 |
deleted file mode 100644 |
3201 |
index 1420419..0000000 |
3202 |
--- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch |
3203 |
+++ /dev/null |
3204 |
@@ -1,87 +0,0 @@ |
3205 |
---- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 |
3206 |
-+++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 |
3207 |
-@@ -623,45 +623,45 @@ |
3208 |
- # echo "! Beware -- the $system installation isn't properly tested." ; } |
3209 |
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' |
3210 |
- |
3211 |
--if test -z "$onlylibs" ; then |
3212 |
-- for i in CCP4_SCR BINSORT_SCR; do |
3213 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3214 |
-- else |
3215 |
-- eval echo "! No directory \$$i and can\'t create it." |
3216 |
-- echo " Check the value of $i." |
3217 |
-- badvar=1 |
3218 |
-- fi |
3219 |
-- done |
3220 |
-- |
3221 |
-- for i in libdir bindir; do |
3222 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3223 |
-- else |
3224 |
-- eval echo "! No directory \$$i and can\'t create it." |
3225 |
-- echo " Check the argument of --$i." |
3226 |
-- badvar=1 |
3227 |
-- fi |
3228 |
-- done |
3229 |
-- |
3230 |
-- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
3231 |
-- if test -d $i || mkdir $i; then : |
3232 |
-- else |
3233 |
-- eval echo "! No directory $i and can\'t create it." |
3234 |
-- badvar=1 |
3235 |
-- fi |
3236 |
-- done |
3237 |
--else |
3238 |
-- # Kludge to fool the "Makefile" target in the top-level CCP4 |
3239 |
-- # Makefile into not trying to remake src/Makefile.in |
3240 |
-- for i in $srcdir/src $srcdir/lib/src ; do |
3241 |
-- if test -d $i || mkdir $i; then |
3242 |
-- if ! test -f $i/Makefile.in ; then |
3243 |
-- echo |
3244 |
-- echo "onlylibs: making dummy file $i/Makefile.in" |
3245 |
-- touch $i/Makefile.in |
3246 |
-- fi |
3247 |
-- fi |
3248 |
-- done |
3249 |
--fi |
3250 |
-+#if test -z "$onlylibs" ; then |
3251 |
-+# for i in CCP4_SCR BINSORT_SCR; do |
3252 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3253 |
-+# else |
3254 |
-+# eval echo "! No directory \$$i and can\'t create it." |
3255 |
-+# echo " Check the value of $i." |
3256 |
-+# badvar=1 |
3257 |
-+# fi |
3258 |
-+# done |
3259 |
-+# |
3260 |
-+# for i in libdir bindir; do |
3261 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3262 |
-+# else |
3263 |
-+# eval echo "! No directory \$$i and can\'t create it." |
3264 |
-+# echo " Check the argument of --$i." |
3265 |
-+# badvar=1 |
3266 |
-+# fi |
3267 |
-+# done |
3268 |
-+# |
3269 |
-+# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
3270 |
-+# if test -d $i || mkdir $i; then : |
3271 |
-+# else |
3272 |
-+# eval echo "! No directory $i and can\'t create it." |
3273 |
-+# badvar=1 |
3274 |
-+# fi |
3275 |
-+# done |
3276 |
-+#else |
3277 |
-+# # Kludge to fool the "Makefile" target in the top-level CCP4 |
3278 |
-+# # Makefile into not trying to remake src/Makefile.in |
3279 |
-+# for i in $srcdir/src $srcdir/lib/src ; do |
3280 |
-+# if test -d $i || mkdir $i; then |
3281 |
-+# if ! test -f $i/Makefile.in ; then |
3282 |
-+# echo |
3283 |
-+# echo "onlylibs: making dummy file $i/Makefile.in" |
3284 |
-+# touch $i/Makefile.in |
3285 |
-+# fi |
3286 |
-+# fi |
3287 |
-+# done |
3288 |
-+#fi |
3289 |
- |
3290 |
- ### sanity checks |
3291 |
- |
3292 |
|
3293 |
diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch |
3294 |
deleted file mode 100644 |
3295 |
index a77d949..0000000 |
3296 |
--- a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch |
3297 |
+++ /dev/null |
3298 |
@@ -1,11 +0,0 @@ |
3299 |
---- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 |
3300 |
-+++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 |
3301 |
-@@ -716,7 +716,7 @@ |
3302 |
- |
3303 |
- #endif /* end of apple xlf support */ |
3304 |
- |
3305 |
--#if ( defined (__linux__) && defined (_CALL_SYSV) ) |
3306 |
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) |
3307 |
- /* linuxppc xlf support */ |
3308 |
- void gerror_ (str, Lstr) |
3309 |
- char *str; |
3310 |
|
3311 |
diff --git a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch |
3312 |
deleted file mode 100644 |
3313 |
index 1420419..0000000 |
3314 |
--- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch |
3315 |
+++ /dev/null |
3316 |
@@ -1,87 +0,0 @@ |
3317 |
---- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 |
3318 |
-+++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 |
3319 |
-@@ -623,45 +623,45 @@ |
3320 |
- # echo "! Beware -- the $system installation isn't properly tested." ; } |
3321 |
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' |
3322 |
- |
3323 |
--if test -z "$onlylibs" ; then |
3324 |
-- for i in CCP4_SCR BINSORT_SCR; do |
3325 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3326 |
-- else |
3327 |
-- eval echo "! No directory \$$i and can\'t create it." |
3328 |
-- echo " Check the value of $i." |
3329 |
-- badvar=1 |
3330 |
-- fi |
3331 |
-- done |
3332 |
-- |
3333 |
-- for i in libdir bindir; do |
3334 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3335 |
-- else |
3336 |
-- eval echo "! No directory \$$i and can\'t create it." |
3337 |
-- echo " Check the argument of --$i." |
3338 |
-- badvar=1 |
3339 |
-- fi |
3340 |
-- done |
3341 |
-- |
3342 |
-- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
3343 |
-- if test -d $i || mkdir $i; then : |
3344 |
-- else |
3345 |
-- eval echo "! No directory $i and can\'t create it." |
3346 |
-- badvar=1 |
3347 |
-- fi |
3348 |
-- done |
3349 |
--else |
3350 |
-- # Kludge to fool the "Makefile" target in the top-level CCP4 |
3351 |
-- # Makefile into not trying to remake src/Makefile.in |
3352 |
-- for i in $srcdir/src $srcdir/lib/src ; do |
3353 |
-- if test -d $i || mkdir $i; then |
3354 |
-- if ! test -f $i/Makefile.in ; then |
3355 |
-- echo |
3356 |
-- echo "onlylibs: making dummy file $i/Makefile.in" |
3357 |
-- touch $i/Makefile.in |
3358 |
-- fi |
3359 |
-- fi |
3360 |
-- done |
3361 |
--fi |
3362 |
-+#if test -z "$onlylibs" ; then |
3363 |
-+# for i in CCP4_SCR BINSORT_SCR; do |
3364 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3365 |
-+# else |
3366 |
-+# eval echo "! No directory \$$i and can\'t create it." |
3367 |
-+# echo " Check the value of $i." |
3368 |
-+# badvar=1 |
3369 |
-+# fi |
3370 |
-+# done |
3371 |
-+# |
3372 |
-+# for i in libdir bindir; do |
3373 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
3374 |
-+# else |
3375 |
-+# eval echo "! No directory \$$i and can\'t create it." |
3376 |
-+# echo " Check the argument of --$i." |
3377 |
-+# badvar=1 |
3378 |
-+# fi |
3379 |
-+# done |
3380 |
-+# |
3381 |
-+# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
3382 |
-+# if test -d $i || mkdir $i; then : |
3383 |
-+# else |
3384 |
-+# eval echo "! No directory $i and can\'t create it." |
3385 |
-+# badvar=1 |
3386 |
-+# fi |
3387 |
-+# done |
3388 |
-+#else |
3389 |
-+# # Kludge to fool the "Makefile" target in the top-level CCP4 |
3390 |
-+# # Makefile into not trying to remake src/Makefile.in |
3391 |
-+# for i in $srcdir/src $srcdir/lib/src ; do |
3392 |
-+# if test -d $i || mkdir $i; then |
3393 |
-+# if ! test -f $i/Makefile.in ; then |
3394 |
-+# echo |
3395 |
-+# echo "onlylibs: making dummy file $i/Makefile.in" |
3396 |
-+# touch $i/Makefile.in |
3397 |
-+# fi |
3398 |
-+# fi |
3399 |
-+# done |
3400 |
-+#fi |
3401 |
- |
3402 |
- ### sanity checks |
3403 |
- |
3404 |
|
3405 |
diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch |
3406 |
deleted file mode 100644 |
3407 |
index c118cc5..0000000 |
3408 |
--- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch |
3409 |
+++ /dev/null |
3410 |
@@ -1,14 +0,0 @@ |
3411 |
-https://bugs.gentoo.org/show_bug.cgi?id=175630 |
3412 |
-JTRiley |
3413 |
- |
3414 |
---- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f 2005-09-06 07:29:56.000000000 -0400 |
3415 |
-+++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f 2007-05-02 20:03:46.000000000 -0400 |
3416 |
-@@ -97,7 +97,7 @@ |
3417 |
- |
3418 |
- READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2) |
3419 |
- |
3420 |
-- CALL IDATE(IMON,IDAY,IYR) |
3421 |
-+ CALL UIDATE(IMON,IDAY,IYR) |
3422 |
- IF(IYR.GE.99) THEN |
3423 |
- IYR=IYR+1900 |
3424 |
- ELSE |
3425 |
|
3426 |
diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch |
3427 |
deleted file mode 100644 |
3428 |
index a77d949..0000000 |
3429 |
--- a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch |
3430 |
+++ /dev/null |
3431 |
@@ -1,11 +0,0 @@ |
3432 |
---- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 |
3433 |
-+++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 |
3434 |
-@@ -716,7 +716,7 @@ |
3435 |
- |
3436 |
- #endif /* end of apple xlf support */ |
3437 |
- |
3438 |
--#if ( defined (__linux__) && defined (_CALL_SYSV) ) |
3439 |
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) |
3440 |
- /* linuxppc xlf support */ |
3441 |
- void gerror_ (str, Lstr) |
3442 |
- char *str; |
3443 |
|
3444 |
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch |
3445 |
deleted file mode 100644 |
3446 |
index 106db89..0000000 |
3447 |
--- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch |
3448 |
+++ /dev/null |
3449 |
@@ -1,13 +0,0 @@ |
3450 |
---- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 |
3451 |
-+++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 |
3452 |
-@@ -54,8 +54,8 @@ |
3453 |
- MESSAGE _text "" |
3454 |
- BLT_LIBRARY _text "" |
3455 |
- MENU_LENGTH _positiveint 25 |
3456 |
--HYPERTEXT_VIEWER _text netscape |
3457 |
--START_NETSCAPE _text netscape |
3458 |
-+HYPERTEXT_VIEWER _text firefox |
3459 |
-+START_NETSCAPE _text firefox |
3460 |
- O_MAPMAN _text mapman |
3461 |
- MAPMAN_MAXSIZE _positiveint 4194304 |
3462 |
- QUANTA_MBKALL _text mbkall |
3463 |
|
3464 |
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch |
3465 |
deleted file mode 100644 |
3466 |
index 02a2aa6..0000000 |
3467 |
--- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch |
3468 |
+++ /dev/null |
3469 |
@@ -1,103 +0,0 @@ |
3470 |
---- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 |
3471 |
-+++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 |
3472 |
-@@ -2410,12 +2410,12 @@ |
3473 |
- end |
3474 |
- EOF |
3475 |
- #firslty test without -lblas |
3476 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" |
3477 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" |
3478 |
- echo $test_compile |
3479 |
- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then |
3480 |
- # Compilation was okay |
3481 |
-- echo "... only -llapack needed" |
3482 |
-- XLAPACK_LIB="-llapack" |
3483 |
-+ echo "... only -llapack -lpthread needed" |
3484 |
-+ XLAPACK_LIB="-llapack -lpthread" |
3485 |
- # Set the next two variables so that configure |
3486 |
- # doesn't try to build netlib libraries |
3487 |
- LAPACKLIB="lapack" |
3488 |
-@@ -2424,12 +2424,12 @@ |
3489 |
- tryblas= |
3490 |
- else |
3491 |
- echo "more than just -llapack needed...." |
3492 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" |
3493 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" |
3494 |
- echo $test_compile |
3495 |
- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
3496 |
- # Compilation was okay |
3497 |
-- echo "...-llapack and -lblas were needed" |
3498 |
-- XLAPACK_LIB="-llapack -lblas" |
3499 |
-+ echo "...-llapack, -lpthread and -lblas were needed" |
3500 |
-+ XLAPACK_LIB="-llapack -lpthread -lblas" |
3501 |
- # Set the next two variables so that configure |
3502 |
- # doesn't try to build netlib libraries |
3503 |
- LAPACKLIB="lapack blas" |
3504 |
-@@ -2720,8 +2720,8 @@ |
3505 |
- STOP |
3506 |
- END |
3507 |
- EOF |
3508 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
3509 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
3510 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" |
3511 |
-+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" |
3512 |
- echo $test_compile |
3513 |
- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
3514 |
- have_lapack=yes |
3515 |
-@@ -2738,7 +2738,7 @@ |
3516 |
- LAPACKDIR="$testdir" |
3517 |
- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" |
3518 |
- # |
3519 |
-- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" |
3520 |
-+ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" |
3521 |
- # |
3522 |
- # Test to see if we need BLAS too |
3523 |
- # Do this by trying to compile a test program |
3524 |
-@@ -2750,8 +2750,8 @@ |
3525 |
- if test -f testlsame ; then |
3526 |
- rm -f testsame testlsame.o |
3527 |
- fi |
3528 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" |
3529 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" |
3530 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" |
3531 |
-+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" |
3532 |
- echo $test_compile |
3533 |
- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then |
3534 |
- have_blas=yes |
3535 |
-@@ -2830,8 +2830,8 @@ |
3536 |
- STOP |
3537 |
- END |
3538 |
- EOF |
3539 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
3540 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
3541 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" |
3542 |
-+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" |
3543 |
- echo $test_compile |
3544 |
- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then |
3545 |
- have_blas=yes |
3546 |
-@@ -3033,7 +3033,7 @@ |
3547 |
- if test -f testlsame ; then |
3548 |
- rm -f testsame testlsame.o |
3549 |
- fi |
3550 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" |
3551 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" |
3552 |
- echo $test_compile |
3553 |
- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then |
3554 |
- echo "Found LSAME in lib$BLASLIB" |
3555 |
-@@ -3046,7 +3046,7 @@ |
3556 |
- if test -f testxerbla ; then |
3557 |
- rm -f testxerbla testxerbla.o |
3558 |
- fi |
3559 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" |
3560 |
-+ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" |
3561 |
- echo $test_compile |
3562 |
- if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then |
3563 |
- # Found lsame |
3564 |
-@@ -3080,7 +3080,7 @@ |
3565 |
- cd ../.. |
3566 |
- # |
3567 |
- lapackdir=lib/lapack |
3568 |
-- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" |
3569 |
-+ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" |
3570 |
- # netlib lapack is in fortran, so we may need the fortran libraries when |
3571 |
- # we are linking using the C or C++ compilers |
3572 |
- case $system in |
3573 |
|
3574 |
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch |
3575 |
deleted file mode 100644 |
3576 |
index 3bf5a06..0000000 |
3577 |
--- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch |
3578 |
+++ /dev/null |
3579 |
@@ -1,11 +0,0 @@ |
3580 |
---- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 |
3581 |
-+++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 |
3582 |
-@@ -21751,7 +21751,7 @@ |
3583 |
- |
3584 |
- if test "x$mccp4_prefix" != x; then |
3585 |
- # ie. mccp4=thing was given (thing is what we're checking for) |
3586 |
-- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" |
3587 |
-+ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" |
3588 |
- ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" |
3589 |
- else |
3590 |
- # treat as standard lib/include |
3591 |
|
3592 |
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch |
3593 |
deleted file mode 100644 |
3594 |
index 34d6197..0000000 |
3595 |
--- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch |
3596 |
+++ /dev/null |
3597 |
@@ -1,10 +0,0 @@ |
3598 |
---- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 |
3599 |
-+++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 |
3600 |
-@@ -158,6 +158,7 @@ |
3601 |
- install_obj = ipdisp.exe hklview xdldataman xdlmapman \ |
3602 |
- rotgen ipmosflm |
3603 |
- install: all |
3604 |
-+ mkdir -p $(bindir) |
3605 |
- $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) |
3606 |
- $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) |
3607 |
- $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) |
3608 |
|
3609 |
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch |
3610 |
deleted file mode 100644 |
3611 |
index 8da54fd..0000000 |
3612 |
--- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch |
3613 |
+++ /dev/null |
3614 |
@@ -1,19 +0,0 @@ |
3615 |
---- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 |
3616 |
-+++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 |
3617 |
-@@ -35,7 +35,7 @@ |
3618 |
- # |
3619 |
- # all |
3620 |
- # |
3621 |
--all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm |
3622 |
-+all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm |
3623 |
- # |
3624 |
- # xdl_view |
3625 |
- # |
3626 |
-@@ -161,7 +161,6 @@ |
3627 |
- $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) |
3628 |
- $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) |
3629 |
- cd $(srcdir)/XCCPJIFFY ; $(MAKE) install |
3630 |
-- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) |
3631 |
- cd $(rotgen_dir); $(MAKE) install |
3632 |
- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) |
3633 |
- cd $(xdlview_dir); $(MAKE) install |
3634 |
|
3635 |
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch |
3636 |
deleted file mode 100644 |
3637 |
index 7813141..0000000 |
3638 |
--- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch |
3639 |
+++ /dev/null |
3640 |
@@ -1,10 +0,0 @@ |
3641 |
---- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 |
3642 |
-+++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 |
3643 |
-@@ -37,6 +37,7 @@ |
3644 |
- ${F77} ${FFLAGS} -o $@ $< |
3645 |
- |
3646 |
- ipmosflm: ${OBJS} |
3647 |
-+ mkdir -p ${DPSBIN} |
3648 |
- ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ |
3649 |
- -o ${DPSBIN}/ipmosflm ${LDFLAGS} |
3650 |
- |
3651 |
|
3652 |
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch |
3653 |
deleted file mode 100644 |
3654 |
index ae4b763..0000000 |
3655 |
--- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch |
3656 |
+++ /dev/null |
3657 |
@@ -1,11 +0,0 @@ |
3658 |
---- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 |
3659 |
-+++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 |
3660 |
-@@ -132,7 +132,7 @@ |
3661 |
- # |
3662 |
- # CBF library |
3663 |
- # |
3664 |
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) |
3665 |
-+$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) |
3666 |
- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) |
3667 |
- $(AR) cr $@ *.o |
3668 |
- $(RANLIB) $@ |
3669 |
|
3670 |
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch |
3671 |
deleted file mode 100644 |
3672 |
index 97607b6..0000000 |
3673 |
--- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch |
3674 |
+++ /dev/null |
3675 |
@@ -1,10 +0,0 @@ |
3676 |
---- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 |
3677 |
-+++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 |
3678 |
-@@ -76,6 +76,7 @@ |
3679 |
- |
3680 |
- # local version of libdps_index.a |
3681 |
- ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} |
3682 |
-+ mkdir -p ${LIB} |
3683 |
- ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} |
3684 |
- |
3685 |
- ${LIB}/libpeak.a: |
3686 |
|
3687 |
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch |
3688 |
deleted file mode 100644 |
3689 |
index eac1b9f..0000000 |
3690 |
--- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch |
3691 |
+++ /dev/null |
3692 |
@@ -1,10 +0,0 @@ |
3693 |
---- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 |
3694 |
-+++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 |
3695 |
-@@ -42,6 +42,7 @@ |
3696 |
- $(LOCALLIBS) $(LIBS) |
3697 |
- |
3698 |
- index: $(IOBJS) |
3699 |
-+ mkdir -p $(LIBDIR) |
3700 |
- ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) |
3701 |
- chmod 644 $(LIBDIR)/libdps_index.a |
3702 |
- |
3703 |
|
3704 |
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch |
3705 |
deleted file mode 100644 |
3706 |
index 3e1a8b0..0000000 |
3707 |
--- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch |
3708 |
+++ /dev/null |
3709 |
@@ -1,11 +0,0 @@ |
3710 |
---- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 |
3711 |
-+++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 |
3712 |
-@@ -3210,7 +3210,7 @@ |
3713 |
- #ccp4 setup |
3714 |
- xopts="${xopts} --with-ccp4=${srcdir}" |
3715 |
- #interface setup |
3716 |
-- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" |
3717 |
-+ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" |
3718 |
- echo |
3719 |
- echo "********* CLIPPER CONFIGURATION ***********" |
3720 |
- echo |
3721 |
|
3722 |
diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml |
3723 |
deleted file mode 100644 |
3724 |
index d37774e..0000000 |
3725 |
--- a/sci-chemistry/ccp4/metadata.xml |
3726 |
+++ /dev/null |
3727 |
@@ -1,9 +0,0 @@ |
3728 |
-<?xml version="1.0" encoding="UTF-8"?> |
3729 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
3730 |
-<pkgmetadata> |
3731 |
- <herd>sci-chemistry</herd> |
3732 |
- <use> |
3733 |
- <flag name="balbes">Install sci-chemistry/balbes</flag> |
3734 |
- <flag name="arpwarp">Add binary arp-warp for molecular replacement</flag> |
3735 |
- </use> |
3736 |
-</pkgmetadata> |
3737 |
|
3738 |
diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest |
3739 |
deleted file mode 100644 |
3740 |
index e082cb4..0000000 |
3741 |
--- a/sci-chemistry/ccp4i/Manifest |
3742 |
+++ /dev/null |
3743 |
@@ -1,3 +0,0 @@ |
3744 |
-DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 |
3745 |
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c |
3746 |
-DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8 |
3747 |
|
3748 |
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild |
3749 |
deleted file mode 100644 |
3750 |
index bdfba78..0000000 |
3751 |
--- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild |
3752 |
+++ /dev/null |
3753 |
@@ -1,99 +0,0 @@ |
3754 |
-# Copyright 1999-2015 Gentoo Foundation |
3755 |
-# Distributed under the terms of the GNU General Public License v2 |
3756 |
-# $Id$ |
3757 |
- |
3758 |
-EAPI=5 |
3759 |
- |
3760 |
-PYTHON_COMPAT=( python2_7 ) |
3761 |
- |
3762 |
-inherit eutils multilib python-single-r1 virtualx |
3763 |
- |
3764 |
-MY_PN="${PN%i}" |
3765 |
-MY_P="${MY_PN}-${PV}" |
3766 |
- |
3767 |
-#UPDATE="04_03_09" |
3768 |
-#PATCHDATE="090511" |
3769 |
- |
3770 |
-SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
3771 |
- |
3772 |
-DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" |
3773 |
-HOMEPAGE="http://www.ccp4.ac.uk/" |
3774 |
-SRC_URI=" |
3775 |
- ${SRC}/${PV}/${MY_P}-core-src.tar.gz |
3776 |
- mirror://gentoo/${P}-arpwarp.patch.bz2 |
3777 |
- https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" |
3778 |
-[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
3779 |
-[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
3780 |
- |
3781 |
-SLOT="0" |
3782 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
3783 |
-LICENSE="ccp4" |
3784 |
-IUSE="" |
3785 |
- |
3786 |
-RDEPEND=" |
3787 |
- app-shells/tcsh |
3788 |
- media-gfx/graphviz |
3789 |
- >=dev-lang/tk-8.3:0 |
3790 |
- >=dev-tcltk/blt-2.4 |
3791 |
- sci-libs/ccp4-libs" |
3792 |
-DEPEND="${RDEPEND}" |
3793 |
- |
3794 |
-S="${WORKDIR}/${MY_P}" |
3795 |
- |
3796 |
-PATCHES=( |
3797 |
- "${FILESDIR}"/${PV}-fix-baubles.patch |
3798 |
- "${WORKDIR}"/${P}-arpwarp.patch |
3799 |
- ) |
3800 |
- |
3801 |
-src_prepare() { |
3802 |
- epatch ${PATCHES[@]} |
3803 |
- |
3804 |
- [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
3805 |
- |
3806 |
- epatch "${WORKDIR}"/${PV}-oasis4.0.patch |
3807 |
- python_fix_shebang ccp4i/ share/dbccp4i/ |
3808 |
-} |
3809 |
- |
3810 |
-src_configure() { |
3811 |
- : |
3812 |
-} |
3813 |
- |
3814 |
-src_compile() { |
3815 |
- : |
3816 |
-} |
3817 |
- |
3818 |
-src_install() { |
3819 |
- # rm imosflm stuff |
3820 |
- rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die |
3821 |
- |
3822 |
- rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die |
3823 |
- |
3824 |
- # This is installed by mrbump |
3825 |
- rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die |
3826 |
- |
3827 |
- # CCP4Interface - GUI |
3828 |
- insinto /usr/$(get_libdir)/ccp4 |
3829 |
- doins -r "${S}"/ccp4i |
3830 |
- exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin |
3831 |
- doexe "${S}"/ccp4i/bin/* |
3832 |
- dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i |
3833 |
- |
3834 |
- dodir /usr/$(get_libdir)/ccp4/ccp4i/unix |
3835 |
- |
3836 |
- # dbccp4i |
3837 |
- insinto /usr/share/ccp4 |
3838 |
- doins -r "${S}"/share/dbccp4i |
3839 |
-} |
3840 |
- |
3841 |
-pkg_postinst() { |
3842 |
- _ccp4-setup() { |
3843 |
- source "${EPREFIX}/etc/profile" |
3844 |
- export USER=root |
3845 |
- bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null |
3846 |
- } |
3847 |
- VIRTUALX_COMMAND="_ccp4-setup" virtualmake |
3848 |
- echo "" |
3849 |
- elog "ccp4i needs some enviromental settings. So please" |
3850 |
- elog "\t source ${EPREFIX}/etc/profile" |
3851 |
- echo "" |
3852 |
-} |
3853 |
|
3854 |
diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch |
3855 |
deleted file mode 100644 |
3856 |
index 2c5f659..0000000 |
3857 |
--- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch |
3858 |
+++ /dev/null |
3859 |
@@ -1,22 +0,0 @@ |
3860 |
---- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 |
3861 |
-+++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 |
3862 |
-@@ -53,8 +53,8 @@ |
3863 |
- RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" |
3864 |
- RUN_CCP4MG _text "ccp4mg" |
3865 |
- RUN_COOT _text "coot" |
3866 |
--RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" |
3867 |
--RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" |
3868 |
-+RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" |
3869 |
-+RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" |
3870 |
- ENABLE_BUBBLE_HELP _logical 1 |
3871 |
- DISABLE_TASKS _logical 1 |
3872 |
- CCP4_SETUP_COMMAND _text setup_ccp4 |
3873 |
-@@ -62,7 +62,7 @@ |
3874 |
- BLT_LIBRARY _text "" |
3875 |
- MENU_LENGTH _positiveint 25 |
3876 |
- HYPERTEXT_VIEWER _text firefox |
3877 |
--START_NETSCAPE _text netscape |
3878 |
-+START_NETSCAPE _text firefox |
3879 |
- O_MAPMAN _text mapman |
3880 |
- MAPMAN_MAXSIZE _positiveint 4194304 |
3881 |
- QUANTA_MBKALL _text mbkall |
3882 |
|
3883 |
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch |
3884 |
deleted file mode 100644 |
3885 |
index 9f5cfb4..0000000 |
3886 |
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch |
3887 |
+++ /dev/null |
3888 |
@@ -1,61 +0,0 @@ |
3889 |
-diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script |
3890 |
-index def44bc..dd4bb7e 100755 |
3891 |
---- a/ccp4i/scripts/check.script |
3892 |
-+++ b/ccp4i/scripts/check.script |
3893 |
-@@ -24,7 +24,7 @@ |
3894 |
- if $RUN_RAMPAGE { |
3895 |
- |
3896 |
- # Generate command line |
3897 |
-- set cmd "[BinPath rapper]" |
3898 |
-+ set cmd "[BinPath rappermc]" |
3899 |
- |
3900 |
- set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] |
3901 |
- set paramsfile [FileJoin $rapperdatadir params.xml] |
3902 |
-diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script |
3903 |
-index cdae1e2..faae226 100755 |
3904 |
---- a/ccp4i/scripts/rapper.script |
3905 |
-+++ b/ccp4i/scripts/rapper.script |
3906 |
-@@ -17,7 +17,7 @@ |
3907 |
- |
3908 |
- #set up command line |
3909 |
- |
3910 |
--set cmd "[BinPath rapper]" |
3911 |
-+set cmd "[BinPath rappermc]" |
3912 |
- |
3913 |
- set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] |
3914 |
- set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] |
3915 |
-@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT" |
3916 |
- |
3917 |
- # Run RAPPER to join loop back to framework and out put to defined pdb file |
3918 |
- # Also need to sort out multimodel files join - FIX ME |
3919 |
--set cmd2 "[BinPath rapper]" |
3920 |
-+set cmd2 "[BinPath rappermc]" |
3921 |
- append cmd2 " $paramsfile joinpdb " |
3922 |
- append cmd2 " --pdb2 \"$root\-loop.pdb\" " |
3923 |
- append cmd2 " --pdb \"$root\-framework.pdb\" " |
3924 |
-diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl |
3925 |
-index ae88ff2..ee3307b 100755 |
3926 |
---- a/ccp4i/tasks/check.tcl |
3927 |
-+++ b/ccp4i/tasks/check.tcl |
3928 |
-@@ -46,7 +46,7 @@ proc check_run { arrayname } { |
3929 |
- # Check for Rampage program. If it is not found, we switch off the option. |
3930 |
- # If it was the only option, script will fail with next check. |
3931 |
- if { $array(RUN_RAMPAGE) == 1 } { |
3932 |
-- if { [FindExecutable "rapper"] == "" } { |
3933 |
-+ if { [FindExecutable "rappermc"] == "" } { |
3934 |
- WarningMessage "Input Error: Rapper_Rampage program not found in system path." |
3935 |
- set array(RUN_RAMPAGE) 0 |
3936 |
- } |
3937 |
-diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl |
3938 |
-index e299057..8843a3f 100755 |
3939 |
---- a/ccp4i/tasks/rapper.tcl |
3940 |
-+++ b/ccp4i/tasks/rapper.tcl |
3941 |
-@@ -28,7 +28,7 @@ proc rapper_run { arrayname } { |
3942 |
- # Check for RAPPER program. If it is not found, we switch off the option. |
3943 |
- # If it was the only option, script will fail with next check. |
3944 |
- if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} { |
3945 |
-- if { [FindExecutable "rapper"] == "" } { |
3946 |
-+ if { [FindExecutable "rappermc"] == "" } { |
3947 |
- WarningMessage "Input Error: RAPPER program not found in system path." |
3948 |
- set build_type 0 |
3949 |
- } |
3950 |
|
3951 |
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch |
3952 |
deleted file mode 100644 |
3953 |
index 74cd2b9..0000000 |
3954 |
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch |
3955 |
+++ /dev/null |
3956 |
@@ -1,26 +0,0 @@ |
3957 |
-diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script |
3958 |
-index 3483c97..5027536 100755 |
3959 |
---- a/ccp4i/scripts/superpose.script |
3960 |
-+++ b/ccp4i/scripts/superpose.script |
3961 |
-@@ -21,7 +21,7 @@ |
3962 |
- |
3963 |
- if { [regexp SSM $SUPERPOSE_MODE ] } { |
3964 |
- |
3965 |
-- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" |
3966 |
-+ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" |
3967 |
- set status [Execute $cmd "" program_status report ] |
3968 |
- |
3969 |
- } elseif { [regexp TOP $SUPERPOSE_MODE ] } { |
3970 |
-diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl |
3971 |
-index 748bf6e..c92122a 100755 |
3972 |
---- a/ccp4i/tasks/superpose.tcl |
3973 |
-+++ b/ccp4i/tasks/superpose.tcl |
3974 |
-@@ -100,7 +100,7 @@ proc superpose_run { arrayname } { |
3975 |
- # If user is match equivalent named residues/atoms then fit in the match fields |
3976 |
- switch [GetValue $arrayname SUPERPOSE_MODE] \ |
3977 |
- SSM { |
3978 |
-- if { ![file exists [FindExecutable superpose]] } { |
3979 |
-+ if { ![file exists [FindExecutable superpose-ccp4]] } { |
3980 |
- WarningMessage "The program \"superpose\" is not on your path. |
3981 |
- Check your installation for \"superpose\" program and \"ssm\" library." |
3982 |
- return 0 |
3983 |
|
3984 |
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch |
3985 |
deleted file mode 100644 |
3986 |
index 9af60b7..0000000 |
3987 |
--- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch |
3988 |
+++ /dev/null |
3989 |
@@ -1,91 +0,0 @@ |
3990 |
-diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl |
3991 |
-index 7d05905..d01f1dc 100755 |
3992 |
---- a/ccp4i/crank/plugins/prep/crank_prep.tcl |
3993 |
-+++ b/ccp4i/crank/plugins/prep/crank_prep.tcl |
3994 |
-@@ -226,7 +226,7 @@ proc run_truncate { i j } { |
3995 |
- set script "$script\n$labout" |
3996 |
- set script "$script\nEND\n" |
3997 |
- |
3998 |
-- set run_command "truncate $command << \"$script\"" |
3999 |
-+ set run_command "ftruncate $command << \"$script\"" |
4000 |
- puts $run_command |
4001 |
- catch {eval exec $run_command } output |
4002 |
- puts $output |
4003 |
-diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script |
4004 |
-index e74aa0d..a2a1adb 100755 |
4005 |
---- a/ccp4i/scripts/dtrek2mtz.script |
4006 |
-+++ b/ccp4i/scripts/dtrek2mtz.script |
4007 |
-@@ -36,7 +36,7 @@ |
4008 |
- set HKL_TRUNCATE [GetTmpFileName -ext mtz] |
4009 |
- |
4010 |
- CreateComScript truncate truncate_script |
4011 |
-- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4012 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4013 |
- set status [Execute $cmd $truncate_script program_status report] |
4014 |
- |
4015 |
- HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
4016 |
-diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script |
4017 |
-index 90cba83..1c90c33 100755 |
4018 |
---- a/ccp4i/scripts/import.script |
4019 |
-+++ b/ccp4i/scripts/import.script |
4020 |
-@@ -144,7 +144,7 @@ if { $FORMAT == "MTZ" } { |
4021 |
- |
4022 |
- set truncatemtz [GetTmpFileName -ext mtz ] |
4023 |
- CreateComScript truncate truncate_script |
4024 |
-- set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" |
4025 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" |
4026 |
- set status [Execute $cmd $truncate_script program_status report] |
4027 |
- |
4028 |
- |
4029 |
-diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script |
4030 |
-index dcc619b..7250513 100755 |
4031 |
---- a/ccp4i/scripts/import_scaled.script |
4032 |
-+++ b/ccp4i/scripts/import_scaled.script |
4033 |
-@@ -62,7 +62,7 @@ |
4034 |
- |
4035 |
- } else { |
4036 |
- CreateComScript truncate truncate_script |
4037 |
-- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4038 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4039 |
- set status [Execute $cmd $truncate_script program_status report] |
4040 |
- |
4041 |
- HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
4042 |
-diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script |
4043 |
-index 6940ccd..bde10d6 100755 |
4044 |
---- a/ccp4i/scripts/scala.script |
4045 |
-+++ b/ccp4i/scripts/scala.script |
4046 |
-@@ -275,7 +275,7 @@ END" |
4047 |
- |
4048 |
- } else { |
4049 |
- CreateComScript truncate truncate_script |
4050 |
-- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4051 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4052 |
- set status [Execute $cmd $truncate_script $LOG_FILE program_status report ] |
4053 |
- } |
4054 |
- |
4055 |
-diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script |
4056 |
-index 986e06c..a1947a6 100755 |
4057 |
---- a/ccp4i/scripts/scalepack2mtz.script |
4058 |
-+++ b/ccp4i/scripts/scalepack2mtz.script |
4059 |
-@@ -35,7 +35,7 @@ |
4060 |
- |
4061 |
- set HKL_TRUNCATE [GetTmpFileName -ext mtz] |
4062 |
- CreateComScript truncate truncate_script |
4063 |
-- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4064 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" |
4065 |
- set status [Execute $cmd $truncate_script program_status report] |
4066 |
- |
4067 |
- HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate |
4068 |
-diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script |
4069 |
-index e0e09ce..2d448a2 100755 |
4070 |
---- a/ccp4i/scripts/truncate.script |
4071 |
-+++ b/ccp4i/scripts/truncate.script |
4072 |
-@@ -45,7 +45,7 @@ |
4073 |
- |
4074 |
- CreateComScript truncate truncate_script |
4075 |
- |
4076 |
-- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" |
4077 |
-+ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" |
4078 |
- if { ![StringSame $INPUT_DATA AMPLITUDES] } { |
4079 |
- append cmd " HKLOUT \"$HKL_TRUNCATE\"" |
4080 |
- } |
4081 |
|
4082 |
diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml |
4083 |
deleted file mode 100644 |
4084 |
index 51fdeda..0000000 |
4085 |
--- a/sci-chemistry/ccp4i/metadata.xml |
4086 |
+++ /dev/null |
4087 |
@@ -1,5 +0,0 @@ |
4088 |
-<?xml version="1.0" encoding="UTF-8"?> |
4089 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
4090 |
-<pkgmetadata> |
4091 |
- <herd>sci-chemistry</herd> |
4092 |
-</pkgmetadata> |
4093 |
|
4094 |
diff --git a/sci-chemistry/coot/coot-0.7.1-r1.ebuild b/sci-chemistry/coot/coot-0.7.1-r1.ebuild |
4095 |
deleted file mode 100644 |
4096 |
index 001145e..0000000 |
4097 |
--- a/sci-chemistry/coot/coot-0.7.1-r1.ebuild |
4098 |
+++ /dev/null |
4099 |
@@ -1,167 +0,0 @@ |
4100 |
-# Copyright 1999-2015 Gentoo Foundation |
4101 |
-# Distributed under the terms of the GNU General Public License v2 |
4102 |
-# $Id$ |
4103 |
- |
4104 |
-EAPI=5 |
4105 |
- |
4106 |
-PYTHON_COMPAT=( python2_7 ) |
4107 |
- |
4108 |
-AUTOTOOLS_AUTORECONF="true" |
4109 |
- |
4110 |
-inherit autotools-utils python-single-r1 toolchain-funcs versionator |
4111 |
- |
4112 |
-MY_S2_PV=$(replace_version_separator 2 - ${PV}) |
4113 |
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} |
4114 |
-MY_S_P=${MY_S2_P}-${PR/r/revision-} |
4115 |
-MY_PV=${PV} |
4116 |
-MY_P=${PN}-${MY_PV} |
4117 |
- |
4118 |
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" |
4119 |
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" |
4120 |
-SRC_URI=" |
4121 |
- http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz |
4122 |
- test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" |
4123 |
- |
4124 |
-SLOT="0" |
4125 |
-LICENSE="GPL-3" |
4126 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
4127 |
-IUSE="+openmp static-libs test" |
4128 |
- |
4129 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
4130 |
- |
4131 |
-AUTOTOOLS_IN_SOURCE_BUILD=1 |
4132 |
- |
4133 |
-SCIDEPS=" |
4134 |
- >=sci-libs/ccp4-libs-6.1 |
4135 |
- sci-libs/clipper |
4136 |
- >=sci-libs/coot-data-2 |
4137 |
- >=sci-libs/gsl-1.3 |
4138 |
- >=sci-libs/mmdb-1.23:0 |
4139 |
- sci-libs/ssm |
4140 |
- sci-libs/monomer-db |
4141 |
- sci-chemistry/reduce |
4142 |
- sci-chemistry/refmac |
4143 |
- sci-chemistry/probe" |
4144 |
- |
4145 |
-XDEPS=" |
4146 |
- gnome-base/libgnomecanvas |
4147 |
- gnome-base/librsvg:2 |
4148 |
- media-libs/libpng |
4149 |
- media-libs/freeglut |
4150 |
- x11-libs/gtk+:2 |
4151 |
- x11-libs/goocanvas:0 |
4152 |
- x11-libs/gtkglext" |
4153 |
- |
4154 |
-SCHEMEDEPS=" |
4155 |
- dev-scheme/net-http |
4156 |
- dev-scheme/guile-gui |
4157 |
- >=dev-scheme/guile-lib-0.1.6 |
4158 |
- dev-scheme/guile-www |
4159 |
- >=x11-libs/guile-gtk-2.1" |
4160 |
- |
4161 |
-RDEPEND=" |
4162 |
- ${SCIDEPS} |
4163 |
- ${XDEPS} |
4164 |
- ${SCHEMEDEPS} |
4165 |
- ${PYTHON_DEPS} |
4166 |
- dev-python/pygtk:2[${PYTHON_USEDEP}] |
4167 |
- >=dev-libs/gmp-4.2.2-r2 |
4168 |
- >=net-misc/curl-7.19.6 |
4169 |
- net-dns/libidn" |
4170 |
-DEPEND="${RDEPEND} |
4171 |
- >=sys-devel/libtool-2.4-r2 |
4172 |
- dev-lang/swig |
4173 |
- sys-devel/bc |
4174 |
- test? ( dev-scheme/greg )" |
4175 |
- |
4176 |
-S="${WORKDIR}/${MY_P}" |
4177 |
- |
4178 |
-pkg_setup() { |
4179 |
- if use openmp; then |
4180 |
- tc-has-openmp || die "Please use an OPENMP capable compiler" |
4181 |
- fi |
4182 |
- python-single-r1_pkg_setup |
4183 |
-} |
4184 |
- |
4185 |
-PATCHES=( |
4186 |
- "${FILESDIR}"/${PN}-0.7-clipper-config.patch |
4187 |
- "${FILESDIR}"/${PN}-0.7-goocanvas.patch |
4188 |
- "${FILESDIR}"/${PN}-0.7-mmdb-config.patch |
4189 |
- "${FILESDIR}"/${PN}-0.7-ssm.patch |
4190 |
- ) |
4191 |
- |
4192 |
-src_prepare() { |
4193 |
- sed \ |
4194 |
- -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ |
4195 |
- -i configure.in || die |
4196 |
- |
4197 |
- autotools-utils_src_prepare |
4198 |
-} |
4199 |
- |
4200 |
-src_configure() { |
4201 |
- # All the --with's are used to activate various parts. |
4202 |
- # Yes, this is broken behavior. |
4203 |
- local myeconfargs=( |
4204 |
- --includedir='${prefix}/include/coot' |
4205 |
- --with-goocanvas-prefix="${EPREFIX}/usr" |
4206 |
- --with-guile |
4207 |
- --with-python="${EPREFIX}/usr" |
4208 |
- --with-guile-gtk |
4209 |
- --with-gtk2 |
4210 |
- --with-pygtk |
4211 |
- $(use_enable openmp) |
4212 |
- ) |
4213 |
- autotools-utils_src_configure |
4214 |
-} |
4215 |
- |
4216 |
-src_test() { |
4217 |
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" |
4218 |
- mkdir "${T}"/coot_test |
4219 |
- |
4220 |
- export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" |
4221 |
- export COOT_SCHEME_DIR="${S}/scheme/" |
4222 |
- export COOT_RESOURCES_FILE="${S}/cootrc" |
4223 |
- export COOT_PIXMAPS_DIR="${S}/pixmaps/" |
4224 |
- export COOT_DATA_DIR="${S}/" |
4225 |
- export COOT_PYTHON_DIR="${S}/python/" |
4226 |
- export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" |
4227 |
- export PYTHONHOME="${EPREFIX}"/usr/ |
4228 |
- export CCP4_SCR="${T}"/coot_test/ |
4229 |
- export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" |
4230 |
- export SYMINFO="${S}/syminfo.lib" |
4231 |
- |
4232 |
- export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data |
4233 |
- |
4234 |
- cat > command-line-greg.scm <<- EOF |
4235 |
- (use-modules (ice-9 greg)) |
4236 |
- (set! greg-tools (list "greg-tests")) |
4237 |
- (set! greg-debug #t) |
4238 |
- (set! greg-verbose 5) |
4239 |
- (let ((r (greg-test-run))) |
4240 |
- (if r |
4241 |
- (coot-real-exit 0) |
4242 |
- (coot-real-exit 1))) |
4243 |
- EOF |
4244 |
- |
4245 |
- einfo "Running test with following paths ..." |
4246 |
- einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" |
4247 |
- einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" |
4248 |
- einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" |
4249 |
- einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" |
4250 |
- einfo "COOT_DATA_DIR $COOT_DATA_DIR" |
4251 |
- einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" |
4252 |
- einfo "PYTHONPATH $PYTHONPATH" |
4253 |
- einfo "PYTHONHOME $PYTHONHOME" |
4254 |
- einfo "CCP4_SCR ${CCP4_SCR}" |
4255 |
- einfo "CLIBD_MON ${CLIBD_MON}" |
4256 |
- einfo "SYMINFO ${SYMINFO}" |
4257 |
- |
4258 |
- "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die |
4259 |
- "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die |
4260 |
-} |
4261 |
- |
4262 |
-src_install() { |
4263 |
- autotools-utils_src_install |
4264 |
- insinto /usr/share/${PN} |
4265 |
- doins syminfo.lib |
4266 |
-} |
4267 |
|
4268 |
diff --git a/sci-chemistry/coot/coot-0.7.2.ebuild b/sci-chemistry/coot/coot-0.7.2.ebuild |
4269 |
deleted file mode 100644 |
4270 |
index 0e14d44..0000000 |
4271 |
--- a/sci-chemistry/coot/coot-0.7.2.ebuild |
4272 |
+++ /dev/null |
4273 |
@@ -1,165 +0,0 @@ |
4274 |
-# Copyright 1999-2015 Gentoo Foundation |
4275 |
-# Distributed under the terms of the GNU General Public License v2 |
4276 |
-# $Id$ |
4277 |
- |
4278 |
-EAPI=5 |
4279 |
- |
4280 |
-PYTHON_COMPAT=( python2_7 ) |
4281 |
- |
4282 |
-AUTOTOOLS_AUTORECONF="true" |
4283 |
- |
4284 |
-inherit autotools-utils python-single-r1 toolchain-funcs versionator |
4285 |
- |
4286 |
-MY_S2_PV=$(replace_version_separator 2 - ${PV}) |
4287 |
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} |
4288 |
-MY_S_P=${MY_S2_P}-${PR/r/revision-} |
4289 |
-MY_PV=${PV} |
4290 |
-MY_P=${PN}-${MY_PV} |
4291 |
- |
4292 |
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" |
4293 |
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" |
4294 |
-SRC_URI=" |
4295 |
- http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz |
4296 |
- test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" |
4297 |
- |
4298 |
-SLOT="0" |
4299 |
-LICENSE="GPL-3" |
4300 |
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" |
4301 |
-IUSE="+openmp static-libs test" |
4302 |
- |
4303 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
4304 |
- |
4305 |
-AUTOTOOLS_IN_SOURCE_BUILD=1 |
4306 |
- |
4307 |
-SCIDEPS=" |
4308 |
- >=sci-libs/ccp4-libs-6.1 |
4309 |
- sci-libs/clipper |
4310 |
- >=sci-libs/coot-data-2 |
4311 |
- >=sci-libs/gsl-1.3 |
4312 |
- >=sci-libs/mmdb-1.23:0 |
4313 |
- sci-libs/ssm |
4314 |
- sci-libs/monomer-db |
4315 |
- sci-chemistry/reduce |
4316 |
- sci-chemistry/refmac |
4317 |
- sci-chemistry/probe" |
4318 |
- |
4319 |
-XDEPS=" |
4320 |
- gnome-base/libgnomecanvas |
4321 |
- gnome-base/librsvg:2 |
4322 |
- media-libs/libpng |
4323 |
- media-libs/freeglut |
4324 |
- x11-libs/gtk+:2 |
4325 |
- x11-libs/goocanvas:0 |
4326 |
- x11-libs/gtkglext" |
4327 |
- |
4328 |
-SCHEMEDEPS=" |
4329 |
- dev-scheme/net-http |
4330 |
- dev-scheme/guile-gui |
4331 |
- >=dev-scheme/guile-lib-0.1.6 |
4332 |
- dev-scheme/guile-www |
4333 |
- >=x11-libs/guile-gtk-2.1" |
4334 |
- |
4335 |
-RDEPEND=" |
4336 |
- ${SCIDEPS} |
4337 |
- ${XDEPS} |
4338 |
- ${SCHEMEDEPS} |
4339 |
- ${PYTHON_DEPS} |
4340 |
- dev-python/pygtk:2[${PYTHON_USEDEP}] |
4341 |
- >=dev-libs/gmp-4.2.2-r2 |
4342 |
- >=net-misc/curl-7.19.6 |
4343 |
- net-dns/libidn" |
4344 |
-DEPEND="${RDEPEND} |
4345 |
- >=sys-devel/libtool-2.4-r2 |
4346 |
- dev-lang/swig |
4347 |
- sys-devel/bc |
4348 |
- test? ( dev-scheme/greg )" |
4349 |
- |
4350 |
-S="${WORKDIR}/${MY_P}" |
4351 |
- |
4352 |
-pkg_setup() { |
4353 |
- if use openmp; then |
4354 |
- tc-has-openmp || die "Please use an OPENMP capable compiler" |
4355 |
- fi |
4356 |
- python-single-r1_pkg_setup |
4357 |
-} |
4358 |
- |
4359 |
-PATCHES=( |
4360 |
- "${FILESDIR}"/${PN}-0.7-clipper-config.patch |
4361 |
- "${FILESDIR}"/${PN}-0.7-goocanvas.patch |
4362 |
- "${FILESDIR}"/${PN}-0.7-mmdb-config.patch |
4363 |
- ) |
4364 |
- |
4365 |
-src_prepare() { |
4366 |
- sed \ |
4367 |
- -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ |
4368 |
- -i configure.in || die |
4369 |
- |
4370 |
- autotools-utils_src_prepare |
4371 |
-} |
4372 |
- |
4373 |
-src_configure() { |
4374 |
- # All the --with's are used to activate various parts. |
4375 |
- # Yes, this is broken behavior. |
4376 |
- local myeconfargs=( |
4377 |
- --includedir='${prefix}/include/coot' |
4378 |
- --with-goocanvas-prefix="${EPREFIX}/usr" |
4379 |
- --with-guile |
4380 |
- --with-python="${EPREFIX}/usr" |
4381 |
- --with-guile-gtk |
4382 |
- --with-gtk2 |
4383 |
- --with-pygtk |
4384 |
- $(use_enable openmp) |
4385 |
- ) |
4386 |
- autotools-utils_src_configure |
4387 |
-} |
4388 |
- |
4389 |
-src_compile() { |
4390 |
- autotools-utils_src_compile |
4391 |
- cp "${S}"/src/coot_gtk2.py python/coot.py || die |
4392 |
-} |
4393 |
- |
4394 |
-src_test() { |
4395 |
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" |
4396 |
- mkdir "${T}"/coot_test |
4397 |
- |
4398 |
- export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" |
4399 |
- export COOT_SCHEME_DIR="${S}/scheme/" |
4400 |
- export COOT_RESOURCES_FILE="${S}/cootrc" |
4401 |
- export COOT_PIXMAPS_DIR="${S}/pixmaps/" |
4402 |
- export COOT_DATA_DIR="${S}/" |
4403 |
- export COOT_PYTHON_DIR="${S}/python/" |
4404 |
- export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" |
4405 |
- export PYTHONHOME="${EPREFIX}"/usr/ |
4406 |
- export CCP4_SCR="${T}"/coot_test/ |
4407 |
- export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" |
4408 |
- export SYMINFO="${S}/syminfo.lib" |
4409 |
- |
4410 |
- export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data |
4411 |
- |
4412 |
- cat > command-line-greg.scm <<- EOF |
4413 |
- (use-modules (ice-9 greg)) |
4414 |
- (set! greg-tools (list "greg-tests")) |
4415 |
- (set! greg-debug #t) |
4416 |
- (set! greg-verbose 5) |
4417 |
- (let ((r (greg-test-run))) |
4418 |
- (if r |
4419 |
- (coot-real-exit 0) |
4420 |
- (coot-real-exit 1))) |
4421 |
- EOF |
4422 |
- |
4423 |
- einfo "Running test with following paths ..." |
4424 |
- einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" |
4425 |
- einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" |
4426 |
- einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" |
4427 |
- einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" |
4428 |
- einfo "COOT_DATA_DIR $COOT_DATA_DIR" |
4429 |
- einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" |
4430 |
- einfo "PYTHONPATH $PYTHONPATH" |
4431 |
- einfo "PYTHONHOME $PYTHONHOME" |
4432 |
- einfo "CCP4_SCR ${CCP4_SCR}" |
4433 |
- einfo "CLIBD_MON ${CLIBD_MON}" |
4434 |
- einfo "SYMINFO ${SYMINFO}" |
4435 |
- |
4436 |
- "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die |
4437 |
- "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die |
4438 |
-} |
4439 |
|
4440 |
diff --git a/sci-chemistry/coot/coot-0.7.ebuild b/sci-chemistry/coot/coot-0.7.ebuild |
4441 |
deleted file mode 100644 |
4442 |
index f5cdfa5..0000000 |
4443 |
--- a/sci-chemistry/coot/coot-0.7.ebuild |
4444 |
+++ /dev/null |
4445 |
@@ -1,159 +0,0 @@ |
4446 |
-# Copyright 1999-2014 Gentoo Foundation |
4447 |
-# Distributed under the terms of the GNU General Public License v2 |
4448 |
-# $Id$ |
4449 |
- |
4450 |
-EAPI=4 |
4451 |
- |
4452 |
-PYTHON_DEPEND="2" |
4453 |
- |
4454 |
-AUTOTOOLS_AUTORECONF="true" |
4455 |
- |
4456 |
-inherit autotools-utils python toolchain-funcs versionator |
4457 |
- |
4458 |
-MY_S2_PV=$(replace_version_separator 2 - ${PV}) |
4459 |
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} |
4460 |
-MY_S_P=${MY_S2_P}-${PR/r/revision-} |
4461 |
-MY_PV=${PV} |
4462 |
-MY_P=${PN}-${MY_PV} |
4463 |
- |
4464 |
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" |
4465 |
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" |
4466 |
-SRC_URI=" |
4467 |
- http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz |
4468 |
- test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" |
4469 |
- |
4470 |
-SLOT="0" |
4471 |
-LICENSE="GPL-3" |
4472 |
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" |
4473 |
-IUSE="+openmp static-libs test" |
4474 |
- |
4475 |
-AUTOTOOLS_IN_SOURCE_BUILD=1 |
4476 |
- |
4477 |
-SCIDEPS=" |
4478 |
- >=sci-libs/ccp4-libs-6.1 |
4479 |
- sci-libs/clipper |
4480 |
- >=sci-libs/coot-data-2 |
4481 |
- >=sci-libs/gsl-1.3 |
4482 |
- >=sci-libs/mmdb-1.23:0 |
4483 |
- sci-libs/ssm |
4484 |
- <sci-libs/monomer-db-1 |
4485 |
- sci-chemistry/reduce |
4486 |
- <sci-chemistry/refmac-5.6 |
4487 |
- sci-chemistry/probe" |
4488 |
- |
4489 |
-XDEPS=" |
4490 |
- gnome-base/libgnomecanvas |
4491 |
- gnome-base/librsvg:2 |
4492 |
- media-libs/libpng |
4493 |
- media-libs/freeglut |
4494 |
- x11-libs/gtk+:2 |
4495 |
- x11-libs/goocanvas:0 |
4496 |
- x11-libs/gtkglext" |
4497 |
- |
4498 |
-SCHEMEDEPS=" |
4499 |
- dev-scheme/net-http |
4500 |
- dev-scheme/guile-gui |
4501 |
- >=dev-scheme/guile-lib-0.1.6 |
4502 |
- dev-scheme/guile-www |
4503 |
- >=x11-libs/guile-gtk-2.1" |
4504 |
- |
4505 |
-RDEPEND=" |
4506 |
- ${SCIDEPS} |
4507 |
- ${XDEPS} |
4508 |
- ${SCHEMEDEPS} |
4509 |
- dev-python/pygtk:2 |
4510 |
- >=dev-libs/gmp-4.2.2-r2 |
4511 |
- >=net-misc/curl-7.19.6 |
4512 |
- net-dns/libidn" |
4513 |
-DEPEND="${RDEPEND} |
4514 |
- >=sys-devel/libtool-2.4-r2 |
4515 |
- dev-lang/swig |
4516 |
- sys-devel/bc |
4517 |
- test? ( dev-scheme/greg )" |
4518 |
- |
4519 |
-S="${WORKDIR}/${MY_P}" |
4520 |
- |
4521 |
-pkg_setup() { |
4522 |
- if use openmp; then |
4523 |
- tc-has-openmp || die "Please use an OPENMP capable compiler" |
4524 |
- fi |
4525 |
- python_set_active_version 2 |
4526 |
- python_pkg_setup |
4527 |
-} |
4528 |
- |
4529 |
-PATCHES=( |
4530 |
- "${FILESDIR}"/${P}-clipper-config.patch |
4531 |
- "${FILESDIR}"/${P}-goocanvas.patch |
4532 |
- "${FILESDIR}"/${P}-mmdb-config.patch |
4533 |
- "${FILESDIR}"/${P}-ssm.patch |
4534 |
- ) |
4535 |
- |
4536 |
-src_prepare() { |
4537 |
- sed \ |
4538 |
- -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ |
4539 |
- -i configure.in || die |
4540 |
- |
4541 |
- autotools-utils_src_prepare |
4542 |
-} |
4543 |
- |
4544 |
-src_configure() { |
4545 |
- # All the --with's are used to activate various parts. |
4546 |
- # Yes, this is broken behavior. |
4547 |
- local myeconfargs=( |
4548 |
- --includedir='${prefix}/include/coot' |
4549 |
- --with-goocanvas-prefix="${EPREFIX}/usr" |
4550 |
- --with-guile |
4551 |
- --with-python="${EPREFIX}/usr" |
4552 |
- --with-guile-gtk |
4553 |
- --with-gtk2 |
4554 |
- --with-pygtk |
4555 |
- $(use_enable openmp) |
4556 |
- ) |
4557 |
- autotools-utils_src_configure |
4558 |
-} |
4559 |
- |
4560 |
-src_test() { |
4561 |
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" |
4562 |
- mkdir "${T}"/coot_test |
4563 |
- |
4564 |
- export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" |
4565 |
- export COOT_SCHEME_DIR="${S}/scheme/" |
4566 |
- export COOT_RESOURCES_FILE="${S}/cootrc" |
4567 |
- export COOT_PIXMAPS_DIR="${S}/pixmaps/" |
4568 |
- export COOT_DATA_DIR="${S}/" |
4569 |
- export COOT_PYTHON_DIR="${S}/python/" |
4570 |
- export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" |
4571 |
- export PYTHONHOME="${EPREFIX}"/usr/ |
4572 |
- export CCP4_SCR="${T}"/coot_test/ |
4573 |
- export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" |
4574 |
- export SYMINFO="${S}/syminfo.lib" |
4575 |
- |
4576 |
- export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data |
4577 |
- |
4578 |
- cat > command-line-greg.scm <<- EOF |
4579 |
- (use-modules (ice-9 greg)) |
4580 |
- (set! greg-tools (list "greg-tests")) |
4581 |
- (set! greg-debug #t) |
4582 |
- (set! greg-verbose 5) |
4583 |
- (let ((r (greg-test-run))) |
4584 |
- (if r |
4585 |
- (coot-real-exit 0) |
4586 |
- (coot-real-exit 1))) |
4587 |
- EOF |
4588 |
- |
4589 |
- einfo "Running test with following paths ..." |
4590 |
- einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" |
4591 |
- einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" |
4592 |
- einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" |
4593 |
- einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" |
4594 |
- einfo "COOT_DATA_DIR $COOT_DATA_DIR" |
4595 |
- einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" |
4596 |
- einfo "PYTHONPATH $PYTHONPATH" |
4597 |
- einfo "PYTHONHOME $PYTHONHOME" |
4598 |
- einfo "CCP4_SCR ${CCP4_SCR}" |
4599 |
- einfo "CLIBD_MON ${CLIBD_MON}" |
4600 |
- einfo "SYMINFO ${SYMINFO}" |
4601 |
- |
4602 |
- "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die |
4603 |
- "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die |
4604 |
-} |
4605 |
|
4606 |
diff --git a/sci-chemistry/imosflm/Manifest b/sci-chemistry/imosflm/Manifest |
4607 |
deleted file mode 100644 |
4608 |
index 2ce7d89..0000000 |
4609 |
--- a/sci-chemistry/imosflm/Manifest |
4610 |
+++ /dev/null |
4611 |
@@ -1 +0,0 @@ |
4612 |
-DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c |
4613 |
|
4614 |
diff --git a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch |
4615 |
deleted file mode 100644 |
4616 |
index 5d0dd70..0000000 |
4617 |
--- a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch |
4618 |
+++ /dev/null |
4619 |
@@ -1,12 +0,0 @@ |
4620 |
-diff --git a/c/tkImageLoad.c b/c/tkImageLoad.c |
4621 |
-index e7c46f0..1496a15 100755 |
4622 |
---- a/c/tkImageLoad.c |
4623 |
-+++ b/c/tkImageLoad.c |
4624 |
-@@ -12,6 +12,7 @@ |
4625 |
- #include <tcl.h> |
4626 |
- #include <tk.h> |
4627 |
- #include <assert.h> |
4628 |
-+#include <stdlib.h> |
4629 |
- |
4630 |
- #define HEADER_LINE_LENGTH 512 |
4631 |
- #define BYTES_PER_PIXEL 2 |
4632 |
|
4633 |
diff --git a/sci-chemistry/imosflm/files/1.0.4-tk.patch b/sci-chemistry/imosflm/files/1.0.4-tk.patch |
4634 |
deleted file mode 100644 |
4635 |
index a901751..0000000 |
4636 |
--- a/sci-chemistry/imosflm/files/1.0.4-tk.patch |
4637 |
+++ /dev/null |
4638 |
@@ -1,50 +0,0 @@ |
4639 |
---- c/tkImageLoad.c 2009-08-14 21:10:19.000000000 +0200 |
4640 |
-+++ c/tkImageLoad.c.new 2009-08-14 21:10:55.000000000 +0200 |
4641 |
-@@ -19,6 +19,7 @@ |
4642 |
- //#define BLOCKED 1 |
4643 |
- //#define UNBLOCKED 1 |
4644 |
- #define IN_BLOCK_FLIP 1 |
4645 |
-+#define USE_COMPOSITELESS_PHOTO_PUT_BLOCK |
4646 |
- |
4647 |
- /* *********************************************************************/ |
4648 |
- |
4649 |
---- c/tkImageLoad.c 2009-08-14 21:13:29.000000000 +0200 |
4650 |
-+++ c/tkImageLoad.c.new 2009-08-14 21:14:59.000000000 +0200 |
4651 |
-@@ -272,9 +272,11 @@ |
4652 |
- } |
4653 |
- /* put the photo block into the image */ |
4654 |
- #ifdef __alpha |
4655 |
-- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height); |
4656 |
-+ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, |
4657 |
-+ TK_PHOTO_COMPOSITE_OVERLAY); |
4658 |
- #else |
4659 |
-- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET); |
4660 |
-+ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET, |
4661 |
-+ TK_PHOTO_COMPOSITE_OVERLAY); |
4662 |
- #endif |
4663 |
- |
4664 |
- /* Free the photo block's memory now it is finished with */ |
4665 |
-@@ -417,9 +419,11 @@ |
4666 |
- |
4667 |
- /* put the photo block back into the image */ |
4668 |
- #ifdef __alpha |
4669 |
-- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height); |
4670 |
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height, |
4671 |
-+ TK_PHOTO_COMPOSITE_OVERLAY); |
4672 |
- #else |
4673 |
-- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET); |
4674 |
-+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET, |
4675 |
-+ TK_PHOTO_COMPOSITE_OVERLAY); |
4676 |
- #endif |
4677 |
- /* Free the photo block's memory now it is finished with */ |
4678 |
- if (block.pixelPtr) { |
4679 |
---- c/tkImageLoad.c 2009-08-14 21:15:06.000000000 +0200 |
4680 |
-+++ c/tkImageLoad.c.new 2009-08-14 21:16:53.000000000 +0200 |
4681 |
-@@ -9,6 +9,7 @@ |
4682 |
- \************************************************************************/ |
4683 |
- |
4684 |
- #include <stdio.h> |
4685 |
-+#include <string.h> |
4686 |
- #include <tcl.h> |
4687 |
- #include <tk.h> |
4688 |
- #include <assert.h> |
4689 |
|
4690 |
diff --git a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch |
4691 |
deleted file mode 100644 |
4692 |
index 27efc6f..0000000 |
4693 |
--- a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch |
4694 |
+++ /dev/null |
4695 |
@@ -1,13 +0,0 @@ |
4696 |
-http://bugs.gentoo.org/467036 |
4697 |
- |
4698 |
---- src/contrast.tcl |
4699 |
-+++ src/contrast.tcl |
4700 |
-@@ -3,7 +3,7 @@ |
4701 |
- |
4702 |
- package require palette |
4703 |
- |
4704 |
--image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUKJGtVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPlXtupMAAAAASUVORK5CYII=" |
4705 |
-+image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUeJytVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPv4fGP4AAAAASUVORK5CYII=" |
4706 |
- |
4707 |
- class Contrast { |
4708 |
- inherit Palette |
4709 |
|
4710 |
diff --git a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild |
4711 |
deleted file mode 100644 |
4712 |
index e49667e..0000000 |
4713 |
--- a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild |
4714 |
+++ /dev/null |
4715 |
@@ -1,54 +0,0 @@ |
4716 |
-# Copyright 1999-2015 Gentoo Foundation |
4717 |
-# Distributed under the terms of the GNU General Public License v2 |
4718 |
-# $Id$ |
4719 |
- |
4720 |
-EAPI=5 |
4721 |
- |
4722 |
-inherit eutils multilib toolchain-funcs versionator |
4723 |
- |
4724 |
-MY_PV="$(delete_all_version_separators ${PV})" |
4725 |
- |
4726 |
-DESCRIPTION="A new GUI for the Mosflm crystallographic data processing tool" |
4727 |
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/imosflm" |
4728 |
-SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip" |
4729 |
- |
4730 |
-LICENSE="ccp4" |
4731 |
-SLOT="0" |
4732 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
4733 |
-IUSE="" |
4734 |
- |
4735 |
-RDEPEND=" |
4736 |
- dev-lang/tcl:0= |
4737 |
- >=dev-tcltk/itcl-3.3 |
4738 |
- >=dev-tcltk/itk-3.3 |
4739 |
- >=dev-tcltk/iwidgets-4 |
4740 |
- >=dev-tcltk/tdom-0.8 |
4741 |
- >=dev-tcltk/tkimg-1.3 |
4742 |
- >=dev-tcltk/tktreectrl-2.1 |
4743 |
- dev-tcltk/anigif |
4744 |
- dev-tcltk/combobox |
4745 |
- dev-tcltk/tablelist |
4746 |
- >=sci-chemistry/mosflm-7.0.9" |
4747 |
-DEPEND="app-arch/unzip" |
4748 |
- |
4749 |
-S=${WORKDIR}/${PN} |
4750 |
- |
4751 |
-src_prepare() { |
4752 |
- epatch "${FILESDIR}"/${PV}-libpng16.patch |
4753 |
-} |
4754 |
- |
4755 |
-src_install(){ |
4756 |
- rm -rf lib/{*.so,anigif,combobox} |
4757 |
- |
4758 |
- insinto /usr/$(get_libdir)/${PN} |
4759 |
- doins -r "${S}"/{src,bitmaps,lib} |
4760 |
- fperms 775 /usr/$(get_libdir)/${PN}/src/imosflm |
4761 |
- |
4762 |
- cat >> "${T}"/23imosflm <<- EOF |
4763 |
- IMOSFLM_VERSION="${PV}" |
4764 |
- EOF |
4765 |
- |
4766 |
- doenvd "${T}"/23imosflm |
4767 |
- |
4768 |
- make_wrapper imosflm /usr/$(get_libdir)/${PN}/src/imosflm |
4769 |
-} |
4770 |
|
4771 |
diff --git a/sci-chemistry/imosflm/metadata.xml b/sci-chemistry/imosflm/metadata.xml |
4772 |
deleted file mode 100644 |
4773 |
index 51fdeda..0000000 |
4774 |
--- a/sci-chemistry/imosflm/metadata.xml |
4775 |
+++ /dev/null |
4776 |
@@ -1,5 +0,0 @@ |
4777 |
-<?xml version="1.0" encoding="UTF-8"?> |
4778 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
4779 |
-<pkgmetadata> |
4780 |
- <herd>sci-chemistry</herd> |
4781 |
-</pkgmetadata> |
4782 |
|
4783 |
diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest |
4784 |
deleted file mode 100644 |
4785 |
index b489a33..0000000 |
4786 |
--- a/sci-chemistry/makecif/Manifest |
4787 |
+++ /dev/null |
4788 |
@@ -1 +0,0 @@ |
4789 |
-DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7 |
4790 |
|
4791 |
diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch |
4792 |
deleted file mode 100644 |
4793 |
index 186abb9..0000000 |
4794 |
--- a/sci-chemistry/makecif/files/5.6.6-makefile.patch |
4795 |
+++ /dev/null |
4796 |
@@ -1,49 +0,0 @@ |
4797 |
-diff --git a/src/makefile b/src/makefile |
4798 |
-index 6c8264a..acdec20 100755 |
4799 |
---- a/src/makefile |
4800 |
-+++ b/src/makefile |
4801 |
-@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/ |
4802 |
- # setenv BLANC_FORT "f77 -O1" |
4803 |
- # |
4804 |
- |
4805 |
-+all: makecif_all libcheck_all modcheck_all emin_all |
4806 |
-+ |
4807 |
- clean: |
4808 |
- rm -f temp_makecif_path.fh |
4809 |
- rm -f ../bin/* |
4810 |
-@@ -118,7 +120,7 @@ makecif.o: makecif.f lib_com.fh crd_com.fh |
4811 |
- $(BLANC_FORT) -c makecif.f |
4812 |
- |
4813 |
- mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o |
4814 |
-- $(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o |
4815 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o |
4816 |
- # ------------- |
4817 |
- libcheck.o: libcheck.f lib_com.fh crd_com.fh |
4818 |
- $(BLANC_FORT) -c libcheck.f |
4819 |
-@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh |
4820 |
- $(BLANC_FORT) -c main_libcheck.f |
4821 |
- |
4822 |
- lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o |
4823 |
-- $(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o |
4824 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o |
4825 |
- # ------------ |
4826 |
- |
4827 |
- emin.o: emin.f crd_com.fh atom_com.fh |
4828 |
-@@ -143,7 +145,7 @@ main_emin.o: main_emin.f |
4829 |
- $(BLANC_FORT) -c main_emin.f |
4830 |
- |
4831 |
- emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o |
4832 |
-- $(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o |
4833 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o |
4834 |
- |
4835 |
- # ------------- |
4836 |
- |
4837 |
-@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f |
4838 |
- $(BLANC_FORT) -c main_modcheck.f |
4839 |
- |
4840 |
- mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o |
4841 |
-- $(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o |
4842 |
-+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o |
4843 |
- |
4844 |
- |
4845 |
- # ====================================== |
4846 |
|
4847 |
diff --git a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild |
4848 |
deleted file mode 100644 |
4849 |
index 509117f..0000000 |
4850 |
--- a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild |
4851 |
+++ /dev/null |
4852 |
@@ -1,40 +0,0 @@ |
4853 |
-# Copyright 1999-2013 Gentoo Foundation |
4854 |
-# Distributed under the terms of the GNU General Public License v2 |
4855 |
-# $Id$ |
4856 |
- |
4857 |
-EAPI=4 |
4858 |
- |
4859 |
-inherit eutils fortran-2 toolchain-funcs |
4860 |
- |
4861 |
-DESCRIPTION="PDB --> CIF convertor" |
4862 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" |
4863 |
-SRC_URI="mirror://gentoo/${P}.tar.gz" |
4864 |
- |
4865 |
-SLOT="0" |
4866 |
-KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
4867 |
-LICENSE="ccp4" |
4868 |
-IUSE="" |
4869 |
- |
4870 |
-S="${WORKDIR}"/${PN} |
4871 |
- |
4872 |
-DEPEND="" |
4873 |
-RDEPEND=" |
4874 |
- !>=sci-chemistry/refmac-5.6 |
4875 |
- sci-libs/monomer-db" |
4876 |
- |
4877 |
-src_prepare() { |
4878 |
- epatch "${FILESDIR}"/${PV}-makefile.patch |
4879 |
-} |
4880 |
- |
4881 |
-src_compile() { |
4882 |
- emake -C src clean |
4883 |
- emake \ |
4884 |
- -C src \ |
4885 |
- BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ |
4886 |
- LDFLAGS="${LDFLAGS}" |
4887 |
-} |
4888 |
- |
4889 |
-src_install() { |
4890 |
- dobin bin/* |
4891 |
- dodoc readme |
4892 |
-} |
4893 |
|
4894 |
diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild |
4895 |
deleted file mode 100644 |
4896 |
index 3a5f70a..0000000 |
4897 |
--- a/sci-chemistry/makecif/makecif-5.6.6.ebuild |
4898 |
+++ /dev/null |
4899 |
@@ -1,39 +0,0 @@ |
4900 |
-# Copyright 1999-2012 Gentoo Foundation |
4901 |
-# Distributed under the terms of the GNU General Public License v2 |
4902 |
-# $Id$ |
4903 |
- |
4904 |
-EAPI=4 |
4905 |
- |
4906 |
-inherit eutils fortran-2 toolchain-funcs |
4907 |
- |
4908 |
-DESCRIPTION="PDB --> CIF convertor" |
4909 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" |
4910 |
-SRC_URI="mirror://gentoo/${P}.tar.gz" |
4911 |
- |
4912 |
-SLOT="0" |
4913 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
4914 |
-LICENSE="ccp4" |
4915 |
-IUSE="" |
4916 |
- |
4917 |
-S="${WORKDIR}"/${PN} |
4918 |
- |
4919 |
-DEPEND="" |
4920 |
-RDEPEND=" |
4921 |
- !>=sci-chemistry/refmac-5.6 |
4922 |
- sci-libs/monomer-db" |
4923 |
- |
4924 |
-src_prepare() { |
4925 |
- epatch "${FILESDIR}"/${PV}-makefile.patch |
4926 |
-} |
4927 |
- |
4928 |
-src_compile() { |
4929 |
- cd src && emake clean |
4930 |
- emake \ |
4931 |
- BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ |
4932 |
- LDFLAGS="${LDFLAGS}" |
4933 |
-} |
4934 |
- |
4935 |
-src_install() { |
4936 |
- dobin bin/* |
4937 |
- dodoc readme |
4938 |
-} |
4939 |
|
4940 |
diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml |
4941 |
deleted file mode 100644 |
4942 |
index 993c1d1..0000000 |
4943 |
--- a/sci-chemistry/makecif/metadata.xml |
4944 |
+++ /dev/null |
4945 |
@@ -1,18 +0,0 @@ |
4946 |
-<?xml version="1.0" encoding="UTF-8"?> |
4947 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
4948 |
-<pkgmetadata> |
4949 |
- <herd>sci-chemistry</herd> |
4950 |
- <maintainer> |
4951 |
- <email>jlec@g.o</email> |
4952 |
- </maintainer> |
4953 |
- <longdescription> |
4954 |
-PDB - CIF convertor |
4955 |
-check and create correct structure description |
4956 |
-create the list of restraints |
4957 |
-create dictionary description of new ligands |
4958 |
-rebuild missing atoms |
4959 |
-create tree like structure |
4960 |
-also the part of REFMAC |
4961 |
-can use additional user's dictionary |
4962 |
-</longdescription> |
4963 |
-</pkgmetadata> |
4964 |
|
4965 |
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest |
4966 |
deleted file mode 100644 |
4967 |
index d91b8a4..0000000 |
4968 |
--- a/sci-chemistry/molrep/Manifest |
4969 |
+++ /dev/null |
4970 |
@@ -1,2 +0,0 @@ |
4971 |
-DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce SHA512 e22636e2d6b5558b66877960a64c0b990bb50d9e1b42016981b64e1311f83d5942fde7c1cd2dc8462ef1be814ce94ef566028079a7a091c9b3d7300f2d6ce03f WHIRLPOOL e507108a38be703e882ab3fd25e817c53c2d57b76fce578de3d308f10a85fce7a9febed39f748667a01c631b35787955d7d0290c944d4bfabfc936eab620daaf |
4972 |
-DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6 |
4973 |
|
4974 |
diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch |
4975 |
deleted file mode 100644 |
4976 |
index d81ec79..0000000 |
4977 |
--- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch |
4978 |
+++ /dev/null |
4979 |
@@ -1,61 +0,0 @@ |
4980 |
---- src/makefile 2009-02-27 16:51:46.492890717 +0100 |
4981 |
-+++ src/makefile.new 2009-02-27 16:52:18.295619642 +0100 |
4982 |
-@@ -5,8 +5,8 @@ |
4983 |
- |
4984 |
- BIN = $(MOLREP)/bin |
4985 |
- |
4986 |
--OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o |
4987 |
--OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o |
4988 |
-+OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o |
4989 |
-+OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o |
4990 |
- |
4991 |
- |
4992 |
- all: molrep |
4993 |
-@@ -19,31 +19,31 @@ |
4994 |
- # ----------------------------- |
4995 |
- |
4996 |
- molrep.o: molrep.f |
4997 |
-- $(MR_FORT) -c molrep.f |
4998 |
-+ $(MR_FORT) $(FFLAGS) -c molrep.f |
4999 |
- molrep1.o: molrep1.f |
5000 |
-- $(MR_FORT) -c molrep1.f |
5001 |
-+ $(MR_FORT) $(FFLAGS) -c molrep1.f |
5002 |
- molrep2.o: molrep2.f |
5003 |
-- $(MR_FORT) -c molrep2.f |
5004 |
-+ $(MR_FORT) $(FFLAGS) -c molrep2.f |
5005 |
- molrep3.o: molrep3.f |
5006 |
-- $(MR_FORT) -c molrep3.f |
5007 |
-+ $(MR_FORT) $(FFLAGS) -c molrep3.f |
5008 |
- molrep_prog.o: molrep_prog.f |
5009 |
-- $(MR_FORT) -c molrep_prog.f |
5010 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog.f |
5011 |
- molrep_prog1.o: molrep_prog1.f |
5012 |
-- $(MR_FORT) -c molrep_prog1.f |
5013 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog1.f |
5014 |
- molrep_prog2.o: molrep_prog2.f |
5015 |
-- $(MR_FORT) -c molrep_prog2.f |
5016 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_prog2.f |
5017 |
- molrep_subr.o: molrep_subr.f |
5018 |
-- $(MR_FORT) -c molrep_subr.f |
5019 |
--molrep_sym.o: molrep_sym.f |
5020 |
-- $(MR_FORT) -c molrep_sym.f |
5021 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_subr.f |
5022 |
-+molrep_sym_ccp4.o: molrep_sym.f |
5023 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f |
5024 |
- main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh |
5025 |
-- $(MR_FORT) -c main_molrep_mtz.f |
5026 |
--molrep_unix.o: molrep_unix.f |
5027 |
-- $(MR_FORT) -c molrep_unix.f |
5028 |
-+ $(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f |
5029 |
-+molrep_unix_ccp4.o: molrep_unix.f |
5030 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f |
5031 |
- molrep_dummy.o: molrep_dummy.f |
5032 |
-- $(MR_FORT) -c molrep_dummy.f |
5033 |
-+ $(MR_FORT) $(FFLAGS) -c molrep_dummy.f |
5034 |
- |
5035 |
- molrep: $(OBJS) |
5036 |
-- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) |
5037 |
-+ $(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) |
5038 |
- |
5039 |
- # -------------------------------- |
5040 |
- |
5041 |
|
5042 |
diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch |
5043 |
deleted file mode 100644 |
5044 |
index c18b9a1..0000000 |
5045 |
--- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch |
5046 |
+++ /dev/null |
5047 |
@@ -1,12 +0,0 @@ |
5048 |
-diff --git a/src/makefile b/src/makefile |
5049 |
-index 30d0de7..10dd68f 100755 |
5050 |
---- a/src/makefile |
5051 |
-+++ b/src/makefile |
5052 |
-@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f |
5053 |
- $(MR_FORT) -c molrep_dummy.f |
5054 |
- |
5055 |
- molrep: $(OBJS) |
5056 |
-- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) |
5057 |
-+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) |
5058 |
- |
5059 |
- # -------------------------------- |
5060 |
|
5061 |
diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch |
5062 |
deleted file mode 100644 |
5063 |
index d90cfb8..0000000 |
5064 |
--- a/sci-chemistry/molrep/files/11.0.00-test.patch |
5065 |
+++ /dev/null |
5066 |
@@ -1,191 +0,0 @@ |
5067 |
-diff --git a/molrep_check/em.bat b/molrep_check/em.bat |
5068 |
-index 2f0f992..96ddd75 100755 |
5069 |
---- a/molrep_check/em.bat |
5070 |
-+++ b/molrep_check/em.bat |
5071 |
-@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop |
5072 |
- # -------------------------------- |
5073 |
- _NMON 6 |
5074 |
- stop |
5075 |
-+echo $? |
5076 |
-+[[ $? ]] || exit 1 |
5077 |
- # -------------------------------- |
5078 |
- # |
5079 |
- # 2. Atomic model --> EM map |
5080 |
-@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop |
5081 |
- _NMON 6 |
5082 |
- _prf y |
5083 |
- stop |
5084 |
-+[[ $? ]] || exit 1 |
5085 |
- # -------------------------------- |
5086 |
- # |
5087 |
- # 3. Atomic model --> EM map |
5088 |
-@@ -36,6 +39,7 @@ _ncs 322 |
5089 |
- _centre 0.500 0.490 0.490 |
5090 |
- _angles 0.0 0.0 90.0 |
5091 |
- stop |
5092 |
-+[[ $? ]] || exit 1 |
5093 |
- # -------------------------------- |
5094 |
- # |
5095 |
- cp out/molrep.pdb hexamer.pdb |
5096 |
-@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop |
5097 |
- # -------------------------------- |
5098 |
- _DOM s |
5099 |
- stop |
5100 |
-+[[ $? ]] || exit 1 |
5101 |
- # -------------------------------- |
5102 |
- # |
5103 |
- # 5. EM --> X-ray |
5104 |
-@@ -60,6 +65,7 @@ stop |
5105 |
- $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop |
5106 |
- # -------------------------------- |
5107 |
- stop |
5108 |
-+[[ $? ]] || exit 1 |
5109 |
- # -------------------------------- |
5110 |
- # |
5111 |
- # 6. Placing the model to a particular orientation and position. |
5112 |
-@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop |
5113 |
- _fun s |
5114 |
- _file_t ../em/tab |
5115 |
- stop |
5116 |
-+[[ $? ]] || exit 1 |
5117 |
- #========================================== |
5118 |
-diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat |
5119 |
-index 284a4cd..6e00695 100755 |
5120 |
---- a/molrep_check/mr.bat |
5121 |
-+++ b/molrep_check/mr.bat |
5122 |
-@@ -10,6 +10,7 @@ |
5123 |
- $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop |
5124 |
- # -------------------------------- |
5125 |
- stop |
5126 |
-+[[ $? ]] || exit 1 |
5127 |
- # |
5128 |
- # ================================================================= |
5129 |
- # |
5130 |
-@@ -26,6 +27,7 @@ _nmon 2 |
5131 |
- _COMPL .5 |
5132 |
- _SIM .7 |
5133 |
- stop |
5134 |
-+[[ $? ]] || exit 1 |
5135 |
- # |
5136 |
- # ================================================================= |
5137 |
- # |
5138 |
-@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod |
5139 |
- # -------------------------------- |
5140 |
- _NP 3 |
5141 |
- stop |
5142 |
-+[[ $? ]] || exit 1 |
5143 |
- # |
5144 |
- # ================================================================= |
5145 |
- # |
5146 |
-@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i |
5147 |
- _NMON 2 |
5148 |
- _NP 3 |
5149 |
- stop |
5150 |
-+[[ $? ]] || exit 1 |
5151 |
- # |
5152 |
- # ================================================================= |
5153 |
- # |
5154 |
-@@ -85,6 +89,7 @@ _NPT 3 |
5155 |
- _NPTD 3 |
5156 |
- _DYAD D |
5157 |
- stop |
5158 |
-+[[ $? ]] || exit 1 |
5159 |
- # |
5160 |
- # ================================================================= |
5161 |
- # |
5162 |
-@@ -103,6 +108,7 @@ _NP 3 |
5163 |
- _NPT 10 |
5164 |
- _NMR 3 |
5165 |
- stop |
5166 |
-+[[ $? ]] || exit 1 |
5167 |
- # |
5168 |
- # ================================================================= |
5169 |
- # |
5170 |
-@@ -118,6 +124,7 @@ _PRF Y |
5171 |
- _compl 1. |
5172 |
- _sim .2 |
5173 |
- stop |
5174 |
-+[[ $? ]] || exit 1 |
5175 |
- # |
5176 |
- # ================================================================= |
5177 |
- # |
5178 |
-@@ -136,6 +143,7 @@ _ph PH |
5179 |
- _fom FOM |
5180 |
- # |
5181 |
- stop |
5182 |
-+[[ $? ]] || exit 1 |
5183 |
- # ================================================================= |
5184 |
- # |
5185 |
- # 9. use sequence |
5186 |
-@@ -145,6 +153,7 @@ stop |
5187 |
- $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop |
5188 |
- # -------------------------------- |
5189 |
- stop |
5190 |
-+[[ $? ]] || exit 1 |
5191 |
- # ================================================================= |
5192 |
- # |
5193 |
- # 10. Locked RF |
5194 |
-@@ -157,6 +166,7 @@ _lock y |
5195 |
- _file_tsrf ../data/srf.tab |
5196 |
- _nsrf 1 |
5197 |
- stop |
5198 |
-+[[ $? ]] || exit 1 |
5199 |
- # ================================================================= |
5200 |
- # |
5201 |
- # 11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and |
5202 |
-@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p |
5203 |
- _self a |
5204 |
- _nsrf 1 |
5205 |
- stop |
5206 |
-+[[ $? ]] || exit 1 |
5207 |
- # ================================================================= |
5208 |
- # |
5209 |
- # 12. use pst |
5210 |
-@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i |
5211 |
- # -------------------------------- |
5212 |
- # |
5213 |
- stop |
5214 |
-+[[ $? ]] || exit 1 |
5215 |
- # ================================================================= |
5216 |
- # |
5217 |
- # 13. space group check |
5218 |
-@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i |
5219 |
- # -------------------------------- |
5220 |
- _sg all |
5221 |
- # |
5222 |
--stop |
5223 |
-+s[[ $? ]] || exit 1 |
5224 |
-+top |
5225 |
- # ========================================================== |
5226 |
- # |
5227 |
- # 14. Example for finding HA position by MR solution. |
5228 |
-@@ -206,6 +219,7 @@ _SIGFD SIGFD3 |
5229 |
- # |
5230 |
- _FUN d |
5231 |
- stop |
5232 |
-+[[ $? ]] || exit 1 |
5233 |
- # ========================================================== |
5234 |
- # |
5235 |
- # 15. Example for HA search by multi-copy search |
5236 |
-@@ -225,6 +239,7 @@ _diff h |
5237 |
- _dyad y |
5238 |
- _nmon 4 |
5239 |
- stop |
5240 |
-+[[ $? ]] || exit 1 |
5241 |
- # ========================================================== |
5242 |
- # |
5243 |
- # 16. Example HA for search by translation function |
5244 |
-@@ -242,6 +257,7 @@ _FUN t |
5245 |
- _diff h |
5246 |
- _nmon 4 |
5247 |
- stop |
5248 |
-+[[ $? ]] || exit 1 |
5249 |
- # ========================================================== |
5250 |
- # |
5251 |
- # 17. Example for Self RF for Heavy Atom structure in derivative. |
5252 |
-@@ -258,4 +274,5 @@ _SIGFD SIGFD3 |
5253 |
- _FUN r |
5254 |
- _diff h |
5255 |
- stop |
5256 |
-+[[ $? ]] || exit 1 |
5257 |
- # ========================================================== |
5258 |
|
5259 |
diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch |
5260 |
deleted file mode 100644 |
5261 |
index 430629e..0000000 |
5262 |
--- a/sci-chemistry/molrep/files/11.0.03-EOR.patch |
5263 |
+++ /dev/null |
5264 |
@@ -1,16 +0,0 @@ |
5265 |
- src/molrep.f | 2 +- |
5266 |
- 1 files changed, 1 insertions(+), 1 deletions(-) |
5267 |
- |
5268 |
-diff --git a/src/molrep.f b/src/molrep.f |
5269 |
-index eac0cfc..94f74c6 100755 |
5270 |
---- a/src/molrep.f |
5271 |
-+++ b/src/molrep.f |
5272 |
-@@ -1257,7 +1257,7 @@ C CHECK_DENS_FILE( 2 ) |
5273 |
- LEN1 = 1 |
5274 |
- IF(LEN.GT.60) LEN1 = LEN - 59 |
5275 |
- WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') |
5276 |
-- * NAME2(LEN11:LEN) |
5277 |
-+ * NAME2(LEN1:LEN) |
5278 |
- CALL MSGDOC(MDoc,LINE) |
5279 |
- |
5280 |
- ENDIF |
5281 |
|
5282 |
diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml |
5283 |
deleted file mode 100644 |
5284 |
index ae9ec7c..0000000 |
5285 |
--- a/sci-chemistry/molrep/metadata.xml |
5286 |
+++ /dev/null |
5287 |
@@ -1,8 +0,0 @@ |
5288 |
-<?xml version="1.0" encoding="UTF-8"?> |
5289 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
5290 |
-<pkgmetadata> |
5291 |
- <herd>sci-chemistry</herd> |
5292 |
- <maintainer> |
5293 |
- <email>jlec@g.o</email> |
5294 |
- </maintainer> |
5295 |
-</pkgmetadata> |
5296 |
|
5297 |
diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild |
5298 |
deleted file mode 100644 |
5299 |
index 51ff6cb..0000000 |
5300 |
--- a/sci-chemistry/molrep/molrep-11.0.02.ebuild |
5301 |
+++ /dev/null |
5302 |
@@ -1,57 +0,0 @@ |
5303 |
-# Copyright 1999-2013 Gentoo Foundation |
5304 |
-# Distributed under the terms of the GNU General Public License v2 |
5305 |
-# $Id$ |
5306 |
- |
5307 |
-EAPI=4 |
5308 |
- |
5309 |
-inherit eutils fortran-2 multilib toolchain-funcs |
5310 |
- |
5311 |
-DESCRIPTION="molecular replacement program" |
5312 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" |
5313 |
-SRC_URI="mirror://gentoo/${P}.tar.gz" |
5314 |
- |
5315 |
-LICENSE="ccp4" |
5316 |
-SLOT="0" |
5317 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
5318 |
-IUSE="" |
5319 |
- |
5320 |
-RDEPEND=" |
5321 |
- >=sci-libs/ccp4-libs-6.1.3 |
5322 |
- sci-libs/mmdb |
5323 |
- virtual/lapack" |
5324 |
-DEPEND="${RDEPEND} |
5325 |
- virtual/pkgconfig" |
5326 |
- |
5327 |
-S="${WORKDIR}/${PN}" |
5328 |
- |
5329 |
-src_prepare() { |
5330 |
- epatch \ |
5331 |
- "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ |
5332 |
- "${FILESDIR}"/11.0.00-test.patch |
5333 |
-} |
5334 |
- |
5335 |
-src_compile() { |
5336 |
- cd "${S}"/src |
5337 |
- emake clean |
5338 |
- emake \ |
5339 |
- MR_FORT="$(tc-getFC) ${FFLAGS}" \ |
5340 |
- FFLAGS="${FFLAGS}" \ |
5341 |
- LDFLAGS="${LDFLAGS}" \ |
5342 |
- MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" |
5343 |
-} |
5344 |
- |
5345 |
-src_test() { |
5346 |
- export MR_TEST="${S}/bin/" |
5347 |
- cd "${S}"/molrep_check/work |
5348 |
- mkdir out scr |
5349 |
- cp ../*.bat . |
5350 |
- bash em.bat || die |
5351 |
- bash mr.bat || die |
5352 |
-} |
5353 |
- |
5354 |
-src_install() { |
5355 |
- exeinto /usr/libexec/ccp4/bin/ |
5356 |
- doexe bin/${PN} |
5357 |
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} |
5358 |
- dodoc readme doc/${PN}.rtf |
5359 |
-} |
5360 |
|
5361 |
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild |
5362 |
deleted file mode 100644 |
5363 |
index 3373bbb..0000000 |
5364 |
--- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild |
5365 |
+++ /dev/null |
5366 |
@@ -1,59 +0,0 @@ |
5367 |
-# Copyright 1999-2013 Gentoo Foundation |
5368 |
-# Distributed under the terms of the GNU General Public License v2 |
5369 |
-# $Id$ |
5370 |
- |
5371 |
-EAPI=4 |
5372 |
- |
5373 |
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs |
5374 |
- |
5375 |
-DESCRIPTION="molecular replacement program" |
5376 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" |
5377 |
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz" |
5378 |
- |
5379 |
-LICENSE="ccp4" |
5380 |
-SLOT="0" |
5381 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
5382 |
-IUSE="" |
5383 |
- |
5384 |
-RDEPEND=" |
5385 |
- >=sci-libs/ccp4-libs-6.1.3 |
5386 |
- sci-libs/mmdb |
5387 |
- virtual/lapack" |
5388 |
-DEPEND="${RDEPEND} |
5389 |
- virtual/pkgconfig" |
5390 |
- |
5391 |
-S="${WORKDIR}/${PN}" |
5392 |
- |
5393 |
-src_prepare() { |
5394 |
- epatch \ |
5395 |
- "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ |
5396 |
- "${FILESDIR}"/11.0.00-test.patch \ |
5397 |
- "${FILESDIR}"/${PV}-EOR.patch |
5398 |
- [[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore |
5399 |
-} |
5400 |
- |
5401 |
-src_compile() { |
5402 |
- cd "${S}"/src |
5403 |
- emake clean |
5404 |
- emake \ |
5405 |
- MR_FORT="$(tc-getFC) ${FFLAGS}" \ |
5406 |
- FFLAGS="${FFLAGS}" \ |
5407 |
- LDFLAGS="${LDFLAGS}" \ |
5408 |
- MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" |
5409 |
-} |
5410 |
- |
5411 |
-src_test() { |
5412 |
- export MR_TEST="${S}/bin/" |
5413 |
- cd "${S}"/molrep_check/work |
5414 |
- mkdir out scr |
5415 |
- cp ../*.bat . |
5416 |
- bash em.bat || die |
5417 |
- bash mr.bat || die |
5418 |
-} |
5419 |
- |
5420 |
-src_install() { |
5421 |
- exeinto /usr/libexec/ccp4/bin/ |
5422 |
- doexe bin/${PN} |
5423 |
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} |
5424 |
- dodoc readme doc/${PN}.rtf |
5425 |
-} |
5426 |
|
5427 |
diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest |
5428 |
deleted file mode 100644 |
5429 |
index 80df134..0000000 |
5430 |
--- a/sci-chemistry/mosflm/Manifest |
5431 |
+++ /dev/null |
5432 |
@@ -1 +0,0 @@ |
5433 |
-DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8 |
5434 |
|
5435 |
diff --git a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch |
5436 |
deleted file mode 100644 |
5437 |
index a35232f..0000000 |
5438 |
--- a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch |
5439 |
+++ /dev/null |
5440 |
@@ -1,13 +0,0 @@ |
5441 |
---- Makefile 2008-10-17 16:15:30.000000000 +0200 |
5442 |
-+++ Makefile.new 2009-02-20 21:52:34.000000000 +0100 |
5443 |
-@@ -22,7 +22,7 @@ |
5444 |
- CBFLIBS = cbf/lib/libcbf.a |
5445 |
- JPGLIBS = jpg/libjpeg.a |
5446 |
- |
5447 |
--all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) |
5448 |
-- cd mosflm ; make |
5449 |
-+all: dpslibs cbflibs |
5450 |
-+ +make -C mosflm |
5451 |
- |
5452 |
- ########################################################################## |
5453 |
- |
5454 |
|
5455 |
diff --git a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch |
5456 |
deleted file mode 100644 |
5457 |
index da393eb..0000000 |
5458 |
--- a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch |
5459 |
+++ /dev/null |
5460 |
@@ -1,36 +0,0 @@ |
5461 |
-diff --git a/mosflm/bravais_fortran.c b/mosflm/bravais_fortran.c |
5462 |
-index 3d68cad..800bd0e 100644 |
5463 |
---- a/mosflm/bravais_fortran.c |
5464 |
-+++ b/mosflm/bravais_fortran.c |
5465 |
-@@ -2,6 +2,7 @@ |
5466 |
- #include <stdlib.h> |
5467 |
- #include <math.h> |
5468 |
- #include "../util/util.h" |
5469 |
-+#include "../util/bravais.h" |
5470 |
- |
5471 |
- /* bravais_fortran_(): This routine converts array from FORTRAN program |
5472 |
- to structure for call to bravais |
5473 |
-diff --git a/mosflm/chelp.c b/mosflm/chelp.c |
5474 |
-index b2aaefc..fa44ab0 100644 |
5475 |
---- a/mosflm/chelp.c |
5476 |
-+++ b/mosflm/chelp.c |
5477 |
-@@ -5,6 +5,7 @@ |
5478 |
- /* modified for Linux by Joachim Meyer jmeyer@×××××××××××××××.de 1998.05.19 */ |
5479 |
- |
5480 |
- #include "chelp.h" |
5481 |
-+#include <stdio.h> |
5482 |
- |
5483 |
- #if CALL_LIKE_HPUX |
5484 |
- void chelp () |
5485 |
-diff --git a/mosflm/pck.c b/mosflm/pck.c |
5486 |
-index ec094fc..288671d 100644 |
5487 |
---- a/mosflm/pck.c |
5488 |
-+++ b/mosflm/pck.c |
5489 |
-@@ -17,6 +17,7 @@ |
5490 |
- #include <math.h> |
5491 |
- #include <ctype.h> |
5492 |
- #include <string.h> |
5493 |
-+#include <unistd.h> |
5494 |
- |
5495 |
- #define BYTE char |
5496 |
- #define WORD short int |
5497 |
|
5498 |
diff --git a/sci-chemistry/mosflm/files/7.0.6-parallel.patch b/sci-chemistry/mosflm/files/7.0.6-parallel.patch |
5499 |
deleted file mode 100644 |
5500 |
index f735c7c..0000000 |
5501 |
--- a/sci-chemistry/mosflm/files/7.0.6-parallel.patch |
5502 |
+++ /dev/null |
5503 |
@@ -1,28 +0,0 @@ |
5504 |
---- cbf/Makefile 2009-08-31 09:35:06.000000000 +0200 |
5505 |
-+++ cbf/Makefile.new 2009-08-31 10:44:46.000000000 +0200 |
5506 |
-@@ -362,6 +362,8 @@ |
5507 |
- $(EXAMPLES)/img.h \ |
5508 |
- $(INCLUDE)/md5.h |
5509 |
- |
5510 |
-+OBJ = $(subst .c,.o,$(SOURCE)) |
5511 |
-+ |
5512 |
- # |
5513 |
- # Compile the library and examples |
5514 |
- # |
5515 |
-@@ -379,11 +381,14 @@ |
5516 |
- $(LIB): |
5517 |
- mkdir $(LIB) |
5518 |
- |
5519 |
-+ |
5520 |
-+.c.o: $(SOURCE) $(HEADERS) |
5521 |
-+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< |
5522 |
-+ |
5523 |
- # |
5524 |
- # CBF library |
5525 |
- # |
5526 |
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) |
5527 |
-- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) |
5528 |
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) |
5529 |
- $(AR) cr $@ *.o |
5530 |
- rm *.o |
5531 |
- if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi |
5532 |
|
5533 |
diff --git a/sci-chemistry/mosflm/files/7.0.7-parallel.patch b/sci-chemistry/mosflm/files/7.0.7-parallel.patch |
5534 |
deleted file mode 100644 |
5535 |
index df0a8b6..0000000 |
5536 |
--- a/sci-chemistry/mosflm/files/7.0.7-parallel.patch |
5537 |
+++ /dev/null |
5538 |
@@ -1,92 +0,0 @@ |
5539 |
- Makefile | 21 ++++++++++----------- |
5540 |
- cbf/Makefile | 9 +++++++-- |
5541 |
- 2 files changed, 17 insertions(+), 13 deletions(-) |
5542 |
- |
5543 |
-diff --git a/Makefile b/Makefile |
5544 |
-index 37f4c7e..51d4164 100644 |
5545 |
---- a/Makefile |
5546 |
-+++ b/Makefile |
5547 |
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a |
5548 |
- CBFLIBS = cbf/lib/libcbf.a |
5549 |
- JPGLIBS = jpg/libjpeg.a |
5550 |
- |
5551 |
--all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) |
5552 |
-- cd mosflm ; make |
5553 |
-+all: $(DPSLIBS) |
5554 |
-+ $(MAKE) -C mosflm |
5555 |
- |
5556 |
- ########################################################################## |
5557 |
- # # |
5558 |
-@@ -47,22 +47,21 @@ dpslibs: |
5559 |
- |
5560 |
- cbflibs: |
5561 |
- rm -f `find ./cbf -name "*.a" -print` |
5562 |
-- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ |
5563 |
-- then $(RANLIB) lib/libcbf.a; fi |
5564 |
-+ $(MAKE) -C cbf all |
5565 |
- |
5566 |
- jpglibs: |
5567 |
-- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a |
5568 |
-+ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a |
5569 |
- |
5570 |
- ${DPSLIBS}: |
5571 |
-- make dpslibs |
5572 |
-+ $(MAKE) dpslibs |
5573 |
- |
5574 |
- ${CBFLIBS}: |
5575 |
-- make cbflibs |
5576 |
-+ $(MAKE) cbflibs |
5577 |
- |
5578 |
- ${JPGLIBS}: |
5579 |
-- make jpglibs |
5580 |
-+ $(MAKE) jpglibs |
5581 |
- |
5582 |
--libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} |
5583 |
-+libs: ${DPSLIBS} ${CBFLIBS} |
5584 |
- @echo "****************************************************************" |
5585 |
- @echo " Making libraries for system ${HOSTTYPE}" |
5586 |
- @echo "****************************************************************" |
5587 |
-@@ -71,11 +70,11 @@ ipmosflm: libs |
5588 |
- @echo "****************************************************************" |
5589 |
- @echo " Making IPMOSFLM for system ${HOSTTYPE}" |
5590 |
- @echo "****************************************************************" |
5591 |
-- cd mosflm ; make ipmosflm |
5592 |
-+ $(MAKE) -C mosflm ipmosflm |
5593 |
- |
5594 |
- force: |
5595 |
- rm bin/ipmosflm |
5596 |
-- make ipmosflm |
5597 |
-+ $(MAKE) ipmosflm |
5598 |
- |
5599 |
- install: |
5600 |
- @echo "the executable is in ${MOSHOME}/bin/ipmosflm" |
5601 |
-diff --git a/cbf/Makefile b/cbf/Makefile |
5602 |
-index e61497c..c3c94ac 100644 |
5603 |
---- a/cbf/Makefile |
5604 |
-+++ b/cbf/Makefile |
5605 |
-@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ |
5606 |
- $(EXAMPLES)/img.h \ |
5607 |
- $(INCLUDE)/md5.h |
5608 |
- |
5609 |
-+OBJ = $(subst .c,.o,$(SOURCE)) |
5610 |
-+ |
5611 |
- # |
5612 |
- # Compile the library and examples |
5613 |
- # |
5614 |
-@@ -379,11 +381,14 @@ $(INSTALLDIR): |
5615 |
- $(LIB): |
5616 |
- mkdir $(LIB) |
5617 |
- |
5618 |
-+ |
5619 |
-+.c.o: $(SOURCE) $(HEADERS) |
5620 |
-+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< |
5621 |
-+ |
5622 |
- # |
5623 |
- # CBF library |
5624 |
- # |
5625 |
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) |
5626 |
-- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) |
5627 |
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) |
5628 |
- $(AR) cr $@ *.o |
5629 |
- rm *.o |
5630 |
- if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi |
5631 |
|
5632 |
diff --git a/sci-chemistry/mosflm/files/7.0.9-parallel.patch b/sci-chemistry/mosflm/files/7.0.9-parallel.patch |
5633 |
deleted file mode 100644 |
5634 |
index 38c6fc4..0000000 |
5635 |
--- a/sci-chemistry/mosflm/files/7.0.9-parallel.patch |
5636 |
+++ /dev/null |
5637 |
@@ -1,92 +0,0 @@ |
5638 |
- Makefile | 21 ++++++++++----------- |
5639 |
- cbf/Makefile | 9 +++++++-- |
5640 |
- 2 files changed, 17 insertions(+), 13 deletions(-) |
5641 |
- |
5642 |
-diff --git a/Makefile b/Makefile |
5643 |
-index 3d2f543..2219d8d 100644 |
5644 |
---- a/Makefile |
5645 |
-+++ b/Makefile |
5646 |
-@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a |
5647 |
- CBFLIBS = cbf/lib/libcbf.a |
5648 |
- JPGLIBS = jpg/libjpeg.a |
5649 |
- |
5650 |
--all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) |
5651 |
-- cd mosflm ; make |
5652 |
-+all: $(DPSLIBS) |
5653 |
-+ $(MAKE) -C mosflm |
5654 |
- |
5655 |
- dpslibs: |
5656 |
- @-find . -name "*a" -delete |
5657 |
-@@ -32,22 +32,21 @@ dpslibs: |
5658 |
- |
5659 |
- cbflibs: |
5660 |
- @-find ./cbf -name "*.a" -delete |
5661 |
-- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ |
5662 |
-- then $(RANLIB) lib/libcbf.a; fi |
5663 |
-+ $(MAKE) -C cbf all |
5664 |
- |
5665 |
- jpglibs: |
5666 |
-- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a |
5667 |
-+ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a |
5668 |
- |
5669 |
- ${DPSLIBS}: |
5670 |
-- make dpslibs |
5671 |
-+ $(MAKE) dpslibs |
5672 |
- |
5673 |
- ${CBFLIBS}: |
5674 |
-- make cbflibs |
5675 |
-+ $(MAKE) cbflibs |
5676 |
- |
5677 |
- ${JPGLIBS}: |
5678 |
-- make jpglibs |
5679 |
-+ $(MAKE) jpglibs |
5680 |
- |
5681 |
--libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} |
5682 |
-+libs: ${DPSLIBS} ${CBFLIBS} |
5683 |
- @echo "****************************************************************" |
5684 |
- @echo " Making libraries for system ${HOSTTYPE}" |
5685 |
- @echo "****************************************************************" |
5686 |
-@@ -56,11 +55,11 @@ ipmosflm: libs |
5687 |
- @echo "****************************************************************" |
5688 |
- @echo " Making IPMOSFLM for system ${HOSTTYPE}" |
5689 |
- @echo "****************************************************************" |
5690 |
-- cd mosflm ; make ipmosflm |
5691 |
-+ $(MAKE) -C mosflm ipmosflm |
5692 |
- |
5693 |
- force: |
5694 |
- @-rm -f bin/ipmosflm |
5695 |
-- make ipmosflm |
5696 |
-+ $(MAKE) ipmosflm |
5697 |
- |
5698 |
- install: |
5699 |
- @echo "the executable is in ${MOSHOME}/bin/ipmosflm" |
5700 |
-diff --git a/cbf/Makefile b/cbf/Makefile |
5701 |
-index e61497c..c3c94ac 100644 |
5702 |
---- a/cbf/Makefile |
5703 |
-+++ b/cbf/Makefile |
5704 |
-@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ |
5705 |
- $(EXAMPLES)/img.h \ |
5706 |
- $(INCLUDE)/md5.h |
5707 |
- |
5708 |
-+OBJ = $(subst .c,.o,$(SOURCE)) |
5709 |
-+ |
5710 |
- # |
5711 |
- # Compile the library and examples |
5712 |
- # |
5713 |
-@@ -379,11 +381,14 @@ $(INSTALLDIR): |
5714 |
- $(LIB): |
5715 |
- mkdir $(LIB) |
5716 |
- |
5717 |
-+ |
5718 |
-+.c.o: $(SOURCE) $(HEADERS) |
5719 |
-+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< |
5720 |
-+ |
5721 |
- # |
5722 |
- # CBF library |
5723 |
- # |
5724 |
--$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) |
5725 |
-- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) |
5726 |
-+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) |
5727 |
- $(AR) cr $@ *.o |
5728 |
- rm *.o |
5729 |
- if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi |
5730 |
|
5731 |
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch |
5732 |
deleted file mode 100644 |
5733 |
index 90158eb..0000000 |
5734 |
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch |
5735 |
+++ /dev/null |
5736 |
@@ -1,16 +0,0 @@ |
5737 |
- mosflm/pilatus_c.c | 2 +- |
5738 |
- 1 files changed, 1 insertions(+), 1 deletions(-) |
5739 |
- |
5740 |
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c |
5741 |
-index 1eaae26..cce5a02 100644 |
5742 |
---- a/mosflm/pilatus_c.c |
5743 |
-+++ b/mosflm/pilatus_c.c |
5744 |
-@@ -34,7 +34,7 @@ delete them later */ |
5745 |
- int cbf_int[16]; |
5746 |
- long cbf_int4[16]; |
5747 |
- double cbf_double[16]; |
5748 |
-- char cbf_char[16][24]; |
5749 |
-+ char cbf_char[16][32]; |
5750 |
- /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll |
5751 |
- delete them later */ |
5752 |
- int id, index, iindex; |
5753 |
|
5754 |
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch |
5755 |
deleted file mode 100644 |
5756 |
index 32f251f..0000000 |
5757 |
--- a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch |
5758 |
+++ /dev/null |
5759 |
@@ -1,29 +0,0 @@ |
5760 |
- mosflm/mosflm_jpeg.c | 1 + |
5761 |
- src/dps/index/ind_gen_direct.c | 2 ++ |
5762 |
- 2 files changed, 3 insertions(+), 0 deletions(-) |
5763 |
- |
5764 |
-diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c |
5765 |
-index 2b32b2e..54684d0 100644 |
5766 |
---- a/mosflm/mosflm_jpeg.c |
5767 |
-+++ b/mosflm/mosflm_jpeg.c |
5768 |
-@@ -76,6 +76,7 @@ G. Winter |
5769 |
- #include <fcntl.h> |
5770 |
- #include <stdio.h> |
5771 |
- #include <stdlib.h> |
5772 |
-+#include <string.h> |
5773 |
- #if (defined _MSC_VER) |
5774 |
- /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/ |
5775 |
- #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC |
5776 |
-diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c |
5777 |
-index 6e143df..2eea61b 100644 |
5778 |
---- a/src/dps/index/ind_gen_direct.c |
5779 |
-+++ b/src/dps/index/ind_gen_direct.c |
5780 |
-@@ -41,6 +41,8 @@ |
5781 |
- /* #include <malloc.h> */ |
5782 |
- #include "util.h" |
5783 |
- #include "ind_gen_direct.h" |
5784 |
-+#include "ind_help.h" |
5785 |
-+#include "ind_sort_merge.h" |
5786 |
- /* char *strcat( char *, const char *); */ |
5787 |
- |
5788 |
- |
5789 |
|
5790 |
diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch |
5791 |
deleted file mode 100644 |
5792 |
index bb4a16b..0000000 |
5793 |
--- a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch |
5794 |
+++ /dev/null |
5795 |
@@ -1,16 +0,0 @@ |
5796 |
- mosflm/pilatus_c.c | 2 +- |
5797 |
- 1 files changed, 1 insertions(+), 1 deletions(-) |
5798 |
- |
5799 |
-diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c |
5800 |
-index 4a85b26..9893e0c 100644 |
5801 |
---- a/mosflm/pilatus_c.c |
5802 |
-+++ b/mosflm/pilatus_c.c |
5803 |
-@@ -34,7 +34,7 @@ delete them later */ |
5804 |
- int cbf_int[16] = {0}; |
5805 |
- long cbf_int4[16] = {0}; |
5806 |
- double cbf_double[16] = {0}; |
5807 |
-- char cbf_char[16][24] = {' '}; |
5808 |
-+ char cbf_char[16][32] = {' '}; |
5809 |
- /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll |
5810 |
- delete them later */ |
5811 |
- int id, index, iindex; |
5812 |
|
5813 |
diff --git a/sci-chemistry/mosflm/metadata.xml b/sci-chemistry/mosflm/metadata.xml |
5814 |
deleted file mode 100644 |
5815 |
index ae9ec7c..0000000 |
5816 |
--- a/sci-chemistry/mosflm/metadata.xml |
5817 |
+++ /dev/null |
5818 |
@@ -1,8 +0,0 @@ |
5819 |
-<?xml version="1.0" encoding="UTF-8"?> |
5820 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
5821 |
-<pkgmetadata> |
5822 |
- <herd>sci-chemistry</herd> |
5823 |
- <maintainer> |
5824 |
- <email>jlec@g.o</email> |
5825 |
- </maintainer> |
5826 |
-</pkgmetadata> |
5827 |
|
5828 |
diff --git a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild |
5829 |
deleted file mode 100644 |
5830 |
index 3aa74ce..0000000 |
5831 |
--- a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild |
5832 |
+++ /dev/null |
5833 |
@@ -1,74 +0,0 @@ |
5834 |
-# Copyright 1999-2015 Gentoo Foundation |
5835 |
-# Distributed under the terms of the GNU General Public License v2 |
5836 |
-# $Id$ |
5837 |
- |
5838 |
-EAPI=5 |
5839 |
- |
5840 |
-inherit eutils fortran-2 toolchain-funcs versionator |
5841 |
- |
5842 |
-MY_PV="$(delete_all_version_separators)" |
5843 |
-MY_P="${PN}${MY_PV}" |
5844 |
- |
5845 |
-DESCRIPTION="A program for integrating single crystal diffraction data from area detectors" |
5846 |
-HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/" |
5847 |
-SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz" |
5848 |
- |
5849 |
-SLOT="0" |
5850 |
-LICENSE="ccp4" |
5851 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
5852 |
-IUSE="" |
5853 |
- |
5854 |
-RDEPEND=" |
5855 |
- app-shells/tcsh |
5856 |
- sci-libs/cbflib |
5857 |
- sci-libs/ccp4-libs |
5858 |
- sys-libs/ncurses |
5859 |
- virtual/jpeg:0= |
5860 |
- x11-libs/libxdl_view" |
5861 |
-DEPEND="${RDEPEND}" |
5862 |
- |
5863 |
-S="${WORKDIR}/${MY_P}" |
5864 |
- |
5865 |
-src_prepare() { |
5866 |
- sed \ |
5867 |
- -e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \ |
5868 |
- -e "s:../jpg/libjpeg.a:-ljpeg:g" \ |
5869 |
- -i ${PN}/Makefile || die |
5870 |
- |
5871 |
- sed \ |
5872 |
- -e '/jinclude.h/d' \ |
5873 |
- -i mosflm/mosflm_jpeg.c || die |
5874 |
- |
5875 |
- cp DATETIME.C mosflm/datetime.c || die |
5876 |
- |
5877 |
- epatch \ |
5878 |
- "${FILESDIR}"/${PV}-parallel.patch \ |
5879 |
- "${FILESDIR}"/7.0.6-impl-dec.patch \ |
5880 |
- "${FILESDIR}"/${P}-buffer-overflow.patch \ |
5881 |
- "${FILESDIR}"/${PN}-7.0.7-impl-dec.patch |
5882 |
- |
5883 |
- rm -rf test.f {cbf,jpg}/*.{h,c} || die |
5884 |
-} |
5885 |
- |
5886 |
-src_compile() { |
5887 |
- emake \ |
5888 |
- MOSHOME="${S}" \ |
5889 |
- DPS="${S}" \ |
5890 |
- FC=$(tc-getFC) \ |
5891 |
- FLINK=$(tc-getFC) \ |
5892 |
- CC=$(tc-getCC) \ |
5893 |
- AR_FLAGS=vru \ |
5894 |
- MOSLIBS="-lccp4f -lccp4c -lxdl_view $($(tc-getPKG_CONFIG) --libs ncurses) -lXt -lmmdb -lccif -lstdc++" \ |
5895 |
- MCFLAGS="-O0 -fno-second-underscore" \ |
5896 |
- MOSFLAGS="${FFLAGS} -fno-second-underscore" \ |
5897 |
- FFLAGS="${FFLAGS} -fno-second-underscore" \ |
5898 |
- CFLAGS="${CFLAGS}" \ |
5899 |
- MOSCFLAGS="${CFLAGS}" \ |
5900 |
- LFLAGS="${LDFLAGS}" |
5901 |
-} |
5902 |
- |
5903 |
-src_install() { |
5904 |
- exeinto /usr/libexec/ccp4/bin/ |
5905 |
- doexe bin/ipmosflm |
5906 |
- dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN} |
5907 |
-} |
5908 |
|
5909 |
diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest |
5910 |
deleted file mode 100644 |
5911 |
index f9887a6..0000000 |
5912 |
--- a/sci-chemistry/mrbump/Manifest |
5913 |
+++ /dev/null |
5914 |
@@ -1 +0,0 @@ |
5915 |
-DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d |
5916 |
|
5917 |
diff --git a/sci-chemistry/mrbump/files/0.4.4-superpose.patch b/sci-chemistry/mrbump/files/0.4.4-superpose.patch |
5918 |
deleted file mode 100644 |
5919 |
index c9941e9..0000000 |
5920 |
--- a/sci-chemistry/mrbump/files/0.4.4-superpose.patch |
5921 |
+++ /dev/null |
5922 |
@@ -1,11 +0,0 @@ |
5923 |
---- share/mrbump/include/mr/Ensemble.py 2008-07-28 16:40:47.000000000 +0200 |
5924 |
-+++ share/mrbump/include/mr/Ensemble.py.new 2009-08-26 22:26:44.000000000 +0200 |
5925 |
-@@ -29,7 +29,7 @@ |
5926 |
- self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose.exe') |
5927 |
- self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset.exe') |
5928 |
- else: |
5929 |
-- self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose') |
5930 |
-+ self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose-ccp4') |
5931 |
- self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset') |
5932 |
- |
5933 |
- self.SPxyz_template='' |
5934 |
|
5935 |
diff --git a/sci-chemistry/mrbump/metadata.xml b/sci-chemistry/mrbump/metadata.xml |
5936 |
deleted file mode 100644 |
5937 |
index 4aaae06..0000000 |
5938 |
--- a/sci-chemistry/mrbump/metadata.xml |
5939 |
+++ /dev/null |
5940 |
@@ -1,10 +0,0 @@ |
5941 |
-<?xml version="1.0" encoding="UTF-8"?> |
5942 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
5943 |
-<pkgmetadata> |
5944 |
- <herd>sci-chemistry</herd> |
5945 |
- <maintainer> |
5946 |
- <email>jlec@g.o</email> |
5947 |
- <name>Justin Lecher (jlec)</name> |
5948 |
- </maintainer> |
5949 |
-</pkgmetadata> |
5950 |
- |
5951 |
|
5952 |
diff --git a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild |
5953 |
deleted file mode 100644 |
5954 |
index 66ec930..0000000 |
5955 |
--- a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild |
5956 |
+++ /dev/null |
5957 |
@@ -1,57 +0,0 @@ |
5958 |
-# Copyright 1999-2012 Gentoo Foundation |
5959 |
-# Distributed under the terms of the GNU General Public License v2 |
5960 |
-# $Id$ |
5961 |
- |
5962 |
-EAPI="3" |
5963 |
- |
5964 |
-PYTHON_DEPEND="2" |
5965 |
- |
5966 |
-inherit eutils multilib python |
5967 |
- |
5968 |
-DESCRIPTION="An automated scheme for Molecular Replacement" |
5969 |
-HOMEPAGE="http://www.ccp4.ac.uk/MrBUMP" |
5970 |
-SRC_URI="${HOMEPAGE}/release/${P}.tar.gz" |
5971 |
- |
5972 |
-LICENSE="ccp4" |
5973 |
-SLOT="0" |
5974 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
5975 |
-IUSE="X perl" |
5976 |
- |
5977 |
-RDEPEND=">=sci-chemistry/ccp4-apps-6.1.3[X?] |
5978 |
- || ( sci-biology/mafft |
5979 |
- sci-biology/clustalw:2 |
5980 |
- sci-biology/probcons |
5981 |
- sci-biology/t-coffee ) |
5982 |
- sci-biology/fasta |
5983 |
- X? ( media-gfx/graphviz ) |
5984 |
- perl? ( dev-perl/SOAP-Lite )" |
5985 |
-DEPEND="${RDEPEND}" |
5986 |
- |
5987 |
-pkg_setup() { |
5988 |
- python_set_active_version 2 |
5989 |
-} |
5990 |
- |
5991 |
-src_unpack(){ |
5992 |
- unpack ${A} |
5993 |
- cd "${S}" |
5994 |
- unpack ./"${PN}".tar.gz |
5995 |
-} |
5996 |
- |
5997 |
-src_prepare() { |
5998 |
- epatch "${FILESDIR}"/${PV}-superpose.patch |
5999 |
- python_convert_shebangs 2 setup_lib/* |
6000 |
-} |
6001 |
- |
6002 |
-src_install(){ |
6003 |
- insinto /usr/$(get_libdir)/ccp4/ccp4i |
6004 |
- doins -r ccp4i/{MrBUMP-ccp4i.tar.gz,MrBUMP/{help,scripts,tasks,templates}} || \ |
6005 |
- die "failed to install interface" |
6006 |
- |
6007 |
- insinto /usr/share/${PN} |
6008 |
- doins -r share/${PN}/{data,include} || die "failed to install mrbump data" |
6009 |
- |
6010 |
- dobin share/${PN}/bin/* || die "failed to install binaries" |
6011 |
- |
6012 |
- dodoc README.txt || die |
6013 |
- dohtml html/mrbump_doc.html || die |
6014 |
-} |
6015 |
|
6016 |
diff --git a/sci-chemistry/oasis/Manifest b/sci-chemistry/oasis/Manifest |
6017 |
deleted file mode 100644 |
6018 |
index e87a831..0000000 |
6019 |
--- a/sci-chemistry/oasis/Manifest |
6020 |
+++ /dev/null |
6021 |
@@ -1 +0,0 @@ |
6022 |
-DIST oasis4.0_Linux.zip 6714528 SHA256 56da70ce0c2750aaddf64ad2cd7852fc341d2022209484beb356b4e73dec61ba SHA512 b43b8315e8e3bc8531e11021605100f231635e2363256a19ed0f51015913221eb9e37b3891b9b1239bf83c9ada8f65a1bdc79ec5745201436f8c3b5019bd4bf7 WHIRLPOOL 24d337391997d036bd657ab22aecc77d36f7fa0af573d17433869a29640a8a10368c75ebee114071c577cc0cce34d838271147599d99e2c389088b8c6185f41b |
6023 |
|
6024 |
diff --git a/sci-chemistry/oasis/files/4.0-makefile.patch b/sci-chemistry/oasis/files/4.0-makefile.patch |
6025 |
deleted file mode 100644 |
6026 |
index f27a350..0000000 |
6027 |
--- a/sci-chemistry/oasis/files/4.0-makefile.patch |
6028 |
+++ /dev/null |
6029 |
@@ -1,15 +0,0 @@ |
6030 |
-diff --git a/src/Makefile b/src/Makefile |
6031 |
-index 1e9128f..eb9edaf 100644 |
6032 |
---- a/src/Makefile |
6033 |
-+++ b/src/Makefile |
6034 |
-@@ -20,8 +20,8 @@ IRIX: |
6035 |
- @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o oasis4-0 oasis4-0.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas |
6036 |
- @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o fnp2fp fnp2fp.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas |
6037 |
- Linux: |
6038 |
-- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} |
6039 |
-- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} |
6040 |
-+ ${F77} $(CFLAGS) $(LDFLAGS) -o oasis oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} |
6041 |
-+ ${F77} $(CFLAGS) $(LDFLAGS) -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} |
6042 |
- Darwin: |
6043 |
- @ ${F77} -O2 -fno-second-underscore -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm |
6044 |
- @ ${F77} -O2 -fno-second-underscore -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm |
6045 |
|
6046 |
diff --git a/sci-chemistry/oasis/metadata.xml b/sci-chemistry/oasis/metadata.xml |
6047 |
deleted file mode 100644 |
6048 |
index 8412c2f..0000000 |
6049 |
--- a/sci-chemistry/oasis/metadata.xml |
6050 |
+++ /dev/null |
6051 |
@@ -1,8 +0,0 @@ |
6052 |
-<?xml version="1.0" encoding="UTF-8"?> |
6053 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
6054 |
-<pkgmetadata> |
6055 |
- <herd>sci-chemistry</herd> |
6056 |
- <use> |
6057 |
- <flag name="minimal">Restricts functionality on free software</flag> |
6058 |
- </use> |
6059 |
-</pkgmetadata> |
6060 |
|
6061 |
diff --git a/sci-chemistry/oasis/oasis-4.0-r3.ebuild b/sci-chemistry/oasis/oasis-4.0-r3.ebuild |
6062 |
deleted file mode 100644 |
6063 |
index 98c8aae..0000000 |
6064 |
--- a/sci-chemistry/oasis/oasis-4.0-r3.ebuild |
6065 |
+++ /dev/null |
6066 |
@@ -1,70 +0,0 @@ |
6067 |
-# Copyright 1999-2015 Gentoo Foundation |
6068 |
-# Distributed under the terms of the GNU General Public License v2 |
6069 |
-# $Id$ |
6070 |
- |
6071 |
-EAPI=5 |
6072 |
- |
6073 |
-inherit eutils fortran-2 multilib toolchain-funcs |
6074 |
- |
6075 |
-MY_P="${PN}${PV}_Linux" |
6076 |
- |
6077 |
-DESCRIPTION="A direct-method program for SAD/SIR phasing" |
6078 |
-HOMEPAGE="http://cryst.iphy.ac.cn/Project/protein/protein-I.html" |
6079 |
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${MY_P}.zip" |
6080 |
- |
6081 |
-SLOT="0" |
6082 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
6083 |
-LICENSE="ccp4 oasis" |
6084 |
-IUSE="examples +minimal" |
6085 |
- |
6086 |
-RDEPEND=" |
6087 |
- sci-chemistry/ccp4-apps |
6088 |
- sci-chemistry/pymol |
6089 |
- sci-libs/mmdb:0 |
6090 |
- sci-visualization/gnuplot |
6091 |
- !minimal? ( |
6092 |
- sci-chemistry/solve-resolve-bin |
6093 |
- sci-chemistry/arp-warp-bin |
6094 |
- )" |
6095 |
-DEPEND="${RDEPEND} |
6096 |
- sci-libs/ccp4-libs" |
6097 |
- |
6098 |
-S="${WORKDIR}"/${MY_P} |
6099 |
- |
6100 |
-src_prepare() { |
6101 |
- rm bin/{fnp2fp,gnuplot,oasis4-0,seq} || die |
6102 |
- epatch "${FILESDIR}"/${PV}-makefile.patch |
6103 |
-} |
6104 |
- |
6105 |
-src_compile() { |
6106 |
- emake \ |
6107 |
- -C src \ |
6108 |
- F77="$(tc-getFC)" \ |
6109 |
- CFLAGS="${FFLAGS}" \ |
6110 |
- CCP4_LIB="${EPREFIX}/usr/$(get_libdir)" \ |
6111 |
- Linux |
6112 |
-} |
6113 |
- |
6114 |
-src_install() { |
6115 |
- exeinto /usr/libexec/ccp4/bin/ |
6116 |
- doexe src/{${PN},fnp2fp} |
6117 |
- |
6118 |
- exeinto /usr/$(get_libdir)/${PN} |
6119 |
- doexe bin/*.*sh |
6120 |
- |
6121 |
- insinto /usr/share/doc/${PF}/html |
6122 |
- doins bin/html/* |
6123 |
- dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/html |
6124 |
- chmod 755 "${ED}"/usr/share/doc/${PF}/html/*.{*sh,awk} || die |
6125 |
- |
6126 |
- if use examples; then |
6127 |
- insinto /usr/share/${PN} |
6128 |
- doins -r examples |
6129 |
- fi |
6130 |
- |
6131 |
- cat >> "${T}"/25oasis <<- EOF |
6132 |
- oasisbin="${EPREFIX}/usr/$(get_libdir)/${PN}" |
6133 |
- EOF |
6134 |
- |
6135 |
- doenvd "${T}"/25oasis |
6136 |
-} |
6137 |
|
6138 |
diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest |
6139 |
deleted file mode 100644 |
6140 |
index 9036c79..0000000 |
6141 |
--- a/sci-chemistry/pdb-extract/Manifest |
6142 |
+++ /dev/null |
6143 |
@@ -1,2 +0,0 @@ |
6144 |
-DIST pdb-extract-v3.004-prod-src.tar.gz 942450 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 SHA512 4505fd615324982e741a3656d8a36ffc2cd6524c825d254e0a1ff44b3464aaf63cbdbe4f614a6ace6c0e56af8f452634152edadd0ed5305f0148856affa8cb60 WHIRLPOOL b7077431d75a31a9ac4ea41f7cb76874aa49626a19c1290126405a8cdac4d210f56929f9213512ae4f542286be5cbedc972642b9ef07a4e461ac969c6c0d965f |
6145 |
-DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 SHA512 06ef4110f873d23bcf878877a8b9f714b895a5b269f8d33312387c0bcb569adb2b1d1577eebc30200d5f0d3648959450912911609dab3749e7d5eb4c84d7e12f WHIRLPOOL ea0e643e1d64f344fdd643348b0ce35143e29f27a64b9153d6645c8dbf914e193f700217c0caecb30ea300ae10f47ea09bed61811c3bb293ef63d9e45acf74d3 |
6146 |
|
6147 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch |
6148 |
deleted file mode 100644 |
6149 |
index 3a6f549..0000000 |
6150 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch |
6151 |
+++ /dev/null |
6152 |
@@ -1,46 +0,0 @@ |
6153 |
---- Makefile 2008-12-05 14:36:44.000000000 +0100 |
6154 |
-+++ Makefile.new 2008-12-05 14:37:21.000000000 +0100 |
6155 |
-@@ -19,13 +19,7 @@ |
6156 |
- CHECKOUT_SCRIPT_MODULE = util |
6157 |
- CHECKOUT_SCRIPT = checkout.sh |
6158 |
- |
6159 |
--LIBDIRS = cifobj-common-v4.1 \ |
6160 |
-- tables-v8.0 \ |
6161 |
-- regex-v2.2 \ |
6162 |
-- cif-file-v1.0 \ |
6163 |
-- misclib-v2.2 \ |
6164 |
-- cifparse-obj-v7.0 \ |
6165 |
-- $(EXTRACT) |
6166 |
-+LIBDIRS = $(EXTRACT) |
6167 |
- |
6168 |
- all: compile |
6169 |
- |
6170 |
---- pdb-extract-v3.0/Makefile 2008-12-05 14:42:58.000000000 +0100 |
6171 |
-+++ pdb-extract-v3.0/Makefile.new 2008-12-05 14:42:15.510315392 +0100 |
6172 |
-@@ -6,6 +6,7 @@ |
6173 |
- |
6174 |
- M_INCL_DIR = ../include |
6175 |
- M_LIB_DIR = ../lib |
6176 |
-+M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR |
6177 |
- M_BIN_DIR = ../bin |
6178 |
- |
6179 |
- PROJ_DIR = . |
6180 |
-@@ -37,12 +38,12 @@ |
6181 |
- include ../etc/Makefile.platform |
6182 |
- |
6183 |
- # Dependent libraries for the pdbml-parser |
6184 |
--CIF_FILE_LIB = $(M_LIB_DIR)/cif-file.a |
6185 |
--CIFPARSE_LIB = $(M_LIB_DIR)/cifparse-obj.a |
6186 |
--CIF_TABLE_LIB = $(M_LIB_DIR)/cif-table-obj.a |
6187 |
--CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a |
6188 |
--REGEX_LIB = $(M_LIB_DIR)/regex.a |
6189 |
--MISCLIB_LIB = $(M_LIB_DIR)/misclib.a |
6190 |
-+CIF_FILE_LIB = $(M_LIB_DIR_GENTOO)/cif-file.a |
6191 |
-+CIFPARSE_LIB = $(M_LIB_DIR_GENTOO)/cifparse-obj.a |
6192 |
-+CIF_TABLE_LIB = $(M_LIB_DIR_GENTOO)/tables.a |
6193 |
-+CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a |
6194 |
-+REGEX_LIB = $(M_LIB_DIR_GENTOO)/regex.a |
6195 |
-+MISCLIB_LIB = $(M_LIB_DIR_GENTOO)/misclib.a |
6196 |
- |
6197 |
- ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \ |
6198 |
- $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB) |
6199 |
|
6200 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch |
6201 |
deleted file mode 100644 |
6202 |
index cdf48e4..0000000 |
6203 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch |
6204 |
+++ /dev/null |
6205 |
@@ -1,199 +0,0 @@ |
6206 |
-diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile |
6207 |
---- pdb-extract-v3.004-prod-src/Makefile 2007-09-11 11:19:46.000000000 -0400 |
6208 |
-+++ pdb-extract-v3.004-prod-src.new/Makefile 2009-12-03 21:34:10.000000000 -0500 |
6209 |
-@@ -52,7 +52,7 @@ |
6210 |
- echo "------------------------------------------------------------"; \ |
6211 |
- echo "**** Making $$libdir ****"; \ |
6212 |
- echo "------------------------------------------------------------"; \ |
6213 |
-- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ |
6214 |
-+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ |
6215 |
- done |
6216 |
- |
6217 |
- beta: |
6218 |
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 |
6219 |
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 2007-09-11 11:19:46.000000000 -0400 |
6220 |
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 2009-12-03 21:34:10.000000000 -0500 |
6221 |
-@@ -91,7 +91,7 @@ |
6222 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6223 |
- |
6224 |
- ## Global include directories |
6225 |
--GINCLUDES= |
6226 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6227 |
- |
6228 |
- # Collect all include directories from global include directories and |
6229 |
- # include directories specified in module makefile |
6230 |
-@@ -159,7 +159,7 @@ |
6231 |
- STATIC_LINKING= |
6232 |
- |
6233 |
- # Linker flags |
6234 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6235 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6236 |
- |
6237 |
- # Fortran linker |
6238 |
- F77_LINKER=f77 |
6239 |
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 |
6240 |
---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 2007-09-11 11:19:46.000000000 -0400 |
6241 |
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 2009-12-03 21:34:10.000000000 -0500 |
6242 |
-@@ -92,7 +92,7 @@ |
6243 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6244 |
- |
6245 |
- ## Global include directories |
6246 |
--GINCLUDES= |
6247 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6248 |
- |
6249 |
- # Collect all include directories from global include directories and |
6250 |
- # include directories specified in module makefile |
6251 |
-@@ -160,7 +160,7 @@ |
6252 |
- STATIC_LINKING= |
6253 |
- |
6254 |
- # Linker flags |
6255 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6256 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6257 |
- |
6258 |
- # Fortran linker |
6259 |
- F77_LINKER=f77 |
6260 |
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 |
6261 |
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 2007-09-11 11:19:46.000000000 -0400 |
6262 |
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 2009-12-03 21:34:10.000000000 -0500 |
6263 |
-@@ -6,6 +6,8 @@ |
6264 |
- ## |
6265 |
- ########################################################################## |
6266 |
- |
6267 |
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR |
6268 |
-+ |
6269 |
- #-----Lexer and Parser section-------------------------------------------# |
6270 |
- |
6271 |
- # Lexer executable |
6272 |
-@@ -89,7 +91,7 @@ |
6273 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6274 |
- |
6275 |
- ## Global include directories |
6276 |
--GINCLUDES= |
6277 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6278 |
- |
6279 |
- # Collect all include directories from global include directories and |
6280 |
- # include directories specified in module makefile |
6281 |
-@@ -107,8 +109,8 @@ |
6282 |
- C_WARNINGS=$(WARNINGS) |
6283 |
- |
6284 |
- # C compiler flags |
6285 |
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6286 |
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6287 |
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6288 |
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6289 |
- $(INCLUDES) |
6290 |
- |
6291 |
- ## C++ compiler |
6292 |
-@@ -128,9 +130,9 @@ |
6293 |
- EXT=C |
6294 |
- |
6295 |
- # C++ compiler flags |
6296 |
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6297 |
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6298 |
- $(INCLUDES) |
6299 |
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6300 |
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6301 |
- $(DEFINES) $(INCLUDES) |
6302 |
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party |
6303 |
- # source code that is not maintained by PDB |
6304 |
-@@ -144,7 +146,7 @@ |
6305 |
- F77=f77 |
6306 |
- |
6307 |
- # Fortran compiler flags |
6308 |
--FFLAGS=-O -u |
6309 |
-+FFLAGS=$(F_OPT) |
6310 |
- |
6311 |
- # Additional Fortran libraries |
6312 |
- F77LIBS= |
6313 |
-@@ -154,11 +156,11 @@ |
6314 |
- #-----Linkers section----------------------------------------------------# |
6315 |
- |
6316 |
- # Static linking option. If not defined, dynamic linking is used. |
6317 |
--STATIC_LINKING=-static |
6318 |
-+STATIC_LINKING= |
6319 |
- |
6320 |
- # Linker flags |
6321 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6322 |
--LDFLAGS_NO_STATIC=$(ABI) -w |
6323 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6324 |
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w |
6325 |
- |
6326 |
- # Fortran linker |
6327 |
- F77_LINKER=f77 |
6328 |
-diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 |
6329 |
---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 2007-09-11 11:19:46.000000000 -0400 |
6330 |
-+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 2009-12-03 21:34:10.000000000 -0500 |
6331 |
-@@ -6,6 +6,8 @@ |
6332 |
- ## |
6333 |
- ########################################################################## |
6334 |
- |
6335 |
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR |
6336 |
-+ |
6337 |
- #-----Lexer and Parser section-------------------------------------------# |
6338 |
- |
6339 |
- # Lexer executable |
6340 |
-@@ -34,7 +36,7 @@ |
6341 |
- |
6342 |
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all |
6343 |
- # warnings as errors. |
6344 |
--WARNINGS_AS_ERRORS=-Werror |
6345 |
-+WARNINGS_AS_ERRORS= |
6346 |
- |
6347 |
- # ALL_WARNINGS defines flags to instruct all compilers to report all |
6348 |
- # warnings. |
6349 |
-@@ -90,7 +92,7 @@ |
6350 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6351 |
- |
6352 |
- ## Global include directories |
6353 |
--GINCLUDES= |
6354 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6355 |
- |
6356 |
- # Collect all include directories from global include directories and |
6357 |
- # include directories specified in module makefile |
6358 |
-@@ -108,8 +110,8 @@ |
6359 |
- C_WARNINGS=$(WARNINGS) |
6360 |
- |
6361 |
- # C compiler flags |
6362 |
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6363 |
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6364 |
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6365 |
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6366 |
- $(INCLUDES) |
6367 |
- |
6368 |
- ## C++ compiler |
6369 |
-@@ -129,9 +131,9 @@ |
6370 |
- EXT=C |
6371 |
- |
6372 |
- # C++ compiler flags |
6373 |
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6374 |
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6375 |
- $(INCLUDES) |
6376 |
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6377 |
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6378 |
- $(DEFINES) $(INCLUDES) |
6379 |
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party |
6380 |
- # source code that is not maintained by PDB |
6381 |
-@@ -145,7 +147,7 @@ |
6382 |
- F77=f77 |
6383 |
- |
6384 |
- # Fortran compiler flags |
6385 |
--FFLAGS=-O -u |
6386 |
-+FFLAGS=$(F_OPT) |
6387 |
- |
6388 |
- # Additional Fortran libraries |
6389 |
- F77LIBS= |
6390 |
-@@ -155,11 +157,11 @@ |
6391 |
- #-----Linkers section----------------------------------------------------# |
6392 |
- |
6393 |
- # Static linking option. If not defined, dynamic linking is used. |
6394 |
--STATIC_LINKING=-static |
6395 |
-+STATIC_LINKING= |
6396 |
- |
6397 |
- # Linker flags |
6398 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6399 |
--LDFLAGS_NO_STATIC=$(ABI) -w |
6400 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6401 |
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w |
6402 |
- |
6403 |
- # Fortran linker |
6404 |
- F77_LINKER=f77 |
6405 |
|
6406 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch |
6407 |
deleted file mode 100644 |
6408 |
index 6506713..0000000 |
6409 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch |
6410 |
+++ /dev/null |
6411 |
@@ -1,11 +0,0 @@ |
6412 |
---- pdb-extract-v3.0/src/extract.C 2007-09-11 17:19:48.000000000 +0200 |
6413 |
-+++ pdb-extract-v3.0/src/extract.C.new 2008-12-05 17:49:59.000000000 +0100 |
6414 |
-@@ -1689,7 +1689,7 @@ |
6415 |
- open_file_error(inpfile, "get_mmcif"); |
6416 |
- } |
6417 |
- |
6418 |
-- (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT"); |
6419 |
-+ (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT"); |
6420 |
- if(temp != NULL) { |
6421 |
- strcpy(pdb_extract, ""); |
6422 |
- strcpy(pdb_extract_sf, ""); |
6423 |
|
6424 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch |
6425 |
deleted file mode 100644 |
6426 |
index 6907399..0000000 |
6427 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch |
6428 |
+++ /dev/null |
6429 |
@@ -1,20 +0,0 @@ |
6430 |
---- cifobj-common-v4.1/src/GenString.C 2008-11-13 10:44:01.000000000 +0100 |
6431 |
-+++ cifobj-common-v4.1/src/GenString.C.new 2008-11-13 10:43:54.000000000 +0100 |
6432 |
-@@ -144,6 +144,7 @@ |
6433 |
- #include <string> |
6434 |
- #include <algorithm> |
6435 |
- #include <sstream> |
6436 |
-+#include <string.h> |
6437 |
- |
6438 |
- #include "GenString.h" |
6439 |
- |
6440 |
---- tables-v8.0/src/ISTable.C 2007-09-11 17:19:47.000000000 +0200 |
6441 |
-+++ tables-v8.0/src/ISTable.C.new 2008-11-13 10:48:18.000000000 +0100 |
6442 |
-@@ -150,6 +150,7 @@ |
6443 |
- #include <sstream> |
6444 |
- #include <iostream> |
6445 |
- #include <iomanip> |
6446 |
-+#include <limits.h> |
6447 |
- |
6448 |
- #include "Exceptions.h" |
6449 |
- #include "GenString.h" |
6450 |
|
6451 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch |
6452 |
deleted file mode 100644 |
6453 |
index 7383811..0000000 |
6454 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch |
6455 |
+++ /dev/null |
6456 |
@@ -1,207 +0,0 @@ |
6457 |
- Makefile | 2 +- |
6458 |
- etc/make.platform.darwin3 | 4 ++-- |
6459 |
- etc/make.platform.darwin4 | 4 ++-- |
6460 |
- etc/make.platform.gnu3 | 20 +++++++++++--------- |
6461 |
- etc/make.platform.gnu4 | 20 +++++++++++--------- |
6462 |
- 5 files changed, 27 insertions(+), 23 deletions(-) |
6463 |
- |
6464 |
-diff --git a/Makefile b/Makefile |
6465 |
-index 627d256..72c7e59 100644 |
6466 |
---- a/Makefile |
6467 |
-+++ b/Makefile |
6468 |
-@@ -52,7 +52,7 @@ compile: |
6469 |
- echo "------------------------------------------------------------"; \ |
6470 |
- echo "**** Making $$libdir ****"; \ |
6471 |
- echo "------------------------------------------------------------"; \ |
6472 |
-- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ |
6473 |
-+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ |
6474 |
- done |
6475 |
- |
6476 |
- beta: |
6477 |
-diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3 |
6478 |
-index c5f7b06..4c1c97c 100644 |
6479 |
---- a/etc/make.platform.darwin3 |
6480 |
-+++ b/etc/make.platform.darwin3 |
6481 |
-@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) |
6482 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6483 |
- |
6484 |
- ## Global include directories |
6485 |
--GINCLUDES= |
6486 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6487 |
- |
6488 |
- # Collect all include directories from global include directories and |
6489 |
- # include directories specified in module makefile |
6490 |
-@@ -159,7 +159,7 @@ F77LIBS= |
6491 |
- STATIC_LINKING= |
6492 |
- |
6493 |
- # Linker flags |
6494 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6495 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6496 |
- |
6497 |
- # Fortran linker |
6498 |
- F77_LINKER=f77 |
6499 |
-diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4 |
6500 |
-index 4619b34..f481fdb 100644 |
6501 |
---- a/etc/make.platform.darwin4 |
6502 |
-+++ b/etc/make.platform.darwin4 |
6503 |
-@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) |
6504 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6505 |
- |
6506 |
- ## Global include directories |
6507 |
--GINCLUDES= |
6508 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6509 |
- |
6510 |
- # Collect all include directories from global include directories and |
6511 |
- # include directories specified in module makefile |
6512 |
-@@ -160,7 +160,7 @@ F77LIBS= |
6513 |
- STATIC_LINKING= |
6514 |
- |
6515 |
- # Linker flags |
6516 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6517 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6518 |
- |
6519 |
- # Fortran linker |
6520 |
- F77_LINKER=f77 |
6521 |
-diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 |
6522 |
-index 7fd442e..9bec4dc 100644 |
6523 |
---- a/etc/make.platform.gnu3 |
6524 |
-+++ b/etc/make.platform.gnu3 |
6525 |
-@@ -6,6 +6,8 @@ |
6526 |
- ## |
6527 |
- ########################################################################## |
6528 |
- |
6529 |
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR |
6530 |
-+ |
6531 |
- #-----Lexer and Parser section-------------------------------------------# |
6532 |
- |
6533 |
- # Lexer executable |
6534 |
-@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) |
6535 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6536 |
- |
6537 |
- ## Global include directories |
6538 |
--GINCLUDES= |
6539 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6540 |
- |
6541 |
- # Collect all include directories from global include directories and |
6542 |
- # include directories specified in module makefile |
6543 |
-@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG= |
6544 |
- C_WARNINGS=$(WARNINGS) |
6545 |
- |
6546 |
- # C compiler flags |
6547 |
--CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6548 |
--CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6549 |
-+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6550 |
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ |
6551 |
- $(INCLUDES) |
6552 |
- |
6553 |
- ## C++ compiler |
6554 |
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) |
6555 |
- EXT=C |
6556 |
- |
6557 |
- # C++ compiler flags |
6558 |
--C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6559 |
-+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ |
6560 |
- $(INCLUDES) |
6561 |
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6562 |
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6563 |
- $(DEFINES) $(INCLUDES) |
6564 |
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party |
6565 |
- # source code that is not maintained by PDB |
6566 |
-@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ |
6567 |
- F77=f77 |
6568 |
- |
6569 |
- # Fortran compiler flags |
6570 |
--FFLAGS=-O -u |
6571 |
-+FFLAGS=$(F_OPT) |
6572 |
- |
6573 |
- # Additional Fortran libraries |
6574 |
- F77LIBS= |
6575 |
-@@ -154,11 +156,11 @@ F77LIBS= |
6576 |
- #-----Linkers section----------------------------------------------------# |
6577 |
- |
6578 |
- # Static linking option. If not defined, dynamic linking is used. |
6579 |
--STATIC_LINKING=-static |
6580 |
-+STATIC_LINKING= |
6581 |
- |
6582 |
- # Linker flags |
6583 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6584 |
--LDFLAGS_NO_STATIC=$(ABI) -w |
6585 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6586 |
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w |
6587 |
- |
6588 |
- # Fortran linker |
6589 |
- F77_LINKER=f77 |
6590 |
-diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 |
6591 |
-index 78a0007..bc85308 100644 |
6592 |
---- a/etc/make.platform.gnu4 |
6593 |
-+++ b/etc/make.platform.gnu4 |
6594 |
-@@ -6,6 +6,8 @@ |
6595 |
- ## |
6596 |
- ########################################################################## |
6597 |
- |
6598 |
-+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR |
6599 |
-+ |
6600 |
- #-----Lexer and Parser section-------------------------------------------# |
6601 |
- |
6602 |
- # Lexer executable |
6603 |
-@@ -34,7 +36,7 @@ ABI= |
6604 |
- |
6605 |
- # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all |
6606 |
- # warnings as errors. |
6607 |
--WARNINGS_AS_ERRORS=-Werror |
6608 |
-+WARNINGS_AS_ERRORS= |
6609 |
- |
6610 |
- # ALL_WARNINGS defines flags to instruct all compilers to report all |
6611 |
- # warnings. |
6612 |
-@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) |
6613 |
- DEFINES=$(GDEFINES) $(LDEFINES) |
6614 |
- |
6615 |
- ## Global include directories |
6616 |
--GINCLUDES= |
6617 |
-+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj |
6618 |
- |
6619 |
- # Collect all include directories from global include directories and |
6620 |
- # include directories specified in module makefile |
6621 |
-@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG= |
6622 |
- C_WARNINGS=$(WARNINGS) |
6623 |
- |
6624 |
- # C compiler flags |
6625 |
--CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6626 |
--CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) |
6627 |
-+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) |
6628 |
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) |
6629 |
- |
6630 |
- ## C++ compiler |
6631 |
- ## This part defines C++ compiler information |
6632 |
-@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) |
6633 |
- EXT=C |
6634 |
- |
6635 |
- # C++ compiler flags |
6636 |
--C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6637 |
-+C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ |
6638 |
- $(DEFINES) $(INCLUDES) |
6639 |
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ |
6640 |
-+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ |
6641 |
- $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) |
6642 |
- |
6643 |
- # C++FLAGS_RELAXED should be set to avoid warnings reported by third party |
6644 |
-@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ |
6645 |
- F77=f77 |
6646 |
- |
6647 |
- # Fortran compiler flags |
6648 |
--FFLAGS=-O -u |
6649 |
-+FFLAGS=$(F_OPT) |
6650 |
- |
6651 |
- # Additional Fortran libraries |
6652 |
- F77LIBS= |
6653 |
-@@ -158,8 +160,8 @@ F77LIBS= |
6654 |
- STATIC_LINKING= |
6655 |
- |
6656 |
- # Linker flags |
6657 |
--LDFLAGS=$(ABI) -w $(STATIC_LINKING) |
6658 |
--LDFLAGS_NO_STATIC=$(ABI) -w |
6659 |
-+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) |
6660 |
-+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w |
6661 |
- |
6662 |
- # Fortran linker |
6663 |
- F77_LINKER=f77 |
6664 |
|
6665 |
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch |
6666 |
deleted file mode 100644 |
6667 |
index 5284bd7..0000000 |
6668 |
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch |
6669 |
+++ /dev/null |
6670 |
@@ -1,64 +0,0 @@ |
6671 |
- common-v4.5/src/mapped_ptr_vector.C | 14 +++++++------- |
6672 |
- 1 files changed, 7 insertions(+), 7 deletions(-) |
6673 |
- |
6674 |
-diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C |
6675 |
-index d7c61f3..e20a236 100644 |
6676 |
---- a/common-v4.5/src/mapped_ptr_vector.C |
6677 |
-+++ b/common-v4.5/src/mapped_ptr_vector.C |
6678 |
-@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP, |
6679 |
- _vector.push_back(inP); |
6680 |
- |
6681 |
- typename tIndex::value_type valuePair(inP->GetName(), |
6682 |
-- make_pair(_vector.size() - 1, fileIndex)); |
6683 |
-+ std::make_pair(_vector.size() - 1, fileIndex)); |
6684 |
- |
6685 |
- _index.insert(valuePair); |
6686 |
- |
6687 |
- _currentName = inP->GetName(); |
6688 |
-- _currentIndices = make_pair(_vector.size() - 1, fileIndex); |
6689 |
-+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); |
6690 |
- |
6691 |
- } |
6692 |
- |
6693 |
-@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name, |
6694 |
- _vector.push_back(NULL); |
6695 |
- |
6696 |
- typename tIndex::value_type valuePair(name, |
6697 |
-- make_pair(_vector.size() - 1, fileIndex)); |
6698 |
-+ std::make_pair(_vector.size() - 1, fileIndex)); |
6699 |
- |
6700 |
- _index.insert(valuePair); |
6701 |
- |
6702 |
- _currentName = name; |
6703 |
-- _currentIndices = make_pair(_vector.size() - 1, fileIndex); |
6704 |
-+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); |
6705 |
- } |
6706 |
- |
6707 |
- |
6708 |
-@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name) |
6709 |
- if (is_equal(_currentName, name, keyComp)) |
6710 |
- { |
6711 |
- _currentName.clear(); |
6712 |
-- _currentIndices = make_pair(_vector.size(), (unsigned int)0); |
6713 |
-+ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0); |
6714 |
- } |
6715 |
- |
6716 |
- } |
6717 |
-@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic |
6718 |
- if (_vector.empty()) |
6719 |
- { |
6720 |
- // Empty container. Return invalid index. |
6721 |
-- return(make_pair(_vector.size(), (unsigned int)0)); |
6722 |
-+ return(std::make_pair(_vector.size(), (unsigned int)0)); |
6723 |
- } |
6724 |
- |
6725 |
- typename tIndex::key_compare keyComp = _index.key_comp(); |
6726 |
-@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic |
6727 |
- else |
6728 |
- { |
6729 |
- // Not found. Return invalid index. |
6730 |
-- return(make_pair(_vector.size(), (unsigned int)0)); |
6731 |
-+ return(std::make_pair(_vector.size(), (unsigned int)0)); |
6732 |
- } |
6733 |
- } |
6734 |
- |
6735 |
|
6736 |
diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml |
6737 |
deleted file mode 100644 |
6738 |
index e42d0af..0000000 |
6739 |
--- a/sci-chemistry/pdb-extract/metadata.xml |
6740 |
+++ /dev/null |
6741 |
@@ -1,5 +0,0 @@ |
6742 |
-<?xml version="1.0" encoding="UTF-8"?> |
6743 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
6744 |
-<pkgmetadata> |
6745 |
- <herd>sci-chemistry</herd> |
6746 |
-</pkgmetadata> |
6747 |
|
6748 |
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild |
6749 |
deleted file mode 100644 |
6750 |
index 836d76f..0000000 |
6751 |
--- a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild |
6752 |
+++ /dev/null |
6753 |
@@ -1,71 +0,0 @@ |
6754 |
-# Copyright 1999-2011 Gentoo Foundation |
6755 |
-# Distributed under the terms of the GNU General Public License v2 |
6756 |
-# $Id$ |
6757 |
- |
6758 |
-EAPI=3 |
6759 |
- |
6760 |
-inherit eutils toolchain-funcs multilib prefix |
6761 |
- |
6762 |
-MY_P="${PN}-v${PV}-prod-src" |
6763 |
- |
6764 |
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" |
6765 |
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" |
6766 |
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" |
6767 |
- |
6768 |
-LICENSE="PDB" |
6769 |
-SLOT="0" |
6770 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
6771 |
-IUSE="" |
6772 |
- |
6773 |
-RDEPEND="!<app-text/html-xml-utils-5.3" |
6774 |
-DEPEND="${RDEPEND} |
6775 |
- >=sci-libs/cifparse-obj-7.025" |
6776 |
- |
6777 |
-S="${WORKDIR}/${MY_P}" |
6778 |
- |
6779 |
-src_prepare() { |
6780 |
- epatch \ |
6781 |
- "${FILESDIR}"/${P}-cflags-install.patch \ |
6782 |
- "${FILESDIR}"/${P}-gcc-4.3.patch \ |
6783 |
- "${FILESDIR}"/${P}-Makefile.patch \ |
6784 |
- "${FILESDIR}"/${P}-env.patch |
6785 |
- |
6786 |
- sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \ |
6787 |
- pdb-extract-v3.0/Makefile \ |
6788 |
- || die "Failed to fix libdir" |
6789 |
- |
6790 |
- # Get rid of unneeded directories, to make sure we use system files |
6791 |
- ebegin "Deleting redundant directories" |
6792 |
- rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \ |
6793 |
- misclib-v2.2 regex-v2.2 tables-v8.0 |
6794 |
- eend |
6795 |
- |
6796 |
- sed -i \ |
6797 |
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ |
6798 |
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ |
6799 |
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ |
6800 |
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
6801 |
- "${S}"/etc/make.* \ |
6802 |
- || die "Failed to fix makefiles" |
6803 |
- |
6804 |
- eprefixify pdb-extract-v3.0/Makefile etc/* |
6805 |
-} |
6806 |
- |
6807 |
-src_install() { |
6808 |
- exeinto /usr/libexec/ccp4/bin |
6809 |
- doexe bin/pdb_extract{,_sf} bin/extract \ |
6810 |
- || die "failed to install binaries" |
6811 |
- insinto /usr/include/rcsb |
6812 |
- doins include/* || die "failed to install include files" |
6813 |
- dodoc README* || die "failed to install docs" |
6814 |
- insinto /usr/share/rcsb/ |
6815 |
- doins -r pdb-extract-data || die "failed to install data files" |
6816 |
- |
6817 |
- cat >> "${T}"/envd <<- EOF |
6818 |
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" |
6819 |
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/" |
6820 |
- EOF |
6821 |
- |
6822 |
- newenvd "${T}"/envd 20pdb-extract \ |
6823 |
- || die "failed to install env files" |
6824 |
-} |
6825 |
|
6826 |
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild |
6827 |
deleted file mode 100644 |
6828 |
index 04351c8..0000000 |
6829 |
--- a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild |
6830 |
+++ /dev/null |
6831 |
@@ -1,60 +0,0 @@ |
6832 |
-# Copyright 1999-2012 Gentoo Foundation |
6833 |
-# Distributed under the terms of the GNU General Public License v2 |
6834 |
-# $Id$ |
6835 |
- |
6836 |
-EAPI=4 |
6837 |
- |
6838 |
-inherit eutils toolchain-funcs multilib prefix |
6839 |
- |
6840 |
-MY_P="${PN}-v${PV}-prod-src" |
6841 |
- |
6842 |
-DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" |
6843 |
-HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" |
6844 |
-SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" |
6845 |
- |
6846 |
-LICENSE="PDB" |
6847 |
-SLOT="0" |
6848 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
6849 |
-IUSE="" |
6850 |
- |
6851 |
-RDEPEND="!<app-text/html-xml-utils-5.3" |
6852 |
-DEPEND="${RDEPEND} |
6853 |
- >=sci-libs/cifparse-obj-7.025" |
6854 |
- |
6855 |
-S="${WORKDIR}/${MY_P}" |
6856 |
- |
6857 |
-MAKEOPTS+=" -j1" |
6858 |
- |
6859 |
-src_prepare() { |
6860 |
- epatch \ |
6861 |
- "${FILESDIR}"/${P}-cflags-install.patch \ |
6862 |
- "${FILESDIR}"/${P}-gcc-4.7.patch \ |
6863 |
- "${FILESDIR}"/${PN}-3.004-env.patch |
6864 |
- |
6865 |
- sed -i \ |
6866 |
- -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ |
6867 |
- -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ |
6868 |
- -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ |
6869 |
- -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
6870 |
- "${S}"/etc/make.* \ |
6871 |
- || die "Failed to fix makefiles" |
6872 |
- |
6873 |
- eprefixify pdb-extract-v3.0/Makefile etc/* |
6874 |
-} |
6875 |
- |
6876 |
-src_install() { |
6877 |
- exeinto /usr/libexec/ccp4/bin |
6878 |
- doexe bin/pdb_extract{,_sf} bin/extract |
6879 |
- insinto /usr/include/rcsb |
6880 |
- doins include/* |
6881 |
- dodoc README* |
6882 |
- insinto /usr/share/rcsb/ |
6883 |
- doins -r pdb-extract-data |
6884 |
- |
6885 |
- cat >> "${T}"/envd <<- EOF |
6886 |
- PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" |
6887 |
- PDB_EXTRACT_ROOT="${EPREFIX}/usr/" |
6888 |
- EOF |
6889 |
- |
6890 |
- newenvd "${T}"/envd 20pdb-extract |
6891 |
-} |
6892 |
|
6893 |
diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest |
6894 |
deleted file mode 100644 |
6895 |
index deb3ba9..0000000 |
6896 |
--- a/sci-chemistry/phaser/Manifest |
6897 |
+++ /dev/null |
6898 |
@@ -1 +0,0 @@ |
6899 |
-DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 SHA512 cdf36572613a6e400af0f29da501ccfd2a9f1a7e2d89162aad3fe14929816b41790bb57ba1e77976b9046c6e06a29df2748999db93a2cd0a4d1fde95ac1f9e8b WHIRLPOOL 5aa1a1c6520be90ef02be0e9de9c111a9835cda05a3549c390f62ceef7e68c8392670d91941b823c0ee94f29e6aab9d34a61b90e8bd3d4820a83daa547463fdb |
6900 |
|
6901 |
diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch |
6902 |
deleted file mode 100644 |
6903 |
index 5311cb3..0000000 |
6904 |
--- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch |
6905 |
+++ /dev/null |
6906 |
@@ -1,13 +0,0 @@ |
6907 |
-diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py |
6908 |
-index 3b1bd3a..8939a74 100755 |
6909 |
---- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py |
6910 |
-+++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py |
6911 |
-@@ -802,8 +802,6 @@ class environment: |
6912 |
- else: |
6913 |
- action = self.write_bin_sh_dispatcher |
6914 |
- ext = "" |
6915 |
-- try: os.chmod(source_file, 0755) |
6916 |
-- except OSError: pass |
6917 |
- target_file_ext = target_file + ext |
6918 |
- remove_or_rename(target_file_ext) |
6919 |
- try: action(source_file, target_file_ext) |
6920 |
|
6921 |
diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml |
6922 |
deleted file mode 100644 |
6923 |
index 6b48264..0000000 |
6924 |
--- a/sci-chemistry/phaser/metadata.xml |
6925 |
+++ /dev/null |
6926 |
@@ -1,9 +0,0 @@ |
6927 |
-<?xml version="1.0" encoding="UTF-8"?> |
6928 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
6929 |
-<pkgmetadata> |
6930 |
- <herd>sci-chemistry</herd> |
6931 |
- <maintainer> |
6932 |
- <email>jlec@g.o</email> |
6933 |
- <description>ccp4 maintainer</description> |
6934 |
- </maintainer> |
6935 |
-</pkgmetadata> |
6936 |
|
6937 |
diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild |
6938 |
deleted file mode 100644 |
6939 |
index 86fa57f..0000000 |
6940 |
--- a/sci-chemistry/phaser/phaser-2.1.4.ebuild |
6941 |
+++ /dev/null |
6942 |
@@ -1,115 +0,0 @@ |
6943 |
-# Copyright 1999-2015 Gentoo Foundation |
6944 |
-# Distributed under the terms of the GNU General Public License v2 |
6945 |
-# $Id$ |
6946 |
- |
6947 |
-EAPI=5 |
6948 |
- |
6949 |
-PYTHON_COMPAT=( python2_7 ) |
6950 |
- |
6951 |
-inherit eutils flag-o-matic python-single-r1 toolchain-funcs |
6952 |
- |
6953 |
-CCP4VER="6.1.13" |
6954 |
- |
6955 |
-DESCRIPTION="A program for phasing macromolecular crystal structures" |
6956 |
-HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" |
6957 |
-SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz" |
6958 |
- |
6959 |
-LICENSE="|| ( phaser phaser-com ccp4 )" |
6960 |
-SLOT="0" |
6961 |
-#KEYWORDS="~amd64 ~x86" |
6962 |
-KEYWORDS="" |
6963 |
-IUSE="openmp" |
6964 |
- |
6965 |
-RDEPEND="" |
6966 |
-DEPEND="${RDEPEND} |
6967 |
- app-shells/tcsh" |
6968 |
- |
6969 |
-S="${WORKDIR}"/ccp4-${CCP4VER} |
6970 |
- |
6971 |
-src_prepare() { |
6972 |
- epatch \ |
6973 |
- "${FILESDIR}"/phaser-2.1.4-chmod.patch \ |
6974 |
- "${FILESDIR}"/phaser-2.1.4-ldflags.patch |
6975 |
- |
6976 |
- use openmp && append-flags -fopenmp |
6977 |
- |
6978 |
- for i in ${CXXFLAGS}; do |
6979 |
- OPTS="${OPTS} \"${i}\"," |
6980 |
- done |
6981 |
- |
6982 |
- OPTS=${OPTS%,} |
6983 |
- |
6984 |
- sed -i \ |
6985 |
- -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ |
6986 |
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die |
6987 |
- |
6988 |
- for i in ${LDFLAGS}; do |
6989 |
- OPTSLD="${OPTSLD} \"${i}\"," |
6990 |
- done |
6991 |
- |
6992 |
- sed -i \ |
6993 |
- -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ |
6994 |
- -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \ |
6995 |
- "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die |
6996 |
- |
6997 |
-} |
6998 |
- |
6999 |
-src_configure() { |
7000 |
- local compiler |
7001 |
- local mtype |
7002 |
- local mversion |
7003 |
- local nproc |
7004 |
- |
7005 |
- # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, |
7006 |
- # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, |
7007 |
- # darwin_c++, darwin_gcc. The build systems seems to prepend |
7008 |
- # unix_ all by itself. Can this be derived from $(tc-getCC)? |
7009 |
- compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') |
7010 |
- |
7011 |
- # Breaks cross compilation. |
7012 |
- mtype=$(src/${PN}/bin/machine_type) |
7013 |
- mversion=$(src/${PN}/bin/machine_version) |
7014 |
- |
7015 |
- einfo "Creating build directory" |
7016 |
- mkdir build |
7017 |
- cd build |
7018 |
- ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons |
7019 |
- ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx |
7020 |
- |
7021 |
- einfo "Configuring phaser components" |
7022 |
- $(PYTHON) "libtbx/configure.py" \ |
7023 |
- --build=release \ |
7024 |
- --compiler=${compiler} \ |
7025 |
- --repository="${S}"/src/${PN}/source \ |
7026 |
- --repository="${S}"/lib/cctbx/cctbx_sources \ |
7027 |
- --static_libraries \ |
7028 |
- ccp4io="${S}" \ |
7029 |
- mmtbx \ |
7030 |
- phaser || die "configure.py failed" |
7031 |
-} |
7032 |
- |
7033 |
-src_compile() { |
7034 |
- nproc=`echo "-j1 ${MAKEOPTS}" \ |
7035 |
- | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` |
7036 |
- |
7037 |
- cd build |
7038 |
- einfo "Setting up build environment" |
7039 |
- source setpaths.sh |
7040 |
- |
7041 |
- einfo "Compiling phaser components" |
7042 |
- libtbx.scons -j ${nproc} || die "libtbx.scons failed" |
7043 |
-} |
7044 |
- |
7045 |
-src_install() { |
7046 |
- dobin build/exe/phaser || die |
7047 |
- |
7048 |
- cat >> "${T}"/53${PN} <<- EOF |
7049 |
- PHASER="${EPREFIX}/usr/bin" |
7050 |
- PHASER_ENVIRONMENT="1" |
7051 |
- PHASER_MTYPE="${mtype}" |
7052 |
- PHASER_MVERSION="${mversion}" |
7053 |
- PHASER_VERSION="${PV}" |
7054 |
- EOF |
7055 |
- |
7056 |
- doenvd "${T}"/53${PN} || die |
7057 |
-} |
7058 |
|
7059 |
diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest |
7060 |
deleted file mode 100644 |
7061 |
index 911c448..0000000 |
7062 |
--- a/sci-chemistry/pointless/Manifest |
7063 |
+++ /dev/null |
7064 |
@@ -1,2 +0,0 @@ |
7065 |
-DIST pointless-1.6.14.tar.gz 423657 SHA256 68f0c1f65239b1451310fe885c2b9d51fc558de7b43af1e584750e05dc5635d8 SHA512 9dd524a7c842edc01206450c52ca1a01e8e3ee6f9ff71742789943ee10e006b5452b0be3aa509dd16bb85f1b9c3d7954616a78ec2fef2daea7c0ab42cdaa42b9 WHIRLPOOL 5085afbd88713384039ef2c2b4b2f7fddd8f078dca9df54062b0415e970791868c61df98f4044b4e061077a73b4e129b6e5db34852d64cace48108db9c6ae50f |
7066 |
-DIST pointless-1.6.2.tar.gz 412244 SHA256 5e09ca592ea565e8ace142fc0edff39d0ab723f4ac6e2cadd6ba571d667c80f6 SHA512 2e897a7302ba4d43da69c8ee91254b0632d8a0ae301140a144472f7e466078f0b1abd10362343d7d50d04bd86ae8b83265a20302f7aeae3dc8845f1581211ddd WHIRLPOOL 8953806f68684e882717673ec18263f0ac2093f3cb2cac573b20886f5f0d60c67b756f74bdb3555342bb3d287021b7c70b20c53f0e38e687a5914df935ae35cd |
7067 |
|
7068 |
diff --git a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch |
7069 |
deleted file mode 100644 |
7070 |
index ca67dbd..0000000 |
7071 |
--- a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch |
7072 |
+++ /dev/null |
7073 |
@@ -1,12 +0,0 @@ |
7074 |
-diff --git a/string_util.hh b/string_util.hh |
7075 |
-index 66af6f3..047512b 100644 |
7076 |
---- a/string_util.hh |
7077 |
-+++ b/string_util.hh |
7078 |
-@@ -3,6 +3,7 @@ |
7079 |
- |
7080 |
- #include <string> |
7081 |
- #include <vector> |
7082 |
-+#include <stdio.h> |
7083 |
- #include "range.hh" |
7084 |
- |
7085 |
- //====================================================================== |
7086 |
|
7087 |
diff --git a/sci-chemistry/pointless/metadata.xml b/sci-chemistry/pointless/metadata.xml |
7088 |
deleted file mode 100644 |
7089 |
index ae9ec7c..0000000 |
7090 |
--- a/sci-chemistry/pointless/metadata.xml |
7091 |
+++ /dev/null |
7092 |
@@ -1,8 +0,0 @@ |
7093 |
-<?xml version="1.0" encoding="UTF-8"?> |
7094 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
7095 |
-<pkgmetadata> |
7096 |
- <herd>sci-chemistry</herd> |
7097 |
- <maintainer> |
7098 |
- <email>jlec@g.o</email> |
7099 |
- </maintainer> |
7100 |
-</pkgmetadata> |
7101 |
|
7102 |
diff --git a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild |
7103 |
deleted file mode 100644 |
7104 |
index d983cb2..0000000 |
7105 |
--- a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild |
7106 |
+++ /dev/null |
7107 |
@@ -1,56 +0,0 @@ |
7108 |
-# Copyright 1999-2015 Gentoo Foundation |
7109 |
-# Distributed under the terms of the GNU General Public License v2 |
7110 |
-# $Id$ |
7111 |
- |
7112 |
-EAPI=5 |
7113 |
- |
7114 |
-PYTHON_COMPAT=( python2_7 ) |
7115 |
- |
7116 |
-inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs |
7117 |
- |
7118 |
-DESCRIPTION="Scores crystallographic Laue and space groups" |
7119 |
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" |
7120 |
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" |
7121 |
- |
7122 |
-SLOT="0" |
7123 |
-LICENSE="ccp4" |
7124 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
7125 |
-IUSE="" |
7126 |
- |
7127 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
7128 |
- |
7129 |
-DEPEND=" |
7130 |
- sci-chemistry/ccp4-apps |
7131 |
- >=sci-libs/ccp4-libs-6.1.3-r10 |
7132 |
- sci-libs/clipper |
7133 |
- sci-libs/fftw:2.1 |
7134 |
- sci-libs/mmdb |
7135 |
- >=sci-libs/cctbx-2010.03.29.2334-r3[${PYTHON_USEDEP}]" |
7136 |
-RDEPEND="${DEPEND}" |
7137 |
- |
7138 |
-S="${WORKDIR}" |
7139 |
- |
7140 |
-src_prepare() { |
7141 |
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch |
7142 |
-} |
7143 |
- |
7144 |
-src_compile() { |
7145 |
- emake \ |
7146 |
- -f Makefile.make \ |
7147 |
- CC=$(tc-getCC) \ |
7148 |
- CXX=$(tc-getCXX) \ |
7149 |
- CFLAGS="${CFLAGS}" \ |
7150 |
- CXXFLAGS="${CXXFLAGS}" \ |
7151 |
- LFLAGS="${LDFLAGS}" \ |
7152 |
- CLIB="${EPREFIX}/usr/$(get_libdir)" \ |
7153 |
- CCTBX_VERSION=2010 \ |
7154 |
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ |
7155 |
- ITBX="-I${EPREFIX}/usr/include" \ |
7156 |
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ |
7157 |
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ |
7158 |
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" |
7159 |
-} |
7160 |
- |
7161 |
-src_install() { |
7162 |
- dobin pointless othercell |
7163 |
-} |
7164 |
|
7165 |
diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild |
7166 |
deleted file mode 100644 |
7167 |
index 158bde0..0000000 |
7168 |
--- a/sci-chemistry/pointless/pointless-1.6.14.ebuild |
7169 |
+++ /dev/null |
7170 |
@@ -1,60 +0,0 @@ |
7171 |
-# Copyright 1999-2012 Gentoo Foundation |
7172 |
-# Distributed under the terms of the GNU General Public License v2 |
7173 |
-# $Id$ |
7174 |
- |
7175 |
-EAPI="3" |
7176 |
- |
7177 |
-PYTHON_DEPEND="2" |
7178 |
- |
7179 |
-inherit eutils fortran-2 multilib python toolchain-funcs |
7180 |
- |
7181 |
-DESCRIPTION="Scores crystallographic Laue and space groups" |
7182 |
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" |
7183 |
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" |
7184 |
- |
7185 |
-SLOT="0" |
7186 |
-LICENSE="ccp4" |
7187 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
7188 |
-IUSE="" |
7189 |
- |
7190 |
-DEPEND=" |
7191 |
- sci-chemistry/ccp4-apps |
7192 |
- >=sci-libs/ccp4-libs-6.1.3-r10 |
7193 |
- sci-libs/clipper |
7194 |
- sci-libs/fftw:2.1 |
7195 |
- sci-libs/mmdb |
7196 |
- >=sci-libs/cctbx-2010.03.29.2334-r3" |
7197 |
-RDEPEND="${DEPEND}" |
7198 |
- |
7199 |
-S="${WORKDIR}" |
7200 |
- |
7201 |
-pkg_setup() { |
7202 |
- fortran-2_pkg_setup |
7203 |
- python_set_active_version 2 |
7204 |
-} |
7205 |
- |
7206 |
-src_prepare() { |
7207 |
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch |
7208 |
-} |
7209 |
- |
7210 |
-src_compile() { |
7211 |
- emake \ |
7212 |
- -f Makefile.make \ |
7213 |
- CC=$(tc-getCC) \ |
7214 |
- CXX=$(tc-getCXX) \ |
7215 |
- CFLAGS="${CFLAGS}" \ |
7216 |
- CXXFLAGS="${CXXFLAGS}" \ |
7217 |
- LFLAGS="${LDFLAGS}" \ |
7218 |
- CLIB="${EPREFIX}/usr/$(get_libdir)" \ |
7219 |
- CCTBX_VERSION=2010 \ |
7220 |
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ |
7221 |
- ITBX="-I${EPREFIX}/usr/include" \ |
7222 |
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ |
7223 |
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ |
7224 |
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \ |
7225 |
- || die |
7226 |
-} |
7227 |
- |
7228 |
-src_install() { |
7229 |
- dobin pointless othercell || die |
7230 |
-} |
7231 |
|
7232 |
diff --git a/sci-chemistry/pointless/pointless-1.6.2.ebuild b/sci-chemistry/pointless/pointless-1.6.2.ebuild |
7233 |
deleted file mode 100644 |
7234 |
index 2b9f0ad..0000000 |
7235 |
--- a/sci-chemistry/pointless/pointless-1.6.2.ebuild |
7236 |
+++ /dev/null |
7237 |
@@ -1,60 +0,0 @@ |
7238 |
-# Copyright 1999-2012 Gentoo Foundation |
7239 |
-# Distributed under the terms of the GNU General Public License v2 |
7240 |
-# $Id$ |
7241 |
- |
7242 |
-EAPI=4 |
7243 |
- |
7244 |
-PYTHON_DEPEND="2" |
7245 |
- |
7246 |
-inherit eutils fortran-2 multilib python toolchain-funcs |
7247 |
- |
7248 |
-DESCRIPTION="Scores crystallographic Laue and space groups" |
7249 |
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" |
7250 |
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" |
7251 |
- |
7252 |
-SLOT="0" |
7253 |
-LICENSE="ccp4" |
7254 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
7255 |
-IUSE="" |
7256 |
- |
7257 |
-DEPEND=" |
7258 |
- sci-chemistry/ccp4-apps |
7259 |
- >=sci-libs/ccp4-libs-6.1.3-r10 |
7260 |
- sci-libs/clipper |
7261 |
- sci-libs/fftw:2.1 |
7262 |
- sci-libs/mmdb |
7263 |
- >=sci-libs/cctbx-2010.03.29.2334-r3" |
7264 |
-RDEPEND="${DEPEND}" |
7265 |
- |
7266 |
-S="${WORKDIR}" |
7267 |
- |
7268 |
-pkg_setup() { |
7269 |
- fortran-2_pkg_setup |
7270 |
- python_pkg_setup |
7271 |
- python_set_active_version 2 |
7272 |
-} |
7273 |
- |
7274 |
-src_prepare() { |
7275 |
- epatch "${FILESDIR}"/1.5.1-gcc4.4.patch |
7276 |
-} |
7277 |
- |
7278 |
-src_compile() { |
7279 |
- emake \ |
7280 |
- -f Makefile.make \ |
7281 |
- CC=$(tc-getCC) \ |
7282 |
- CXX=$(tc-getCXX) \ |
7283 |
- CFLAGS="${CFLAGS}" \ |
7284 |
- CXXFLAGS="${CXXFLAGS}" \ |
7285 |
- LFLAGS="${LDFLAGS}" \ |
7286 |
- CLIB="${EPREFIX}/usr/$(get_libdir)" \ |
7287 |
- CCTBX_VERSION=2010 \ |
7288 |
- ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ |
7289 |
- ITBX="-I${EPREFIX}/usr/include" \ |
7290 |
- ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ |
7291 |
- LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ |
7292 |
- SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" |
7293 |
-} |
7294 |
- |
7295 |
-src_install() { |
7296 |
- dobin pointless othercell |
7297 |
-} |
7298 |
|
7299 |
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest |
7300 |
deleted file mode 100644 |
7301 |
index ba3def1..0000000 |
7302 |
--- a/sci-chemistry/refmac/Manifest |
7303 |
+++ /dev/null |
7304 |
@@ -1,2 +0,0 @@ |
7305 |
-DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac |
7306 |
-DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d |
7307 |
|
7308 |
diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch |
7309 |
deleted file mode 100644 |
7310 |
index 61858be..0000000 |
7311 |
--- a/sci-chemistry/refmac/files/5.5-test.log.patch |
7312 |
+++ /dev/null |
7313 |
@@ -1,32 +0,0 @@ |
7314 |
---- test-framework/refmac5/test_refmac5.py 2009-06-29 15:45:37.000000000 +0200 |
7315 |
-+++ test-framework/refmac5/test_refmac5.py.new 2009-06-29 15:48:05.000000000 +0200 |
7316 |
-@@ -88,7 +88,8 @@ |
7317 |
- 'make hydr no', |
7318 |
- 'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag', |
7319 |
- 'labout FC=FC PHIC=PHIC'], |
7320 |
-- working_directory = self.test_dir) |
7321 |
-+ working_directory = self.test_dir, |
7322 |
-+ log_file = 'test_twinned_refinement.log') |
7323 |
- |
7324 |
- self.assertEqual(status, 0) |
7325 |
- |
7326 |
-@@ -123,7 +124,8 @@ |
7327 |
- 'weight auto', |
7328 |
- 'ncyc 20', |
7329 |
- 'labout FC=FC PHIC=PHIC'], |
7330 |
-- working_directory = self.test_dir) |
7331 |
-+ working_directory = self.test_dir, |
7332 |
-+ log_file = 'test_4_domain_tls.log') |
7333 |
- |
7334 |
- self.assertEqual(status, 0) |
7335 |
- |
7336 |
-@@ -156,7 +158,8 @@ |
7337 |
- 'anomalous form SE -9.9 3.9', |
7338 |
- 'anomalous wavelength 0.97966', |
7339 |
- 'labout FC=FC PHIC=PHIC'], |
7340 |
-- working_directory = self.test_dir) |
7341 |
-+ working_directory = self.test_dir, |
7342 |
-+ log_file = 'test_sad_refinement.log') |
7343 |
- |
7344 |
- self.assertEqual(status, 0) |
7345 |
- |
7346 |
|
7347 |
diff --git a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch |
7348 |
deleted file mode 100644 |
7349 |
index 1efbaa0..0000000 |
7350 |
--- a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch |
7351 |
+++ /dev/null |
7352 |
@@ -1,84 +0,0 @@ |
7353 |
-diff --git a/makefile b/makefile |
7354 |
-index 66d4cee..5270677 100644 |
7355 |
---- a/makefile |
7356 |
-+++ b/makefile |
7357 |
-@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static |
7358 |
- XCFLAGS = -DGFORTRAN -DPROTOTYPE |
7359 |
- FFLAGS = $(FOPTIM) $(XFFLAGS) |
7360 |
- CFLAGS = $(COPTIM) $(XCFLAGS) |
7361 |
--CPPFLAGS = $(CFLAGS) |
7362 |
-+CPPFLAGS = $(CXXFLAGS) $(XCFLAGS) |
7363 |
- |
7364 |
- LLIBCIF = |
7365 |
- LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a |
7366 |
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 |
7367 |
-index 371d84d..557077f 100644 |
7368 |
---- a/makefile_refmac.inc1 |
7369 |
-+++ b/makefile_refmac.inc1 |
7370 |
-@@ -68,9 +68,7 @@ messy_pdb.o \ |
7371 |
- bridge.o \ |
7372 |
- i0.o \ |
7373 |
- i1.o \ |
7374 |
--chbevl.o \ |
7375 |
--$(LLIBCIF) \ |
7376 |
--$(LLIBLAPACK) |
7377 |
-+chbevl.o |
7378 |
- #$(LLIBCCP) \ |
7379 |
- #crt0.o \ |
7380 |
- #heavy.o \ |
7381 |
-@@ -95,8 +93,7 @@ make_unix_ccp4.o \ |
7382 |
- emin.o \ |
7383 |
- libcheck_min.o \ |
7384 |
- mol2_file.o \ |
7385 |
--sdf_files.o \ |
7386 |
--$(LLIBCCP) |
7387 |
-+sdf_files.o |
7388 |
- |
7389 |
- SUBM = \ |
7390 |
- main_makecif.o \ |
7391 |
-@@ -116,9 +113,7 @@ make_rst2.o \ |
7392 |
- make_PDB.o \ |
7393 |
- makecif.o \ |
7394 |
- make_unix_ccp4.o \ |
7395 |
--make_vdw.o \ |
7396 |
--$(LLIBCCP) \ |
7397 |
--$(LLIBCIF) |
7398 |
-+make_vdw.o |
7399 |
- |
7400 |
- SUBT = \ |
7401 |
- tlsgroups.o \ |
7402 |
-@@ -142,9 +137,7 @@ make_refmac_dummy.o \ |
7403 |
- inout_routines.o \ |
7404 |
- errwrt_1.o \ |
7405 |
- linalgebra.o \ |
7406 |
--subnumrec.o \ |
7407 |
--$(LLIBCCP) \ |
7408 |
--$(LLIBCIF) |
7409 |
-+subnumrec.o |
7410 |
- #-------------------------------------------------------------------------------- |
7411 |
- |
7412 |
- ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s |
7413 |
-@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s |
7414 |
- all: refmac libcheck makecif |
7415 |
- |
7416 |
- refmac: $(SUBR) |
7417 |
-- $(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) |
7418 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) |
7419 |
- |
7420 |
- libcheck: $(SUBL) |
7421 |
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) |
7422 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) |
7423 |
- |
7424 |
- makecif: $(SUBM) |
7425 |
-- $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM) |
7426 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF) |
7427 |
- |
7428 |
- tlsgroups: $(SUBT) |
7429 |
-- $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT) |
7430 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF) |
7431 |
- |
7432 |
- clean: |
7433 |
- /bin/rm *.o |
7434 |
- |
7435 |
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h |
7436 |
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp |
7437 |
|
7438 |
diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch |
7439 |
deleted file mode 100644 |
7440 |
index 3969cc9..0000000 |
7441 |
--- a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch |
7442 |
+++ /dev/null |
7443 |
@@ -1,17 +0,0 @@ |
7444 |
- hkon_secder_tch.f | 3 ++- |
7445 |
- 1 files changed, 2 insertions(+), 1 deletions(-) |
7446 |
- |
7447 |
-diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f |
7448 |
-index 31794b0..86d2cdf 100644 |
7449 |
---- a/hkon_secder_tch.f |
7450 |
-+++ b/hkon_secder_tch.f |
7451 |
-@@ -3724,7 +3724,8 @@ c---External functions and subprutines |
7452 |
- INTEGER NWORKSPACE |
7453 |
- REAL*8 TOLER |
7454 |
- REAL*8 WORKSPACE(300) |
7455 |
-- REAL LSTLSQ,D2DF_WEIGHT |
7456 |
-+ REAL*8 D2DF_WEIGHT |
7457 |
-+ REAL LSTLSQ |
7458 |
- C |
7459 |
- INTEGER IBIN,IBIN_S |
7460 |
- INTEGER I,J,K |
7461 |
|
7462 |
diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch |
7463 |
deleted file mode 100644 |
7464 |
index 9998b75..0000000 |
7465 |
--- a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch |
7466 |
+++ /dev/null |
7467 |
@@ -1,341 +0,0 @@ |
7468 |
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- |
7469 |
- 1 files changed, 104 insertions(+), 111 deletions(-) |
7470 |
- |
7471 |
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 |
7472 |
-index 0f8bd63..e59fbfb 100644 |
7473 |
---- a/makefile_refmac.inc1 |
7474 |
-+++ b/makefile_refmac.inc1 |
7475 |
-@@ -96,9 +96,7 @@ bridge.o \ |
7476 |
- i0.o \ |
7477 |
- i1.o \ |
7478 |
- chbevl.o \ |
7479 |
--make_unix_ccp4.o \ |
7480 |
--$(LLIBCIF) \ |
7481 |
--$(LLIBLAPACK) |
7482 |
-+make_unix_ccp4.o |
7483 |
- |
7484 |
- |
7485 |
- SUBL = \ |
7486 |
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \ |
7487 |
- iheap_sort.o \ |
7488 |
- linalgebra.o \ |
7489 |
- math_refmac.o \ |
7490 |
--subnumrec.o \ |
7491 |
--$(LLIBLAPACK) \ |
7492 |
--$(LLIBCCP) |
7493 |
-+subnumrec.o |
7494 |
- |
7495 |
- SUB_FREE = \ |
7496 |
- freer_twin.o \ |
7497 |
-@@ -145,9 +141,7 @@ subnumrec.o \ |
7498 |
- libT.o \ |
7499 |
- iheap_sort.o \ |
7500 |
- cell_symm_subrs.o \ |
7501 |
--math_refmac.o \ |
7502 |
--$(LLIBLAPACK) \ |
7503 |
--$(LLIBCCP) |
7504 |
-+math_refmac.o |
7505 |
- |
7506 |
- SUB_HEADER = header2matr.o |
7507 |
- #-------------------------------------------------------------------------------- |
7508 |
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 |
7509 |
- twin77mod.o: twin77mod.f |
7510 |
- $(FC) $(FFLAGS) -c twin77mod.f |
7511 |
- |
7512 |
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 |
7513 |
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 |
7514 |
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 |
7515 |
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 |
7516 |
- |
7517 |
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 |
7518 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f |
7519 |
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o |
7520 |
-+ $(FC) $(FFLAGS) -c max_with_twins.f |
7521 |
- |
7522 |
--merohedr_twin.o: restr_files.f90 merohedr_twin.f |
7523 |
-- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f |
7524 |
-+merohedr_twin.o: restr_files.o merohedr_twin.f |
7525 |
-+ $(FC) $(FFLAGS) -c merohedr_twin.f |
7526 |
- |
7527 |
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 |
7528 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f |
7529 |
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o |
7530 |
-+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f |
7531 |
- |
7532 |
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 |
7533 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f |
7534 |
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o |
7535 |
-+ $(FC) $(FFLAGS) -c ml_params_refine.f |
7536 |
- |
7537 |
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 |
7538 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 |
7539 |
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o |
7540 |
-+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 |
7541 |
- |
7542 |
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 |
7543 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f |
7544 |
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o |
7545 |
-+ $(FC) $(FFLAGS) -c ncs_rest.f |
7546 |
- |
7547 |
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 |
7548 |
-- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 |
7549 |
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o |
7550 |
-+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 |
7551 |
- |
7552 |
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 |
7553 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 |
7554 |
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o |
7555 |
-+ $(FC) $(FFLAGS) -c lsq_exp2.f |
7556 |
- |
7557 |
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 |
7558 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f |
7559 |
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o |
7560 |
-+ $(FC) $(FFLAGS) -c vdw_and_contacts.f |
7561 |
- |
7562 |
- dist_routines.o: dist_routines.f90 |
7563 |
- $(FC) $(FFLAGS) -c dist_routines.f90 |
7564 |
- |
7565 |
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 |
7566 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 |
7567 |
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 |
7568 |
-+ $(FC) $(FFLAGS) -c ncs_simil.f90 |
7569 |
- |
7570 |
- ridge.o: ridge.f90 |
7571 |
- $(FC) $(FFLAGS) -c ridge.f90 |
7572 |
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90 |
7573 |
- align_refmac.o: align_refmac.f90 |
7574 |
- $(FC) $(FFLAGS) -c align_refmac.f90 |
7575 |
- |
7576 |
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 |
7577 |
-- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f |
7578 |
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o |
7579 |
-+ $(FC) $(FFLAGS) -c rigid_allocate.f |
7580 |
- |
7581 |
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 |
7582 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f |
7583 |
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o |
7584 |
-+ $(FC) $(FFLAGS) -c tls_allocate.f |
7585 |
- |
7586 |
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ |
7587 |
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7588 |
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ |
7589 |
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 |
7590 |
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ |
7591 |
-+ restr_files.o weights.o agreem.o rharvest_mod.o |
7592 |
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f |
7593 |
- |
7594 |
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 |
7595 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f |
7596 |
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o |
7597 |
-+ $(FC) $(FFLAGS) -c oppro_allocate.f |
7598 |
- |
7599 |
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 |
7600 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f |
7601 |
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o |
7602 |
-+ $(FC) $(FFLAGS) -c read_extra_restraints.f |
7603 |
- |
7604 |
--coords.o: coords.f90 atomf77mod.f |
7605 |
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 |
7606 |
-+coords.o: coords.f90 atomf77mod.o |
7607 |
-+ $(FC) $(FFLAGS) -c coords.f90 |
7608 |
- |
7609 |
- |
7610 |
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 |
7611 |
-- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 |
7612 |
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o |
7613 |
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f |
7614 |
- |
7615 |
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 |
7616 |
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 |
7617 |
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o |
7618 |
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f |
7619 |
- |
7620 |
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 |
7621 |
-- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 |
7622 |
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o |
7623 |
-+ $(FC) $(FFLAGS) -c calc_stats_twin.f |
7624 |
- |
7625 |
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7626 |
-- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f |
7627 |
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o |
7628 |
-+ $(FC) $(FFLAGS) -c refpre_twin.f |
7629 |
- |
7630 |
- |
7631 |
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f |
7632 |
-- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f |
7633 |
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f |
7634 |
-+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f |
7635 |
- |
7636 |
- automorphism.o: automorphism.f90 |
7637 |
- $(FC) $(FFLAGS) -c automorphism.f90 |
7638 |
- |
7639 |
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 |
7640 |
-- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f |
7641 |
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o |
7642 |
-+ $(FC) $(FFLAGS) -c mtz_write_twin.f |
7643 |
- |
7644 |
- filter_params.o: filter_params.f90 |
7645 |
- $(FC) $(FFLAGS) -c filter_params.f90 |
7646 |
- |
7647 |
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ |
7648 |
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
7649 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ |
7650 |
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f |
7651 |
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ |
7652 |
-+ agreem.o rharvest_mod.o ncs_constr.o |
7653 |
-+ $(FC) $(FFLAGS) -c rcard_tor1.f |
7654 |
- |
7655 |
--inout_routines.o: restr_files.f90 inout_routines.f |
7656 |
-- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f |
7657 |
-+inout_routines.o: restr_files.o inout_routines.f |
7658 |
-+ $(FC) $(FFLAGS) -c inout_routines.f |
7659 |
- |
7660 |
--local_tls.o: local_tls.f90 linalgebra_f90.f90 |
7661 |
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 |
7662 |
-+local_tls.o: local_tls.f90 linalgebra_f90.o |
7663 |
-+ $(FC) $(FFLAGS) -c local_tls.f90 |
7664 |
- |
7665 |
- linalgebra_f90.o: linalgebra_f90.f90 |
7666 |
- $(FC) $(FFLAGS) -c linalgebra_f90.f90 |
7667 |
- |
7668 |
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7669 |
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f |
7670 |
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
7671 |
-+ $(FC) $(FFLAGS) -c make_refmac_dummy.f |
7672 |
- |
7673 |
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7674 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f |
7675 |
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
7676 |
-+ $(FC) $(FFLAGS) -c ml_scaling_double.f |
7677 |
- |
7678 |
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7679 |
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f |
7680 |
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o |
7681 |
-+ $(FC) $(FFLAGS) -c refall_twin.f |
7682 |
- |
7683 |
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7684 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f |
7685 |
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
7686 |
-+ $(FC) $(FFLAGS) -c rharvest_subr.f |
7687 |
- |
7688 |
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
7689 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f |
7690 |
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o |
7691 |
-+ $(FC) $(FFLAGS) -c solvent_contr_mask.f |
7692 |
- |
7693 |
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
7694 |
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f |
7695 |
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o |
7696 |
-+ $(FC) $(FFLAGS) -c subag_scale_hessian.f |
7697 |
- |
7698 |
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 |
7699 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f |
7700 |
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o |
7701 |
-+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f |
7702 |
- |
7703 |
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7704 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f |
7705 |
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
7706 |
-+ $(FC) $(FFLAGS) -c subcf_scale1.f |
7707 |
- |
7708 |
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f |
7709 |
-- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 |
7710 |
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o |
7711 |
-+ $(FC) $(FFLAGS) -c bvalue_routines.f90 |
7712 |
- |
7713 |
--newentry_idealise.o:: newentry_idealise.f weights.f90 |
7714 |
-- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 |
7715 |
-+newentry_idealise.o:: newentry_idealise.f weights.o |
7716 |
-+ $(FC) $(FFLAGS) -c newentry_idealise.f |
7717 |
- |
7718 |
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 |
7719 |
-- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 |
7720 |
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o |
7721 |
-+ $(FC) $(FFLAGS) -c occupancy_only_refine.f |
7722 |
- |
7723 |
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 |
7724 |
-- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 |
7725 |
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 |
7726 |
-+ $(FC) $(FFLAGS) -c refmac_completeness.f90 |
7727 |
- |
7728 |
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7729 |
-- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f |
7730 |
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o |
7731 |
-+ $(FC) $(FFLAGS) -c refmac_xml.f |
7732 |
- |
7733 |
- hkl_pack.o: hkl_pack.f90 |
7734 |
- $(FC) $(FFLAGS) -c hkl_pack.f90 |
7735 |
- |
7736 |
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 |
7737 |
-- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 |
7738 |
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o |
7739 |
-+ $(FC) $(FFLAGS) -c extra_eigen.f |
7740 |
- |
7741 |
--subvag.o: subvag.f hkl_pack.f90 |
7742 |
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f |
7743 |
-+subvag.o: subvag.f hkl_pack.o |
7744 |
-+ $(FC) $(FFLAGS) -c subvag.f |
7745 |
- |
7746 |
--make_PDB.o: make_PDB.f ncs_constr.f90 |
7747 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f |
7748 |
-+make_PDB.o: make_PDB.f ncs_constr.o |
7749 |
-+ $(FC) $(FFLAGS) -c make_PDB.f |
7750 |
- |
7751 |
--make_CIF.o: make_CIF.f ncs_constr.f90 |
7752 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f |
7753 |
-+make_CIF.o: make_CIF.f ncs_constr.o |
7754 |
-+ $(FC) $(FFLAGS) -c make_CIF.f |
7755 |
- |
7756 |
- refmac: $(SUBR) |
7757 |
-- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) |
7758 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) |
7759 |
- |
7760 |
--mol2_file.o: mol2_file.f odb_files.f90 |
7761 |
-- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f |
7762 |
-+mol2_file.o: mol2_file.f odb_files.o |
7763 |
-+ $(FC) $(FFLAGS) -c mol2_file.f |
7764 |
- |
7765 |
--odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f |
7766 |
-- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 |
7767 |
-+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o |
7768 |
-+ $(FC) $(FFLAGS) -c odb_files.f90 |
7769 |
- |
7770 |
- elements_module.o: elements_module.f90 |
7771 |
- $(FC) $(FFLAGS) -c elements_module.f90 |
7772 |
- |
7773 |
--make_lib2.o: make_lib2.f odb_files.f90 |
7774 |
-- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f |
7775 |
-+make_lib2.o: make_lib2.f odb_files.o |
7776 |
-+ $(FC) $(FFLAGS) -c make_lib2.f |
7777 |
- |
7778 |
- pdb2libcheck.o: pdb2libcheck.f90 |
7779 |
- $(FC) $(FFLAGS) -c pdb2libcheck.f90 |
7780 |
- |
7781 |
--libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 |
7782 |
-- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f |
7783 |
-+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o |
7784 |
-+ $(FC) $(FFLAGS) -c libcheck.f |
7785 |
- |
7786 |
- header2matr.o: header2matr.f90 |
7787 |
- $(FC) $(FFLAGS) -c header2matr.f90 |
7788 |
-@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 |
7789 |
- $(FC) $(FFLAGS) -c freer_twin.f90 |
7790 |
- |
7791 |
- libcheck: $(SUBL) |
7792 |
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) |
7793 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) |
7794 |
- |
7795 |
- free_twin: $(SUB_FREE) |
7796 |
-- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) |
7797 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) |
7798 |
- |
7799 |
- |
7800 |
- header2matr: $(SUB_HEADER) |
7801 |
-- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) |
7802 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) |
7803 |
- |
7804 |
- clean: |
7805 |
- /bin/rm *.o *.mod |
7806 |
- |
7807 |
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h |
7808 |
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp |
7809 |
|
7810 |
diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch |
7811 |
deleted file mode 100644 |
7812 |
index 9998b75..0000000 |
7813 |
--- a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch |
7814 |
+++ /dev/null |
7815 |
@@ -1,341 +0,0 @@ |
7816 |
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- |
7817 |
- 1 files changed, 104 insertions(+), 111 deletions(-) |
7818 |
- |
7819 |
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 |
7820 |
-index 0f8bd63..e59fbfb 100644 |
7821 |
---- a/makefile_refmac.inc1 |
7822 |
-+++ b/makefile_refmac.inc1 |
7823 |
-@@ -96,9 +96,7 @@ bridge.o \ |
7824 |
- i0.o \ |
7825 |
- i1.o \ |
7826 |
- chbevl.o \ |
7827 |
--make_unix_ccp4.o \ |
7828 |
--$(LLIBCIF) \ |
7829 |
--$(LLIBLAPACK) |
7830 |
-+make_unix_ccp4.o |
7831 |
- |
7832 |
- |
7833 |
- SUBL = \ |
7834 |
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \ |
7835 |
- iheap_sort.o \ |
7836 |
- linalgebra.o \ |
7837 |
- math_refmac.o \ |
7838 |
--subnumrec.o \ |
7839 |
--$(LLIBLAPACK) \ |
7840 |
--$(LLIBCCP) |
7841 |
-+subnumrec.o |
7842 |
- |
7843 |
- SUB_FREE = \ |
7844 |
- freer_twin.o \ |
7845 |
-@@ -145,9 +141,7 @@ subnumrec.o \ |
7846 |
- libT.o \ |
7847 |
- iheap_sort.o \ |
7848 |
- cell_symm_subrs.o \ |
7849 |
--math_refmac.o \ |
7850 |
--$(LLIBLAPACK) \ |
7851 |
--$(LLIBCCP) |
7852 |
-+math_refmac.o |
7853 |
- |
7854 |
- SUB_HEADER = header2matr.o |
7855 |
- #-------------------------------------------------------------------------------- |
7856 |
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 |
7857 |
- twin77mod.o: twin77mod.f |
7858 |
- $(FC) $(FFLAGS) -c twin77mod.f |
7859 |
- |
7860 |
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 |
7861 |
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 |
7862 |
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 |
7863 |
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 |
7864 |
- |
7865 |
--max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 |
7866 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f |
7867 |
-+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o |
7868 |
-+ $(FC) $(FFLAGS) -c max_with_twins.f |
7869 |
- |
7870 |
--merohedr_twin.o: restr_files.f90 merohedr_twin.f |
7871 |
-- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f |
7872 |
-+merohedr_twin.o: restr_files.o merohedr_twin.f |
7873 |
-+ $(FC) $(FFLAGS) -c merohedr_twin.f |
7874 |
- |
7875 |
--ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 |
7876 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f |
7877 |
-+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o |
7878 |
-+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f |
7879 |
- |
7880 |
--ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 |
7881 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f |
7882 |
-+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o |
7883 |
-+ $(FC) $(FFLAGS) -c ml_params_refine.f |
7884 |
- |
7885 |
--optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 |
7886 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 |
7887 |
-+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o |
7888 |
-+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 |
7889 |
- |
7890 |
--ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 |
7891 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f |
7892 |
-+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o |
7893 |
-+ $(FC) $(FFLAGS) -c ncs_rest.f |
7894 |
- |
7895 |
--ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 |
7896 |
-- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 |
7897 |
-+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o |
7898 |
-+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 |
7899 |
- |
7900 |
--lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 |
7901 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 |
7902 |
-+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o |
7903 |
-+ $(FC) $(FFLAGS) -c lsq_exp2.f |
7904 |
- |
7905 |
--vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 |
7906 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f |
7907 |
-+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o |
7908 |
-+ $(FC) $(FFLAGS) -c vdw_and_contacts.f |
7909 |
- |
7910 |
- dist_routines.o: dist_routines.f90 |
7911 |
- $(FC) $(FFLAGS) -c dist_routines.f90 |
7912 |
- |
7913 |
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 |
7914 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 |
7915 |
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 |
7916 |
-+ $(FC) $(FFLAGS) -c ncs_simil.f90 |
7917 |
- |
7918 |
- ridge.o: ridge.f90 |
7919 |
- $(FC) $(FFLAGS) -c ridge.f90 |
7920 |
-@@ -227,140 +221,138 @@ ridge.o: ridge.f90 |
7921 |
- align_refmac.o: align_refmac.f90 |
7922 |
- $(FC) $(FFLAGS) -c align_refmac.f90 |
7923 |
- |
7924 |
--rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 |
7925 |
-- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f |
7926 |
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o |
7927 |
-+ $(FC) $(FFLAGS) -c rigid_allocate.f |
7928 |
- |
7929 |
--tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 |
7930 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f |
7931 |
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o |
7932 |
-+ $(FC) $(FFLAGS) -c tls_allocate.f |
7933 |
- |
7934 |
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ |
7935 |
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7936 |
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ |
7937 |
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 |
7938 |
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ |
7939 |
-+ restr_files.o weights.o agreem.o rharvest_mod.o |
7940 |
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f |
7941 |
- |
7942 |
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 |
7943 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f |
7944 |
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o |
7945 |
-+ $(FC) $(FFLAGS) -c oppro_allocate.f |
7946 |
- |
7947 |
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 |
7948 |
-- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f |
7949 |
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o |
7950 |
-+ $(FC) $(FFLAGS) -c read_extra_restraints.f |
7951 |
- |
7952 |
--coords.o: coords.f90 atomf77mod.f |
7953 |
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 |
7954 |
-+coords.o: coords.f90 atomf77mod.o |
7955 |
-+ $(FC) $(FFLAGS) -c coords.f90 |
7956 |
- |
7957 |
- |
7958 |
--ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 |
7959 |
-- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 |
7960 |
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o |
7961 |
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f |
7962 |
- |
7963 |
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 |
7964 |
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 |
7965 |
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o |
7966 |
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f |
7967 |
- |
7968 |
--calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 |
7969 |
-- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 |
7970 |
-+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o |
7971 |
-+ $(FC) $(FFLAGS) -c calc_stats_twin.f |
7972 |
- |
7973 |
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
7974 |
-- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f |
7975 |
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o |
7976 |
-+ $(FC) $(FFLAGS) -c refpre_twin.f |
7977 |
- |
7978 |
- |
7979 |
--decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f |
7980 |
-- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f |
7981 |
-+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f |
7982 |
-+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f |
7983 |
- |
7984 |
- automorphism.o: automorphism.f90 |
7985 |
- $(FC) $(FFLAGS) -c automorphism.f90 |
7986 |
- |
7987 |
--mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 |
7988 |
-- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f |
7989 |
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o |
7990 |
-+ $(FC) $(FFLAGS) -c mtz_write_twin.f |
7991 |
- |
7992 |
- filter_params.o: filter_params.f90 |
7993 |
- $(FC) $(FFLAGS) -c filter_params.f90 |
7994 |
- |
7995 |
--rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ |
7996 |
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
7997 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ |
7998 |
-- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f |
7999 |
-+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ |
8000 |
-+ agreem.o rharvest_mod.o ncs_constr.o |
8001 |
-+ $(FC) $(FFLAGS) -c rcard_tor1.f |
8002 |
- |
8003 |
--inout_routines.o: restr_files.f90 inout_routines.f |
8004 |
-- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f |
8005 |
-+inout_routines.o: restr_files.o inout_routines.f |
8006 |
-+ $(FC) $(FFLAGS) -c inout_routines.f |
8007 |
- |
8008 |
--local_tls.o: local_tls.f90 linalgebra_f90.f90 |
8009 |
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 |
8010 |
-+local_tls.o: local_tls.f90 linalgebra_f90.o |
8011 |
-+ $(FC) $(FFLAGS) -c local_tls.f90 |
8012 |
- |
8013 |
- linalgebra_f90.o: linalgebra_f90.f90 |
8014 |
- $(FC) $(FFLAGS) -c linalgebra_f90.f90 |
8015 |
- |
8016 |
--make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8017 |
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f |
8018 |
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
8019 |
-+ $(FC) $(FFLAGS) -c make_refmac_dummy.f |
8020 |
- |
8021 |
--ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8022 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f |
8023 |
-+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
8024 |
-+ $(FC) $(FFLAGS) -c ml_scaling_double.f |
8025 |
- |
8026 |
--refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8027 |
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f |
8028 |
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o |
8029 |
-+ $(FC) $(FFLAGS) -c refall_twin.f |
8030 |
- |
8031 |
--rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8032 |
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f |
8033 |
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
8034 |
-+ $(FC) $(FFLAGS) -c rharvest_subr.f |
8035 |
- |
8036 |
--solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
8037 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f |
8038 |
-+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o |
8039 |
-+ $(FC) $(FFLAGS) -c solvent_contr_mask.f |
8040 |
- |
8041 |
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 |
8042 |
-- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f |
8043 |
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o |
8044 |
-+ $(FC) $(FFLAGS) -c subag_scale_hessian.f |
8045 |
- |
8046 |
--aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 |
8047 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f |
8048 |
-+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o |
8049 |
-+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f |
8050 |
- |
8051 |
--subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8052 |
-- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f |
8053 |
-+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o |
8054 |
-+ $(FC) $(FFLAGS) -c subcf_scale1.f |
8055 |
- |
8056 |
--bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f |
8057 |
-- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 |
8058 |
-+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o |
8059 |
-+ $(FC) $(FFLAGS) -c bvalue_routines.f90 |
8060 |
- |
8061 |
--newentry_idealise.o:: newentry_idealise.f weights.f90 |
8062 |
-- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 |
8063 |
-+newentry_idealise.o:: newentry_idealise.f weights.o |
8064 |
-+ $(FC) $(FFLAGS) -c newentry_idealise.f |
8065 |
- |
8066 |
--occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 |
8067 |
-- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 |
8068 |
-+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o |
8069 |
-+ $(FC) $(FFLAGS) -c occupancy_only_refine.f |
8070 |
- |
8071 |
--refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 |
8072 |
-- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 |
8073 |
-+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 |
8074 |
-+ $(FC) $(FFLAGS) -c refmac_completeness.f90 |
8075 |
- |
8076 |
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 |
8077 |
-- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f |
8078 |
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o |
8079 |
-+ $(FC) $(FFLAGS) -c refmac_xml.f |
8080 |
- |
8081 |
- hkl_pack.o: hkl_pack.f90 |
8082 |
- $(FC) $(FFLAGS) -c hkl_pack.f90 |
8083 |
- |
8084 |
--extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 |
8085 |
-- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 |
8086 |
-+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o |
8087 |
-+ $(FC) $(FFLAGS) -c extra_eigen.f |
8088 |
- |
8089 |
--subvag.o: subvag.f hkl_pack.f90 |
8090 |
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f |
8091 |
-+subvag.o: subvag.f hkl_pack.o |
8092 |
-+ $(FC) $(FFLAGS) -c subvag.f |
8093 |
- |
8094 |
--make_PDB.o: make_PDB.f ncs_constr.f90 |
8095 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f |
8096 |
-+make_PDB.o: make_PDB.f ncs_constr.o |
8097 |
-+ $(FC) $(FFLAGS) -c make_PDB.f |
8098 |
- |
8099 |
--make_CIF.o: make_CIF.f ncs_constr.f90 |
8100 |
-- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f |
8101 |
-+make_CIF.o: make_CIF.f ncs_constr.o |
8102 |
-+ $(FC) $(FFLAGS) -c make_CIF.f |
8103 |
- |
8104 |
- refmac: $(SUBR) |
8105 |
-- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) |
8106 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) |
8107 |
- |
8108 |
--mol2_file.o: mol2_file.f odb_files.f90 |
8109 |
-- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f |
8110 |
-+mol2_file.o: mol2_file.f odb_files.o |
8111 |
-+ $(FC) $(FFLAGS) -c mol2_file.f |
8112 |
- |
8113 |
--odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f |
8114 |
-- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 |
8115 |
-+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o |
8116 |
-+ $(FC) $(FFLAGS) -c odb_files.f90 |
8117 |
- |
8118 |
- elements_module.o: elements_module.f90 |
8119 |
- $(FC) $(FFLAGS) -c elements_module.f90 |
8120 |
- |
8121 |
--make_lib2.o: make_lib2.f odb_files.f90 |
8122 |
-- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f |
8123 |
-+make_lib2.o: make_lib2.f odb_files.o |
8124 |
-+ $(FC) $(FFLAGS) -c make_lib2.f |
8125 |
- |
8126 |
- pdb2libcheck.o: pdb2libcheck.f90 |
8127 |
- $(FC) $(FFLAGS) -c pdb2libcheck.f90 |
8128 |
- |
8129 |
--libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 |
8130 |
-- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f |
8131 |
-+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o |
8132 |
-+ $(FC) $(FFLAGS) -c libcheck.f |
8133 |
- |
8134 |
- header2matr.o: header2matr.f90 |
8135 |
- $(FC) $(FFLAGS) -c header2matr.f90 |
8136 |
-@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 |
8137 |
- $(FC) $(FFLAGS) -c freer_twin.f90 |
8138 |
- |
8139 |
- libcheck: $(SUBL) |
8140 |
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) |
8141 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) |
8142 |
- |
8143 |
- free_twin: $(SUB_FREE) |
8144 |
-- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) |
8145 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) |
8146 |
- |
8147 |
- |
8148 |
- header2matr: $(SUB_HEADER) |
8149 |
-- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) |
8150 |
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) |
8151 |
- |
8152 |
- clean: |
8153 |
- /bin/rm *.o *.mod |
8154 |
- |
8155 |
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h |
8156 |
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp |
8157 |
|
8158 |
diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml |
8159 |
deleted file mode 100644 |
8160 |
index c0432fe..0000000 |
8161 |
--- a/sci-chemistry/refmac/metadata.xml |
8162 |
+++ /dev/null |
8163 |
@@ -1,9 +0,0 @@ |
8164 |
-<?xml version="1.0" encoding="UTF-8"?> |
8165 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
8166 |
-<pkgmetadata> |
8167 |
- <herd>sci-chemistry</herd> |
8168 |
- <maintainer> |
8169 |
- <email>jlec@g.o</email> |
8170 |
- <name>Justin Lecher (jlec)</name> |
8171 |
- </maintainer> |
8172 |
-</pkgmetadata> |
8173 |
|
8174 |
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild |
8175 |
deleted file mode 100644 |
8176 |
index eb8e870..0000000 |
8177 |
--- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild |
8178 |
+++ /dev/null |
8179 |
@@ -1,85 +0,0 @@ |
8180 |
-# Copyright 1999-2014 Gentoo Foundation |
8181 |
-# Distributed under the terms of the GNU General Public License v2 |
8182 |
-# $Id$ |
8183 |
- |
8184 |
-EAPI=4 |
8185 |
- |
8186 |
-inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator |
8187 |
- |
8188 |
-DESCRIPTION="Macromolecular crystallographic refinement program" |
8189 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" |
8190 |
-SRC_URI=" |
8191 |
- ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz |
8192 |
- test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" |
8193 |
- |
8194 |
-SLOT="0" |
8195 |
-LICENSE="ccp4" |
8196 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
8197 |
-IUSE="test" |
8198 |
- |
8199 |
-RDEPEND=" |
8200 |
- sci-chemistry/makecif |
8201 |
- >=sci-libs/ccp4-libs-6.1.3-r7 |
8202 |
- sci-libs/mmdb |
8203 |
- <sci-libs/monomer-db-1 |
8204 |
- virtual/blas |
8205 |
- virtual/lapack" |
8206 |
-DEPEND="${RDEPEND} |
8207 |
- virtual/pkgconfig" |
8208 |
- |
8209 |
-FORTRAN_STANDARD="77 90" |
8210 |
- |
8211 |
-S="${WORKDIR}" |
8212 |
- |
8213 |
-PATCHES=( |
8214 |
- "${FILESDIR}"/${PV}-allow-dynamic-linking.patch |
8215 |
- "${FILESDIR}"/${PV}-gcc4.6.patch |
8216 |
- ) |
8217 |
- |
8218 |
-src_prepare() { |
8219 |
- epatch ${PATCHES[@]} |
8220 |
- |
8221 |
- use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch |
8222 |
- [[ ${FC} == *gfortran* ]] && \ |
8223 |
- append-fflags -fno-second-underscore && \ |
8224 |
- append-cflags -DGFORTRAN -DPROTOTYPE && \ |
8225 |
- append-libs -lgfortran -lgfortranbegin -lstdc++ |
8226 |
- [[ ${FC} == *ifort* ]] && \ |
8227 |
- append-libs -lstdc++ |
8228 |
-} |
8229 |
- |
8230 |
-src_compile() { |
8231 |
- emake \ |
8232 |
- FC=$(tc-getFC) \ |
8233 |
- CC=$(tc-getCC) \ |
8234 |
- CXX=$(tc-getCXX) \ |
8235 |
- COPTIM="${CFLAGS}" \ |
8236 |
- FOPTIM="${FFLAGS:- -O2}" \ |
8237 |
- VERSION="" \ |
8238 |
- XFFLAGS="" \ |
8239 |
- XCFLAGS="" \ |
8240 |
- LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \ |
8241 |
- LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \ |
8242 |
- LLIBOTHERS="${LIBS}" \ |
8243 |
- ${PN} libcheck |
8244 |
-} |
8245 |
- |
8246 |
-src_test() { |
8247 |
- einfo "Starting tests ..." |
8248 |
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" |
8249 |
- export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" |
8250 |
- export CCP4_TEST="${WORKDIR}"/test-framework |
8251 |
- export CCP4_SCR="${T}" |
8252 |
- ln -sf refmac "${S}"/refmac5 |
8253 |
- sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb |
8254 |
- ccp4-run-thorough-tests -v test_refmac5 || die |
8255 |
-} |
8256 |
- |
8257 |
-src_install() { |
8258 |
- exeinto /usr/libexec/ccp4/bin/ |
8259 |
- doexe ${PN} |
8260 |
- dosym refmac /usr/libexec/ccp4/bin/refmac5 |
8261 |
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} |
8262 |
- dosym refmac /usr/bin/refmac5 |
8263 |
- dodoc refmac_keywords.pdf bugs_and_features.pdf |
8264 |
-} |
8265 |
|
8266 |
diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest |
8267 |
deleted file mode 100644 |
8268 |
index e03416a..0000000 |
8269 |
--- a/sci-chemistry/scala/Manifest |
8270 |
+++ /dev/null |
8271 |
@@ -1 +0,0 @@ |
8272 |
-DIST scala-3.3.20.tar.gz 368628 SHA256 0efb108923a4d21fdc75d7ee92567e4bac4ae409f8798fbabd8142b5b026e976 SHA512 9f9812527013d87c80101333baf7ee646f6b3c665cdb477bb4e633c0a1fa57b31b6327913cf712e961c4484a9d9edf1aab5f3cfc66e6834aca1e970a4e0ca898 WHIRLPOOL 7d6082872a9f2f992186a2626dbf7ccd9f827b1322d1399b41ebc1b07267a46cfed5f7ea085403415c01eba4fc44e9d51983080537db04b227469d6871f8f1f9 |
8273 |
|
8274 |
diff --git a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch |
8275 |
deleted file mode 100644 |
8276 |
index 0bb3d40..0000000 |
8277 |
--- a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch |
8278 |
+++ /dev/null |
8279 |
@@ -1,17 +0,0 @@ |
8280 |
- scala.f | 3 ++- |
8281 |
- 1 files changed, 2 insertions(+), 1 deletions(-) |
8282 |
- |
8283 |
-diff --git a/scala.f b/scala.f |
8284 |
-index d7e1cbe..8ed6fd2 100644 |
8285 |
---- a/scala.f |
8286 |
-+++ b/scala.f |
8287 |
-@@ -3955,7 +3955,8 @@ c line buffer |
8288 |
- character*40 key, value |
8289 |
- character*200 realfilename |
8290 |
- |
8291 |
-- integer intfp, i2swap, lenstr |
8292 |
-+ integer intfp, lenstr |
8293 |
-+ integer*2 i2swap |
8294 |
- external intfp, i2swap, lenstr |
8295 |
- logical litend |
8296 |
- external litend |
8297 |
|
8298 |
diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am |
8299 |
deleted file mode 100644 |
8300 |
index 49fd611..0000000 |
8301 |
--- a/sci-chemistry/scala/files/Makefile.am |
8302 |
+++ /dev/null |
8303 |
@@ -1,7 +0,0 @@ |
8304 |
- |
8305 |
-LIBS = -lccp4f $(LAPACK_LIBS) |
8306 |
- |
8307 |
-bin_PROGRAMS = scala |
8308 |
- |
8309 |
-scala_SOURCES = scala.f |
8310 |
- |
8311 |
|
8312 |
diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac |
8313 |
deleted file mode 100644 |
8314 |
index 35c4c7f..0000000 |
8315 |
--- a/sci-chemistry/scala/files/configure.ac |
8316 |
+++ /dev/null |
8317 |
@@ -1,14 +0,0 @@ |
8318 |
-# -*- Autoconf -*- |
8319 |
-# Process this file with autoconf to produce a configure script. |
8320 |
- |
8321 |
-AC_PREREQ(2.59) |
8322 |
-AC_INIT(scala, https://bugs.gentoo.org/) |
8323 |
-AC_CONFIG_SRCDIR([scala.f]) |
8324 |
-AM_INIT_AUTOMAKE([foreign]) |
8325 |
- |
8326 |
-PKG_CHECK_MODULES([LAPACK],[lapack]) |
8327 |
- |
8328 |
-# Checks for programs. |
8329 |
-AC_PROG_FC |
8330 |
-AC_PROG_F77 |
8331 |
-AC_OUTPUT([Makefile]) |
8332 |
|
8333 |
diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml |
8334 |
deleted file mode 100644 |
8335 |
index 2c9359a..0000000 |
8336 |
--- a/sci-chemistry/scala/metadata.xml |
8337 |
+++ /dev/null |
8338 |
@@ -1,13 +0,0 @@ |
8339 |
-<?xml version="1.0" encoding="UTF-8"?> |
8340 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
8341 |
-<pkgmetadata> |
8342 |
- <herd>sci-chemistry</herd> |
8343 |
- <maintainer> |
8344 |
- <email>jlec@g.o</email> |
8345 |
- </maintainer> |
8346 |
- <longdescription> |
8347 |
-This program scales together multiple observations of reflections from |
8348 |
-Xray difraction experiments, and merges multiple observations into an |
8349 |
-average intensity. |
8350 |
-</longdescription> |
8351 |
-</pkgmetadata> |
8352 |
|
8353 |
diff --git a/sci-chemistry/scala/scala-3.3.20.ebuild b/sci-chemistry/scala/scala-3.3.20.ebuild |
8354 |
deleted file mode 100644 |
8355 |
index 3555cc2..0000000 |
8356 |
--- a/sci-chemistry/scala/scala-3.3.20.ebuild |
8357 |
+++ /dev/null |
8358 |
@@ -1,38 +0,0 @@ |
8359 |
-# Copyright 1999-2015 Gentoo Foundation |
8360 |
-# Distributed under the terms of the GNU General Public License v2 |
8361 |
-# $Id$ |
8362 |
- |
8363 |
-EAPI=4 |
8364 |
- |
8365 |
-inherit autotools fortran-2 |
8366 |
- |
8367 |
-DESCRIPTION="Scale together multiple observations of reflections" |
8368 |
-HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html" |
8369 |
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" |
8370 |
- |
8371 |
-LICENSE="ccp4" |
8372 |
-SLOT="0" |
8373 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
8374 |
-IUSE="" |
8375 |
- |
8376 |
-RDEPEND=" |
8377 |
- !<sci-chemistry/ccp4-6.1.2 |
8378 |
- !dev-lang/scala-bin |
8379 |
- !dev-lang/scala |
8380 |
- sci-libs/ccp4-libs |
8381 |
- virtual/lapack" |
8382 |
-DEPEND="${RDEPEND} |
8383 |
- virtual/pkgconfig" |
8384 |
- |
8385 |
-src_prepare() { |
8386 |
- cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}" |
8387 |
- eautoreconf |
8388 |
-} |
8389 |
- |
8390 |
-src_install() { |
8391 |
- exeinto /usr/libexec/ccp4/bin/ |
8392 |
- doexe ${PN} |
8393 |
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} |
8394 |
- dodoc ${PN}.doc |
8395 |
- dohtml ${PN}.html |
8396 |
-} |
8397 |
|
8398 |
diff --git a/sci-chemistry/sfcheck/Manifest b/sci-chemistry/sfcheck/Manifest |
8399 |
deleted file mode 100644 |
8400 |
index 77615ce..0000000 |
8401 |
--- a/sci-chemistry/sfcheck/Manifest |
8402 |
+++ /dev/null |
8403 |
@@ -1 +0,0 @@ |
8404 |
-DIST sfcheck-7.03.18.tar.gz 535707 SHA256 def9ceec86fc50f35b9a729e6f84b45a83560e2c6c20a5105647182e10313148 SHA512 256aa1690e0f5ca6aca0483a7d00c1deeb7b77701d950771a134532a658f7c3189bc6abec620ea6da2af200fc879ac9ff07ef7f4ba8614b6cd4e8455a11bed93 WHIRLPOOL 7b9f99f1a8387c5bc63bdab2078d3fcfab4146046429c56503760ca12a1898e944b5aa3c42b358d303206487e5d493bdcb77fe1795490779e7bd79b8b66a2d7a |
8405 |
|
8406 |
diff --git a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch |
8407 |
deleted file mode 100644 |
8408 |
index 4163cb5..0000000 |
8409 |
--- a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch |
8410 |
+++ /dev/null |
8411 |
@@ -1,12 +0,0 @@ |
8412 |
-diff --git a/src/makefile b/src/makefile |
8413 |
-index ab43d7d..37e469f 100755 |
8414 |
---- a/src/makefile |
8415 |
-+++ b/src/makefile |
8416 |
-@@ -60,6 +60,6 @@ main_sfcheck_ccp4.o: main_sfcheck_ccp4.f sfch_version.fh |
8417 |
- $(MR_FORT) -c main_sfcheck_ccp4.f |
8418 |
- |
8419 |
- sfcheck: $(OBJS) |
8420 |
-- $(MR_FORT) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) |
8421 |
-+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) |
8422 |
- |
8423 |
- # ---------------------------------------- |
8424 |
|
8425 |
diff --git a/sci-chemistry/sfcheck/metadata.xml b/sci-chemistry/sfcheck/metadata.xml |
8426 |
deleted file mode 100644 |
8427 |
index 9ac9ffd..0000000 |
8428 |
--- a/sci-chemistry/sfcheck/metadata.xml |
8429 |
+++ /dev/null |
8430 |
@@ -1,5 +0,0 @@ |
8431 |
-<?xml version="1.0" encoding="UTF-8"?> |
8432 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
8433 |
-<pkgmetadata> |
8434 |
-<herd>sci-chemistry</herd> |
8435 |
-</pkgmetadata> |
8436 |
|
8437 |
diff --git a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild |
8438 |
deleted file mode 100644 |
8439 |
index e18673d..0000000 |
8440 |
--- a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild |
8441 |
+++ /dev/null |
8442 |
@@ -1,42 +0,0 @@ |
8443 |
-# Copyright 1999-2012 Gentoo Foundation |
8444 |
-# Distributed under the terms of the GNU General Public License v2 |
8445 |
-# $Id$ |
8446 |
- |
8447 |
-EAPI=4 |
8448 |
- |
8449 |
-inherit eutils fortran-2 toolchain-funcs |
8450 |
- |
8451 |
-DESCRIPTION="Program for assessing the agreement between the atomic model and X-ray data or EM map" |
8452 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/sfcheck.html" |
8453 |
-#SRC_URI="http://www.ysbl.york.ac.uk/~alexei/downloads/sfcheck.tar.gz" |
8454 |
-SRC_URI="mirror://gentoo/${P}.tar.gz" |
8455 |
- |
8456 |
-SLOT="0" |
8457 |
-LICENSE="ccp4" |
8458 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
8459 |
-IUSE="" |
8460 |
- |
8461 |
-RDEPEND="sci-libs/ccp4-libs" |
8462 |
-DEPEND="${RDEPEND} |
8463 |
- !<sci-chmistry/ccp4-apps-6.1.3" |
8464 |
- |
8465 |
-S="${WORKDIR}"/${PN} |
8466 |
- |
8467 |
-src_prepare() { |
8468 |
- epatch "${FILESDIR}"/7.03.17-ldflags.patch |
8469 |
- |
8470 |
- emake -C src clean |
8471 |
-} |
8472 |
- |
8473 |
-src_compile() { |
8474 |
- MR_FORT="$(tc-getFC) ${FFLAGS}" \ |
8475 |
- MR_LIBRARY="-lccp4f" \ |
8476 |
- emake -C src all |
8477 |
-} |
8478 |
- |
8479 |
-src_install() { |
8480 |
- exeinto /usr/libexec/ccp4/bin/ |
8481 |
- doexe bin/${PN} |
8482 |
- dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} |
8483 |
- dodoc readme ${PN}.com.gz doc/${PN}* |
8484 |
-} |
8485 |
|
8486 |
diff --git a/sci-chemistry/solve-resolve-bin/Manifest b/sci-chemistry/solve-resolve-bin/Manifest |
8487 |
deleted file mode 100644 |
8488 |
index 43fcf71..0000000 |
8489 |
--- a/sci-chemistry/solve-resolve-bin/Manifest |
8490 |
+++ /dev/null |
8491 |
@@ -1,2 +0,0 @@ |
8492 |
-DIST solve-2.13-linux-64.tar.gz 74444830 SHA256 e03250bb550686fc6e5f59d4e885b83b88cd342dfb4975eb31ddf95d9515650e SHA512 8f20715c3fb73940f03ba8a4bb3528f89ba01520cacead001796609bc15259ab7ab7f2d4960ea97efc43029863bc31e630c9e93f528a233652928220dafe0b4d WHIRLPOOL 125efe76024148656f3bb357ad1bc78d17f51eb8268c83241f4da9a94356170d0259fe48fadf6bf1ffe4b10b57bb27ed79199063dc95d0eef8d9e22de653c84a |
8493 |
-DIST solve-2.13-linux.tar.gz 71902534 SHA256 975466fe92d8f6256de20ea0b5101876f3e5a7e3093199946c9f4824236c79d3 SHA512 a3a779ada33bd189fc8c3e6fdc424ef9c032c5540138cce52e0c8dcf5a12847b1325402a2c1715ed4ab217f433169d3612c724f2d178ead576afc44ec4839c6a WHIRLPOOL 0fec411b795a107610e620586cba511a0cbf50400e0bdfef872b22ee05e3992fcc0a4b1cf1d84d450bbeb3838a7bc9633acd8f4cf97d5e4b7a01e6e7959ccd7c |
8494 |
|
8495 |
diff --git a/sci-chemistry/solve-resolve-bin/metadata.xml b/sci-chemistry/solve-resolve-bin/metadata.xml |
8496 |
deleted file mode 100644 |
8497 |
index ae9ec7c..0000000 |
8498 |
--- a/sci-chemistry/solve-resolve-bin/metadata.xml |
8499 |
+++ /dev/null |
8500 |
@@ -1,8 +0,0 @@ |
8501 |
-<?xml version="1.0" encoding="UTF-8"?> |
8502 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
8503 |
-<pkgmetadata> |
8504 |
- <herd>sci-chemistry</herd> |
8505 |
- <maintainer> |
8506 |
- <email>jlec@g.o</email> |
8507 |
- </maintainer> |
8508 |
-</pkgmetadata> |
8509 |
|
8510 |
diff --git a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild |
8511 |
deleted file mode 100644 |
8512 |
index 6deae17..0000000 |
8513 |
--- a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild |
8514 |
+++ /dev/null |
8515 |
@@ -1,68 +0,0 @@ |
8516 |
-# Copyright 1999-2015 Gentoo Foundation |
8517 |
-# Distributed under the terms of the GNU General Public License v2 |
8518 |
-# $Id$ |
8519 |
- |
8520 |
-EAPI=5 |
8521 |
- |
8522 |
-inherit eutils |
8523 |
- |
8524 |
-DESCRIPTION="Automated crystallographic structure solution for MIR, SAD, and MAD" |
8525 |
-HOMEPAGE="http://www.solve.lanl.gov/index.html" |
8526 |
-SRC_URI=" |
8527 |
- x86? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux.tar.gz ) |
8528 |
- amd64? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux-64.tar.gz )" |
8529 |
- |
8530 |
-SLOT="0" |
8531 |
-LICENSE="solve" |
8532 |
-KEYWORDS="-* x86 amd64" |
8533 |
-IUSE="examples" |
8534 |
- |
8535 |
-RDEPEND="sci-libs/ccp4-libs" |
8536 |
-DEPEND="" |
8537 |
- |
8538 |
-RESTRICT="mirror" |
8539 |
- |
8540 |
-S="${WORKDIR}"/solve-${PV} |
8541 |
- |
8542 |
-QA_PREBUILT="opt/solve-resolve/bin/*" |
8543 |
- |
8544 |
-src_install(){ |
8545 |
- local IN_PATH="/opt/solve-resolve/" |
8546 |
- |
8547 |
- exeinto ${IN_PATH}bin/ |
8548 |
- doexe bin/* |
8549 |
- |
8550 |
- insinto ${IN_PATH}lib/ |
8551 |
- doins -r lib/{*sym,sym*,hist*,*dat,segments,patterns} |
8552 |
- |
8553 |
- docinto html |
8554 |
- dodoc -r lib/html/* |
8555 |
- |
8556 |
- sed \ |
8557 |
- -e 's:/usr/local/lib/solve/:${EPREFIX}/opt/solve-resolve/lib/:' \ |
8558 |
- -i lib/examples_solve/p9/solve* || die |
8559 |
- if use examples; then |
8560 |
- sed \ |
8561 |
- -e 's:/usr/local/lib/resolve/:${EPREFIX}/opt/solve-resolve/lib/:' \ |
8562 |
- -i lib/examples_resolve/{resolve.csh,prime_and_switch.csh} || die |
8563 |
- insinto /usr/share/${PF}/ |
8564 |
- doins -r lib/examples_*solve |
8565 |
- fi |
8566 |
- |
8567 |
- cat >> "${T}"/20solve-resolve <<- EOF |
8568 |
- CCP4_OPEN="UNKNOWN" |
8569 |
- SYMOP="${EPREFIX}/usr/share/ccp4/data/symop.lib" |
8570 |
- SYMINFO="${EPREFIX}/usr/share/ccp4/data/syminfo.lib" |
8571 |
- SOLVEDIR="${EPREFIX}/${IN_PATH}lib/" |
8572 |
- PATH="${EPREFIX}/${IN_PATH}bin" |
8573 |
- EOF |
8574 |
- |
8575 |
- doenvd "${T}"/20solve-resolve |
8576 |
-} |
8577 |
- |
8578 |
-pkg_postinst(){ |
8579 |
- einfo "Get a valid license key from" |
8580 |
- einfo "http://solve.lanl.gov/license.html" |
8581 |
- einfo "and place it in" |
8582 |
- einfo "${EPREFIX}${IN_PATH}lib/" |
8583 |
-} |
8584 |
|
8585 |
diff --git a/sci-chemistry/xdsi/Manifest b/sci-chemistry/xdsi/Manifest |
8586 |
deleted file mode 100644 |
8587 |
index e33598d..0000000 |
8588 |
--- a/sci-chemistry/xdsi/Manifest |
8589 |
+++ /dev/null |
8590 |
@@ -1 +0,0 @@ |
8591 |
-DIST xdsi_0.92.tar.gz 886028 SHA256 416403f167d26b56965283b407783ea80927ace533df76e330b51ca37c9bb9e4 |
8592 |
|
8593 |
diff --git a/sci-chemistry/xdsi/files/0.92-gentoo.patch b/sci-chemistry/xdsi/files/0.92-gentoo.patch |
8594 |
deleted file mode 100644 |
8595 |
index f4a37ff..0000000 |
8596 |
--- a/sci-chemistry/xdsi/files/0.92-gentoo.patch |
8597 |
+++ /dev/null |
8598 |
@@ -1,27 +0,0 @@ |
8599 |
- xdsi | 6 +++--- |
8600 |
- 1 files changed, 3 insertions(+), 3 deletions(-) |
8601 |
- |
8602 |
-diff --git a/xdsi b/xdsi |
8603 |
-index cbedee8..1037913 100755 |
8604 |
---- a/xdsi |
8605 |
-+++ b/xdsi |
8606 |
-@@ -20,8 +20,8 @@ |
8607 |
- #################################################################### |
8608 |
- # These are the only two things you should change# |
8609 |
- |
8610 |
--set Templates "/mydir/templates" |
8611 |
--set initial "/mydir/SLS-2009" |
8612 |
-+set Templates "GENTOOTEMPLATE" |
8613 |
-+set initial "./" |
8614 |
- |
8615 |
- |
8616 |
- #################################################################### |
8617 |
-@@ -121,7 +121,7 @@ your system administrator." |
8618 |
- } |
8619 |
- |
8620 |
- |
8621 |
--CheckExecutables "kpdf gnuplot xds_par xdsstat xds-viewer-0.6 convert pointless ipmosflm VIEW" |
8622 |
-+CheckExecutables "kpdf gnuplot xds_par xds-viewer convert pointless ipmosflm" |
8623 |
- |
8624 |
- #wm resizable . 0 0 |
8625 |
- |
8626 |
|
8627 |
diff --git a/sci-chemistry/xdsi/metadata.xml b/sci-chemistry/xdsi/metadata.xml |
8628 |
deleted file mode 100644 |
8629 |
index 431fb2b..0000000 |
8630 |
--- a/sci-chemistry/xdsi/metadata.xml |
8631 |
+++ /dev/null |
8632 |
@@ -1,17 +0,0 @@ |
8633 |
-<?xml version="1.0" encoding="UTF-8"?> |
8634 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
8635 |
-<pkgmetadata> |
8636 |
- <herd>sci-chemistry</herd> |
8637 |
- <maintainer> |
8638 |
- <email>jlec@g.o</email> |
8639 |
- </maintainer> |
8640 |
- <longdescription> |
8641 |
-XDSi offers you the possibility to process all your datasets in a given directory with minimum effort. |
8642 |
-* You just have to provide it with a resultdirectory and the directory where your frames are stored. |
8643 |
-* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. |
8644 |
-* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package |
8645 |
-* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset |
8646 |
-* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated |
8647 |
-* You can also generate plots for datasets that have been processed using XDS without XDSi |
8648 |
-</longdescription> |
8649 |
-</pkgmetadata> |
8650 |
|
8651 |
diff --git a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild |
8652 |
deleted file mode 100644 |
8653 |
index 6a6c9bb..0000000 |
8654 |
--- a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild |
8655 |
+++ /dev/null |
8656 |
@@ -1,54 +0,0 @@ |
8657 |
-# Copyright 1999-2015 Gentoo Foundation |
8658 |
-# Distributed under the terms of the GNU General Public License v2 |
8659 |
-# $Id$ |
8660 |
- |
8661 |
-EAPI=5 |
8662 |
- |
8663 |
-inherit eutils |
8664 |
- |
8665 |
-DESCRIPTION="A crude interface for running the XDS" |
8666 |
-HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi" |
8667 |
-SRC_URI="ftp://turn5.biologie.uni-konstanz.de/pub/${PN}_${PV}.tar.gz" |
8668 |
- |
8669 |
-LICENSE="all-rights-reserved" |
8670 |
-SLOT="0" |
8671 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
8672 |
-IUSE="" |
8673 |
- |
8674 |
-RDEPEND=" |
8675 |
- app-text/mupdf |
8676 |
- dev-lang/tk |
8677 |
- || ( media-gfx/imagemagick media-gfx/graphicsmagick[imagemagick] ) |
8678 |
- sci-chemistry/mosflm |
8679 |
- sci-chemistry/pointless |
8680 |
- sci-chemistry/xds-bin[smp] |
8681 |
- sci-visualization/gnuplot |
8682 |
- sci-visualization/xds-viewer" |
8683 |
-# Need to clarified for licensing |
8684 |
-# sci-chemistry/xdsstat-bin |
8685 |
-DEPEND="" |
8686 |
- |
8687 |
-RESTRICT="mirror bindist" |
8688 |
- |
8689 |
-S="${WORKDIR}" |
8690 |
- |
8691 |
-src_prepare() { |
8692 |
- epatch "${FILESDIR}"/${PV}-gentoo.patch |
8693 |
- sed \ |
8694 |
- -e "s:GENTOOTEMPLATE:${EPREFIX}/usr/share/${PN}/templates:g" \ |
8695 |
- -e "s:kpdf:mupdf:g" \ |
8696 |
- -e "s:xds-viewer-0.6:xds-viewer:g" \ |
8697 |
- -i ${PN} || die |
8698 |
-} |
8699 |
- |
8700 |
-src_install() { |
8701 |
- dobin ${PN} |
8702 |
- insinto /usr/share/${PN}/templates |
8703 |
- doins templates/{*.INP,bohr*,fortran,pauli,info.png,*.pck,tablesf_xdsi} |
8704 |
- dodoc templates/*.pdf |
8705 |
-} |
8706 |
- |
8707 |
-pkg_postinst() { |
8708 |
- elog "Documentation can be found here:" |
8709 |
- elog "ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/xdsi_doc_print.pdf" |
8710 |
-} |
8711 |
|
8712 |
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest |
8713 |
deleted file mode 100644 |
8714 |
index 52cb6c1..0000000 |
8715 |
--- a/sci-chemistry/xia2/Manifest |
8716 |
+++ /dev/null |
8717 |
@@ -1,6 +0,0 @@ |
8718 |
-DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 SHA512 cd595147164e4a281431a1d5a7298588001bb11662b517a5f95366e7b0ba4fdb33adf88dd2672c8c2ee84f48356fccb7cbd07667d5f04417a1564c7ea9f878c5 WHIRLPOOL e5493526d3075a5c61ce582a3bf42e2b4a2a73d7a28b1c8df786f0bdf5c8b1eaee986a60f379559ba556f256057794211a6c1e812b785aa9fe3179357b24b0da |
8719 |
-DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f SHA512 d00ba2c42c88d01522859839cbee6a93662ed7f89fb146babffa1dd5d6af12ca72cc146157e0dc88bba1d6543f8509fc9027e1c42ed3ae15dd3e168ca18e1858 WHIRLPOOL ccedcbf910ec5bed637739f7519e14eb249b89ae6ccd83a632ab8571a3af62f1f168f8dfd88287fed9fe927b98230e083a0d2d4525f47bc49c4074375a46a796 |
8720 |
-DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 SHA512 d25788e6564b0f8f4c8e6723347b7691277b01192ead8f37bc7e6d1cdfbee5b22a1329f4ff82d9287875df2de1358e738de08c6a4d19353ccb40c31343dce7bd WHIRLPOOL 1c7306a54a5262632e0319a289f57610badea3945b61653039c78772399557f895ea57e02bbff6804704df8a08f4aa35fce7746e9e03807143d0e395bcd93c75 |
8721 |
-DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 SHA512 656abd51dc6764dee16423e2ea75f590e7a04046c5ac60ce013615c91b3fd41c0089351ceb948203643bff442753773aa639b036efc089ce26592b52b187f656 WHIRLPOOL f11a6bba359ce9f3095d2993fb331a8c70a44bc1ef31dc08663ee63372db995047d5e1b4693808a347eedeb487a1b799c4e080c05416786209f62e7b619ddec8 |
8722 |
-DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 SHA512 913b5a6e24c3c070cc36b404b987331d8de99756d0f598ef485ba5fef3b4bc42d17bf4b4e648d5c99f014872d554b94880a7542dfb9ab6969e272ec986127561 WHIRLPOOL 5f19e3b06df7d5a83d75296fe9c9956f5c0b995cd5d10f1adb66e519d9dbcdd73edcbec53acb90aede6f2955bbd88991d6283af9a3578ad26a686e8530bfdffa |
8723 |
-DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf SHA512 7d2444cb2acfcd2d7ca4c37d5714e7c249ffc419e9d7e1dbb33ccf18adc07f05a2b043af5aee721c64639b991dbbfd356181630229e91e0f871489870f9a8d51 WHIRLPOOL 14759e436d42e4b5ae558616d297f41eb9a345b19df4a4d02d2cb3c61937320d9161343b126b393049319ab6e37dc3890566b1bd3f2bff1a29cd108931640a90 |
8724 |
|
8725 |
diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch |
8726 |
deleted file mode 100644 |
8727 |
index 9d92af7..0000000 |
8728 |
--- a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch |
8729 |
+++ /dev/null |
8730 |
@@ -1,61 +0,0 @@ |
8731 |
-diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py |
8732 |
-index 1a3b0e2..e0b8a1e 100755 |
8733 |
---- a/xia2-0.3.1.0/Applications/xia2find.py |
8734 |
-+++ b/xia2-0.3.1.0/Applications/xia2find.py |
8735 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
8736 |
- from Experts.FindImages import image2template_directory |
8737 |
- |
8738 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
8739 |
-- 'osc', 'cbf', 'mar2000']] |
8740 |
-+ 'osc', 'cbf', 'mar2000'] |
8741 |
- known_sweeps = { } |
8742 |
- |
8743 |
- def is_image_name(file): |
8744 |
-diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py |
8745 |
-index 28b1dc3..dba3ef7 100644 |
8746 |
---- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py |
8747 |
-+++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py |
8748 |
-@@ -48,24 +48,24 @@ strategy_dict = { |
8749 |
- 'default':{ |
8750 |
- 'score':1, |
8751 |
- 'pipeline':{ |
8752 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8753 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8754 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8755 |
- 'pointless-1.1.0.4']}, |
8756 |
- 'default':{ |
8757 |
- 'score':2, |
8758 |
- 'pipeline':{ |
8759 |
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} |
8760 |
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, |
8761 |
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', |
8762 |
- 'pointless-1.1.0.4']}, |
8763 |
- 'mosaic':{ |
8764 |
- 'score':1, |
8765 |
- 'pipeline':{ |
8766 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8767 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8768 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8769 |
- 'pointless-1.1.0.4']}, |
8770 |
- 'mosaic':{ |
8771 |
- 'score':2, |
8772 |
- 'pipeline':{ |
8773 |
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} |
8774 |
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, |
8775 |
- 'depends-on':['xds', 'xscale']} |
8776 |
- } |
8777 |
-diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py |
8778 |
-index 88f9218..5fb6f2a 100644 |
8779 |
---- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py |
8780 |
-+++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py |
8781 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
8782 |
- self.add_command_line(hklin) |
8783 |
- |
8784 |
- self.set_task('Rewriting reflections %s => %s' % |
8785 |
-- ` (os.path.split(hklin)[-1], |
8786 |
-- ` os.path.split(self.getHklout())[-1])) |
8787 |
-+ (os.path.split(hklin)[-1], |
8788 |
-+ os.path.split(self.getHklout())[-1])) |
8789 |
- |
8790 |
- self.start() |
8791 |
- |
8792 |
|
8793 |
diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch |
8794 |
deleted file mode 100644 |
8795 |
index 7770a53..0000000 |
8796 |
--- a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch |
8797 |
+++ /dev/null |
8798 |
@@ -1,61 +0,0 @@ |
8799 |
-diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py |
8800 |
-index 1a3b0e2..e0b8a1e 100755 |
8801 |
---- a/xia2-0.3.1.6/Applications/xia2find.py |
8802 |
-+++ b/xia2-0.3.1.6/Applications/xia2find.py |
8803 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
8804 |
- from Experts.FindImages import image2template_directory |
8805 |
- |
8806 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
8807 |
-- 'osc', 'cbf', 'mar2000']] |
8808 |
-+ 'osc', 'cbf', 'mar2000'] |
8809 |
- known_sweeps = { } |
8810 |
- |
8811 |
- def is_image_name(file): |
8812 |
-diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py |
8813 |
-index 28b1dc3..dba3ef7 100644 |
8814 |
---- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py |
8815 |
-+++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py |
8816 |
-@@ -48,24 +48,24 @@ strategy_dict = { |
8817 |
- 'default':{ |
8818 |
- 'score':1, |
8819 |
- 'pipeline':{ |
8820 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8821 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8822 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8823 |
- 'pointless-1.1.0.4']}, |
8824 |
- 'default':{ |
8825 |
- 'score':2, |
8826 |
- 'pipeline':{ |
8827 |
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} |
8828 |
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, |
8829 |
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', |
8830 |
- 'pointless-1.1.0.4']}, |
8831 |
- 'mosaic':{ |
8832 |
- 'score':1, |
8833 |
- 'pipeline':{ |
8834 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8835 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8836 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8837 |
- 'pointless-1.1.0.4']}, |
8838 |
- 'mosaic':{ |
8839 |
- 'score':2, |
8840 |
- 'pipeline':{ |
8841 |
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} |
8842 |
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, |
8843 |
- 'depends-on':['xds', 'xscale']} |
8844 |
- } |
8845 |
-diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py |
8846 |
-index 88f9218..5fb6f2a 100644 |
8847 |
---- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py |
8848 |
-+++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py |
8849 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
8850 |
- self.add_command_line(hklin) |
8851 |
- |
8852 |
- self.set_task('Rewriting reflections %s => %s' % |
8853 |
-- ` (os.path.split(hklin)[-1], |
8854 |
-- ` os.path.split(self.getHklout())[-1])) |
8855 |
-+ (os.path.split(hklin)[-1], |
8856 |
-+ os.path.split(self.getHklout())[-1])) |
8857 |
- |
8858 |
- self.start() |
8859 |
- |
8860 |
|
8861 |
diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch |
8862 |
deleted file mode 100644 |
8863 |
index ec8ada4..0000000 |
8864 |
--- a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch |
8865 |
+++ /dev/null |
8866 |
@@ -1,61 +0,0 @@ |
8867 |
-diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py |
8868 |
-index 1a3b0e2..e0b8a1e 100755 |
8869 |
---- a/xia2-0.3.1.7/Applications/xia2find.py |
8870 |
-+++ b/xia2-0.3.1.7/Applications/xia2find.py |
8871 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
8872 |
- from Experts.FindImages import image2template_directory |
8873 |
- |
8874 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
8875 |
-- 'osc', 'cbf', 'mar2000']] |
8876 |
-+ 'osc', 'cbf', 'mar2000'] |
8877 |
- known_sweeps = { } |
8878 |
- |
8879 |
- def is_image_name(file): |
8880 |
-diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py |
8881 |
-index 28b1dc3..dba3ef7 100644 |
8882 |
---- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py |
8883 |
-+++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py |
8884 |
-@@ -48,24 +48,24 @@ strategy_dict = { |
8885 |
- 'default':{ |
8886 |
- 'score':1, |
8887 |
- 'pipeline':{ |
8888 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8889 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8890 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8891 |
- 'pointless-1.1.0.4']}, |
8892 |
- 'default':{ |
8893 |
- 'score':2, |
8894 |
- 'pipeline':{ |
8895 |
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} |
8896 |
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, |
8897 |
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', |
8898 |
- 'pointless-1.1.0.4']}, |
8899 |
- 'mosaic':{ |
8900 |
- 'score':1, |
8901 |
- 'pipeline':{ |
8902 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8903 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8904 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8905 |
- 'pointless-1.1.0.4']}, |
8906 |
- 'mosaic':{ |
8907 |
- 'score':2, |
8908 |
- 'pipeline':{ |
8909 |
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} |
8910 |
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, |
8911 |
- 'depends-on':['xds', 'xscale']} |
8912 |
- } |
8913 |
-diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py |
8914 |
-index 88f9218..5fb6f2a 100644 |
8915 |
---- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py |
8916 |
-+++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py |
8917 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
8918 |
- self.add_command_line(hklin) |
8919 |
- |
8920 |
- self.set_task('Rewriting reflections %s => %s' % |
8921 |
-- ` (os.path.split(hklin)[-1], |
8922 |
-- ` os.path.split(self.getHklout())[-1])) |
8923 |
-+ (os.path.split(hklin)[-1], |
8924 |
-+ os.path.split(self.getHklout())[-1])) |
8925 |
- |
8926 |
- self.start() |
8927 |
- |
8928 |
|
8929 |
diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch |
8930 |
deleted file mode 100644 |
8931 |
index 36cf6bb..0000000 |
8932 |
--- a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch |
8933 |
+++ /dev/null |
8934 |
@@ -1,61 +0,0 @@ |
8935 |
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py |
8936 |
-index 1a3b0e2..e0b8a1e 100755 |
8937 |
---- a/xia2-0.3.3.1/Applications/xia2find.py |
8938 |
-+++ b/xia2-0.3.3.1/Applications/xia2find.py |
8939 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
8940 |
- from Experts.FindImages import image2template_directory |
8941 |
- |
8942 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
8943 |
-- 'osc', 'cbf', 'mar2000']] |
8944 |
-+ 'osc', 'cbf', 'mar2000'] |
8945 |
- known_sweeps = { } |
8946 |
- |
8947 |
- def is_image_name(file): |
8948 |
-diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py |
8949 |
-index 28b1dc3..dba3ef7 100644 |
8950 |
---- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py |
8951 |
-+++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py |
8952 |
-@@ -48,24 +48,24 @@ strategy_dict = { |
8953 |
- 'default':{ |
8954 |
- 'score':1, |
8955 |
- 'pipeline':{ |
8956 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8957 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8958 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8959 |
- 'pointless-1.1.0.4']}, |
8960 |
- 'default':{ |
8961 |
- 'score':2, |
8962 |
- 'pipeline':{ |
8963 |
-- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} |
8964 |
-+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, |
8965 |
- 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', |
8966 |
- 'pointless-1.1.0.4']}, |
8967 |
- 'mosaic':{ |
8968 |
- 'score':1, |
8969 |
- 'pipeline':{ |
8970 |
-- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} |
8971 |
-+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, |
8972 |
- 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', |
8973 |
- 'pointless-1.1.0.4']}, |
8974 |
- 'mosaic':{ |
8975 |
- 'score':2, |
8976 |
- 'pipeline':{ |
8977 |
-- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} |
8978 |
-+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, |
8979 |
- 'depends-on':['xds', 'xscale']} |
8980 |
- } |
8981 |
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py |
8982 |
-index 88f9218..5fb6f2a 100644 |
8983 |
---- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py |
8984 |
-+++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py |
8985 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
8986 |
- self.add_command_line(hklin) |
8987 |
- |
8988 |
- self.set_task('Rewriting reflections %s => %s' % |
8989 |
-- ` (os.path.split(hklin)[-1], |
8990 |
-- ` os.path.split(self.getHklout())[-1])) |
8991 |
-+ (os.path.split(hklin)[-1], |
8992 |
-+ os.path.split(self.getHklout())[-1])) |
8993 |
- |
8994 |
- self.start() |
8995 |
- |
8996 |
|
8997 |
diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch |
8998 |
deleted file mode 100644 |
8999 |
index 53cacbb..0000000 |
9000 |
--- a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch |
9001 |
+++ /dev/null |
9002 |
@@ -1,28 +0,0 @@ |
9003 |
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py |
9004 |
-index 1a3b0e2..e0b8a1e 100755 |
9005 |
---- a/xia2-0.3.3.3/Applications/xia2find.py |
9006 |
-+++ b/xia2-0.3.3.3/Applications/xia2find.py |
9007 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
9008 |
- from Experts.FindImages import image2template_directory |
9009 |
- |
9010 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
9011 |
-- 'osc', 'cbf', 'mar2000']] |
9012 |
-+ 'osc', 'cbf', 'mar2000'] |
9013 |
- known_sweeps = { } |
9014 |
- |
9015 |
- def is_image_name(file): |
9016 |
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py |
9017 |
-index 88f9218..5fb6f2a 100644 |
9018 |
---- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py |
9019 |
-+++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py |
9020 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
9021 |
- self.add_command_line(hklin) |
9022 |
- |
9023 |
- self.set_task('Rewriting reflections %s => %s' % |
9024 |
-- ` (os.path.split(hklin)[-1], |
9025 |
-- ` os.path.split(self.getHklout())[-1])) |
9026 |
-+ (os.path.split(hklin)[-1], |
9027 |
-+ os.path.split(self.getHklout())[-1])) |
9028 |
- |
9029 |
- self.start() |
9030 |
- |
9031 |
|
9032 |
diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch |
9033 |
deleted file mode 100644 |
9034 |
index 9ba4c94..0000000 |
9035 |
--- a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch |
9036 |
+++ /dev/null |
9037 |
@@ -1,28 +0,0 @@ |
9038 |
-diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py |
9039 |
-index 1a3b0e2..e0b8a1e 100755 |
9040 |
---- a/xia2-0.3.4.0/Applications/xia2find.py |
9041 |
-+++ b/xia2-0.3.4.0/Applications/xia2find.py |
9042 |
-@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory |
9043 |
- from Experts.FindImages import image2template_directory |
9044 |
- |
9045 |
- known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', |
9046 |
-- 'osc', 'cbf', 'mar2000']] |
9047 |
-+ 'osc', 'cbf', 'mar2000'] |
9048 |
- known_sweeps = { } |
9049 |
- |
9050 |
- def is_image_name(file): |
9051 |
-diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py |
9052 |
-index 88f9218..5fb6f2a 100644 |
9053 |
---- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py |
9054 |
-+++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py |
9055 |
-@@ -49,8 +49,8 @@ def Cad(DriverType = None): |
9056 |
- self.add_command_line(hklin) |
9057 |
- |
9058 |
- self.set_task('Rewriting reflections %s => %s' % |
9059 |
-- ` (os.path.split(hklin)[-1], |
9060 |
-- ` os.path.split(self.getHklout())[-1])) |
9061 |
-+ (os.path.split(hklin)[-1], |
9062 |
-+ os.path.split(self.getHklout())[-1])) |
9063 |
- |
9064 |
- self.start() |
9065 |
- |
9066 |
|
9067 |
diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml |
9068 |
deleted file mode 100644 |
9069 |
index 9ac9ffd..0000000 |
9070 |
--- a/sci-chemistry/xia2/metadata.xml |
9071 |
+++ /dev/null |
9072 |
@@ -1,5 +0,0 @@ |
9073 |
-<?xml version="1.0" encoding="UTF-8"?> |
9074 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
9075 |
-<pkgmetadata> |
9076 |
-<herd>sci-chemistry</herd> |
9077 |
-</pkgmetadata> |
9078 |
|
9079 |
diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild |
9080 |
deleted file mode 100644 |
9081 |
index 33b3d84..0000000 |
9082 |
--- a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild |
9083 |
+++ /dev/null |
9084 |
@@ -1,59 +0,0 @@ |
9085 |
-# Copyright 1999-2011 Gentoo Foundation |
9086 |
-# Distributed under the terms of the GNU General Public License v2 |
9087 |
-# $Id$ |
9088 |
- |
9089 |
-EAPI="3" |
9090 |
- |
9091 |
-inherit eutils python |
9092 |
- |
9093 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9094 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9095 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9096 |
- |
9097 |
-LICENSE="BSD" |
9098 |
-SLOT="0" |
9099 |
-KEYWORDS="~amd64 ~x86" |
9100 |
-IUSE="" |
9101 |
- |
9102 |
-RDEPEND=" |
9103 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9104 |
- sci-chemistry/mosflm |
9105 |
- sci-chemistry/pointless |
9106 |
- >=sci-libs/ccp4-libs-6.1.2 |
9107 |
- sci-libs/cctbx" |
9108 |
-DEPEND="${RDEPEND}" |
9109 |
- |
9110 |
-src_prepare() { |
9111 |
- find . -name '*.bat' | xargs rm || die |
9112 |
- |
9113 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9114 |
-} |
9115 |
- |
9116 |
-src_install() { |
9117 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9118 |
- |
9119 |
- insinto /usr/share/ccp4/XIAROOT/ |
9120 |
- doins -r * || die |
9121 |
- |
9122 |
- # Set programs executable |
9123 |
-# fperms cannot handle wildcards |
9124 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9125 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9126 |
- |
9127 |
- cat >> "${T}"/23XIA <<- EOF |
9128 |
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT |
9129 |
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} |
9130 |
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} |
9131 |
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications |
9132 |
- EOF |
9133 |
- |
9134 |
- doenvd "${T}"/23XIA |
9135 |
-} |
9136 |
- |
9137 |
-pkg_postinst() { |
9138 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9139 |
-} |
9140 |
- |
9141 |
-pkg_postrm() { |
9142 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9143 |
-} |
9144 |
|
9145 |
diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild |
9146 |
deleted file mode 100644 |
9147 |
index 537735e..0000000 |
9148 |
--- a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild |
9149 |
+++ /dev/null |
9150 |
@@ -1,66 +0,0 @@ |
9151 |
-# Copyright 1999-2011 Gentoo Foundation |
9152 |
-# Distributed under the terms of the GNU General Public License v2 |
9153 |
-# $Id$ |
9154 |
- |
9155 |
-EAPI="3" |
9156 |
- |
9157 |
-PYTHON_DEPEND="2" |
9158 |
- |
9159 |
-inherit eutils python |
9160 |
- |
9161 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9162 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9163 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9164 |
- |
9165 |
-LICENSE="BSD" |
9166 |
-SLOT="0" |
9167 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
9168 |
-IUSE="" |
9169 |
- |
9170 |
-RDEPEND=" |
9171 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9172 |
- sci-chemistry/mosflm |
9173 |
- sci-chemistry/pointless |
9174 |
- >=sci-libs/ccp4-libs-6.1.2 |
9175 |
- sci-libs/cctbx" |
9176 |
-DEPEND="${RDEPEND}" |
9177 |
- |
9178 |
-pkg_setup() { |
9179 |
- python_set_active_version 2 |
9180 |
-} |
9181 |
- |
9182 |
-src_prepare() { |
9183 |
- find . -name '*.bat' -delete || die |
9184 |
- |
9185 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9186 |
- python_convert_shebangs -r $(python_get_version) . |
9187 |
-} |
9188 |
- |
9189 |
-src_install() { |
9190 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9191 |
- |
9192 |
- insinto /usr/share/ccp4/XIAROOT/ |
9193 |
- doins -r * || die |
9194 |
- |
9195 |
- # Set programs executable |
9196 |
-# fperms cannot handle wildcards |
9197 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9198 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9199 |
- |
9200 |
- cat >> "${T}"/23XIA <<- EOF |
9201 |
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT |
9202 |
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} |
9203 |
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} |
9204 |
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications |
9205 |
- EOF |
9206 |
- |
9207 |
- doenvd "${T}"/23XIA |
9208 |
-} |
9209 |
- |
9210 |
-pkg_postinst() { |
9211 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9212 |
-} |
9213 |
- |
9214 |
-pkg_postrm() { |
9215 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9216 |
-} |
9217 |
|
9218 |
diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild |
9219 |
deleted file mode 100644 |
9220 |
index 16fbf79..0000000 |
9221 |
--- a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild |
9222 |
+++ /dev/null |
9223 |
@@ -1,66 +0,0 @@ |
9224 |
-# Copyright 1999-2011 Gentoo Foundation |
9225 |
-# Distributed under the terms of the GNU General Public License v2 |
9226 |
-# $Id$ |
9227 |
- |
9228 |
-EAPI="3" |
9229 |
- |
9230 |
-PYTHON_DEPEND="2" |
9231 |
- |
9232 |
-inherit eutils python |
9233 |
- |
9234 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9235 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9236 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9237 |
- |
9238 |
-LICENSE="BSD" |
9239 |
-SLOT="0" |
9240 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
9241 |
-IUSE="" |
9242 |
- |
9243 |
-RDEPEND=" |
9244 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9245 |
- sci-chemistry/mosflm |
9246 |
- sci-chemistry/pointless |
9247 |
- >=sci-libs/ccp4-libs-6.1.2 |
9248 |
- sci-libs/cctbx" |
9249 |
-DEPEND="${RDEPEND}" |
9250 |
- |
9251 |
-pkg_setup() { |
9252 |
- python_set_active_version 2 |
9253 |
-} |
9254 |
- |
9255 |
-src_prepare() { |
9256 |
- find . -name '*.bat' -delete || die |
9257 |
- |
9258 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9259 |
- python_convert_shebangs -r $(python_get_version) . |
9260 |
-} |
9261 |
- |
9262 |
-src_install() { |
9263 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9264 |
- |
9265 |
- insinto /usr/share/ccp4/XIAROOT/ |
9266 |
- doins -r * || die |
9267 |
- |
9268 |
- # Set programs executable |
9269 |
-# fperms cannot handle wildcards |
9270 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9271 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9272 |
- |
9273 |
- cat >> "${T}"/23XIA <<- EOF |
9274 |
- XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT |
9275 |
- XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} |
9276 |
- XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} |
9277 |
- PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications |
9278 |
- EOF |
9279 |
- |
9280 |
- doenvd "${T}"/23XIA |
9281 |
-} |
9282 |
- |
9283 |
-pkg_postinst() { |
9284 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9285 |
-} |
9286 |
- |
9287 |
-pkg_postrm() { |
9288 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9289 |
-} |
9290 |
|
9291 |
diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild |
9292 |
deleted file mode 100644 |
9293 |
index 26fb7d0..0000000 |
9294 |
--- a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild |
9295 |
+++ /dev/null |
9296 |
@@ -1,70 +0,0 @@ |
9297 |
-# Copyright 1999-2012 Gentoo Foundation |
9298 |
-# Distributed under the terms of the GNU General Public License v2 |
9299 |
-# $Id$ |
9300 |
- |
9301 |
-EAPI=3 |
9302 |
- |
9303 |
-PYTHON_DEPEND="2" |
9304 |
- |
9305 |
-inherit eutils python |
9306 |
- |
9307 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9308 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9309 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9310 |
- |
9311 |
-LICENSE="BSD" |
9312 |
-SLOT="0" |
9313 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
9314 |
-IUSE="" |
9315 |
- |
9316 |
-RDEPEND=" |
9317 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9318 |
- sci-chemistry/mosflm |
9319 |
- sci-chemistry/pointless |
9320 |
- >=sci-libs/ccp4-libs-6.1.2 |
9321 |
- sci-libs/cctbx" |
9322 |
-DEPEND="${RDEPEND}" |
9323 |
- |
9324 |
-pkg_setup() { |
9325 |
- python_set_active_version 2 |
9326 |
-} |
9327 |
- |
9328 |
-src_prepare() { |
9329 |
- find . -name '*.bat' -delete || die |
9330 |
- |
9331 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9332 |
- python_convert_shebangs -r $(python_get_version) . |
9333 |
-} |
9334 |
- |
9335 |
-src_install() { |
9336 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9337 |
- |
9338 |
- insinto /usr/share/ccp4/XIAROOT/ |
9339 |
- doins -r * || die |
9340 |
- |
9341 |
- # Set programs executable |
9342 |
-# fperms cannot handle wildcards |
9343 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9344 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9345 |
- |
9346 |
- cat >> "${T}"/23XIA <<- EOF |
9347 |
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" |
9348 |
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" |
9349 |
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" |
9350 |
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" |
9351 |
- EOF |
9352 |
- |
9353 |
- doenvd "${T}"/23XIA |
9354 |
-} |
9355 |
- |
9356 |
-pkg_postinst() { |
9357 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9358 |
- echo "" |
9359 |
- elog "In order to use the package, you need to" |
9360 |
- elog "\t source ${EPREFIX}/etc/profile" |
9361 |
- echo "" |
9362 |
-} |
9363 |
- |
9364 |
-pkg_postrm() { |
9365 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9366 |
-} |
9367 |
|
9368 |
diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild |
9369 |
deleted file mode 100644 |
9370 |
index 60778aa..0000000 |
9371 |
--- a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild |
9372 |
+++ /dev/null |
9373 |
@@ -1,70 +0,0 @@ |
9374 |
-# Copyright 1999-2011 Gentoo Foundation |
9375 |
-# Distributed under the terms of the GNU General Public License v2 |
9376 |
-# $Id$ |
9377 |
- |
9378 |
-EAPI=3 |
9379 |
- |
9380 |
-PYTHON_DEPEND="2" |
9381 |
- |
9382 |
-inherit eutils python |
9383 |
- |
9384 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9385 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9386 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9387 |
- |
9388 |
-LICENSE="BSD" |
9389 |
-SLOT="0" |
9390 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
9391 |
-IUSE="" |
9392 |
- |
9393 |
-RDEPEND=" |
9394 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9395 |
- sci-chemistry/mosflm |
9396 |
- sci-chemistry/pointless |
9397 |
- >=sci-libs/ccp4-libs-6.1.2 |
9398 |
- sci-libs/cctbx" |
9399 |
-DEPEND="${RDEPEND}" |
9400 |
- |
9401 |
-pkg_setup() { |
9402 |
- python_set_active_version 2 |
9403 |
-} |
9404 |
- |
9405 |
-src_prepare() { |
9406 |
- find . -name '*.bat' -delete || die |
9407 |
- |
9408 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9409 |
- python_convert_shebangs -r $(python_get_version) . |
9410 |
-} |
9411 |
- |
9412 |
-src_install() { |
9413 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9414 |
- |
9415 |
- insinto /usr/share/ccp4/XIAROOT/ |
9416 |
- doins -r * || die |
9417 |
- |
9418 |
- # Set programs executable |
9419 |
-# fperms cannot handle wildcards |
9420 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9421 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9422 |
- |
9423 |
- cat >> "${T}"/23XIA <<- EOF |
9424 |
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" |
9425 |
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" |
9426 |
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" |
9427 |
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" |
9428 |
- EOF |
9429 |
- |
9430 |
- doenvd "${T}"/23XIA |
9431 |
-} |
9432 |
- |
9433 |
-pkg_postinst() { |
9434 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9435 |
- echo "" |
9436 |
- elog "In order to use the package, you need to" |
9437 |
- elog "\t source ${EPREFIX}/etc/profile" |
9438 |
- echo "" |
9439 |
-} |
9440 |
- |
9441 |
-pkg_postrm() { |
9442 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9443 |
-} |
9444 |
|
9445 |
diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild |
9446 |
deleted file mode 100644 |
9447 |
index 1d27abd..0000000 |
9448 |
--- a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild |
9449 |
+++ /dev/null |
9450 |
@@ -1,70 +0,0 @@ |
9451 |
-# Copyright 1999-2012 Gentoo Foundation |
9452 |
-# Distributed under the terms of the GNU General Public License v2 |
9453 |
-# $Id$ |
9454 |
- |
9455 |
-EAPI=3 |
9456 |
- |
9457 |
-PYTHON_DEPEND="2" |
9458 |
- |
9459 |
-inherit eutils python |
9460 |
- |
9461 |
-DESCRIPTION="An automated data reduction system for crystallography" |
9462 |
-HOMEPAGE="http://www.ccp4.ac.uk/xia/" |
9463 |
-SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" |
9464 |
- |
9465 |
-LICENSE="BSD" |
9466 |
-SLOT="0" |
9467 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" |
9468 |
-IUSE="" |
9469 |
- |
9470 |
-RDEPEND=" |
9471 |
- >=sci-chemistry/ccp4-apps-6.1.2 |
9472 |
- sci-chemistry/mosflm |
9473 |
- sci-chemistry/pointless |
9474 |
- >=sci-libs/ccp4-libs-6.1.2 |
9475 |
- sci-libs/cctbx" |
9476 |
-DEPEND="${RDEPEND}" |
9477 |
- |
9478 |
-pkg_setup() { |
9479 |
- python_set_active_version 2 |
9480 |
-} |
9481 |
- |
9482 |
-src_prepare() { |
9483 |
- find . -name '*.bat' -delete || die |
9484 |
- |
9485 |
- epatch "${FILESDIR}"/${PV}-fix-syntax.patch |
9486 |
- python_convert_shebangs -r $(python_get_version) . |
9487 |
-} |
9488 |
- |
9489 |
-src_install() { |
9490 |
- rm -rf ${P}/binaries ${PN}core-${PV}/Test || die |
9491 |
- |
9492 |
- insinto /usr/share/ccp4/XIAROOT/ |
9493 |
- doins -r * || die |
9494 |
- |
9495 |
- # Set programs executable |
9496 |
-# fperms cannot handle wildcards |
9497 |
- chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die |
9498 |
- chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die |
9499 |
- |
9500 |
- cat >> "${T}"/23XIA <<- EOF |
9501 |
- XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" |
9502 |
- XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" |
9503 |
- XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" |
9504 |
- PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" |
9505 |
- EOF |
9506 |
- |
9507 |
- doenvd "${T}"/23XIA |
9508 |
-} |
9509 |
- |
9510 |
-pkg_postinst() { |
9511 |
- python_mod_optimize /usr/share/ccp4/XIAROOT |
9512 |
- echo "" |
9513 |
- elog "In order to use the package, you need to" |
9514 |
- elog "\t source ${EPREFIX}/etc/profile" |
9515 |
- echo "" |
9516 |
-} |
9517 |
- |
9518 |
-pkg_postrm() { |
9519 |
- python_mod_cleanup /usr/share/ccp4/XIAROOT |
9520 |
-} |
9521 |
|
9522 |
diff --git a/sci-libs/balbes-db/Manifest b/sci-libs/balbes-db/Manifest |
9523 |
deleted file mode 100644 |
9524 |
index 86fed7e..0000000 |
9525 |
--- a/sci-libs/balbes-db/Manifest |
9526 |
+++ /dev/null |
9527 |
@@ -1 +0,0 @@ |
9528 |
-DIST ccp4-6.1.3-balbesdb-10-11-08.tar.gz 600856059 SHA256 5606fc5e131138b56fa3a1afce014225a6c07826b99587f132f6c337585f4f0d SHA512 5b7f3b3465312da72ff4816c96244252a6f0bf039fde8ff772ea683e6317053d903cdc2b3b86b78e8edbb1c766d1b3676048ac4e7d4d0db29ed7bf62dfb00ab2 WHIRLPOOL 9a01610c9767aece4c9cc052a8aa2fd5dff9c9967f11688f5e6e206a82e2714751e086a7ddbe6a99da23b70163c7b096f57d281eebe53b8dd7cdb18faed23d63 |
9529 |
|
9530 |
diff --git a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild |
9531 |
deleted file mode 100644 |
9532 |
index bd973c5..0000000 |
9533 |
--- a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild |
9534 |
+++ /dev/null |
9535 |
@@ -1,47 +0,0 @@ |
9536 |
-# Copyright 1999-2015 Gentoo Foundation |
9537 |
-# Distributed under the terms of the GNU General Public License v2 |
9538 |
-# $Id$ |
9539 |
- |
9540 |
-EAPI=5 |
9541 |
- |
9542 |
-MY_P="ccp4-${PV}" |
9543 |
- |
9544 |
-SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
9545 |
-VERSION="10-11-08" |
9546 |
- |
9547 |
-DESCRIPTION="The database for the BALBES automated crystallographic molecular replacement pipeline" |
9548 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/" |
9549 |
-SRC_URI="${SRC}/${PV}/${MY_P}-${PN/-/}-${VERSION}.tar.gz" |
9550 |
- |
9551 |
-LICENSE="ccp4" |
9552 |
-SLOT="0" |
9553 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
9554 |
-IUSE="" |
9555 |
- |
9556 |
-RDEPEND=" |
9557 |
- >=dev-python/pyxml-0.8.4 |
9558 |
- sci-libs/monomer-db" |
9559 |
-DEPEND="${RDEPEND}" |
9560 |
-RESTRICT="binchecks strip" |
9561 |
- |
9562 |
-S="${WORKDIR}/${MY_P}" |
9563 |
- |
9564 |
-src_install() { |
9565 |
- dodir /usr/share/balbes/BALBES_0.0.1 |
9566 |
- rm -rf share/balbes/BALBES_0.0.1/dic || die |
9567 |
- # We don't want to wait around to copy all this, or suck up double |
9568 |
- # the disk space |
9569 |
- einfo "Installing files, which can take some time ..." |
9570 |
- mv "${S}"/share/balbes/BALBES_0.0.1/* "${ED}"/usr/share/balbes/BALBES_0.0.1/ || die |
9571 |
- # db files shouldn't be executable |
9572 |
- find "${ED}"/usr/share/balbes/BALBES_0.0.1/ \ |
9573 |
- -type f \ |
9574 |
- -exec chmod 664 '{}' \; || die |
9575 |
- dosym ../../ccp4/data/monomers /usr/share/balbes/BALBES_0.0.1/dic |
9576 |
- |
9577 |
- cat >> "${T}"/20balbes <<- EOF |
9578 |
- BALBES_ROOT="${EPREFIX}/usr/share/balbes/BALBES_0.0.1/" |
9579 |
- EOF |
9580 |
- |
9581 |
- doenvd "${T}"/20balbes |
9582 |
-} |
9583 |
|
9584 |
diff --git a/sci-libs/balbes-db/metadata.xml b/sci-libs/balbes-db/metadata.xml |
9585 |
deleted file mode 100644 |
9586 |
index 51fdeda..0000000 |
9587 |
--- a/sci-libs/balbes-db/metadata.xml |
9588 |
+++ /dev/null |
9589 |
@@ -1,5 +0,0 @@ |
9590 |
-<?xml version="1.0" encoding="UTF-8"?> |
9591 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
9592 |
-<pkgmetadata> |
9593 |
- <herd>sci-chemistry</herd> |
9594 |
-</pkgmetadata> |
9595 |
|
9596 |
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest |
9597 |
deleted file mode 100644 |
9598 |
index 9d3fe28..0000000 |
9599 |
--- a/sci-libs/ccp4-libs/Manifest |
9600 |
+++ /dev/null |
9601 |
@@ -1 +0,0 @@ |
9602 |
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c |
9603 |
|
9604 |
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild |
9605 |
deleted file mode 100644 |
9606 |
index dcd7416..0000000 |
9607 |
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild |
9608 |
+++ /dev/null |
9609 |
@@ -1,359 +0,0 @@ |
9610 |
-# Copyright 1999-2015 Gentoo Foundation |
9611 |
-# Distributed under the terms of the GNU General Public License v2 |
9612 |
-# $Id$ |
9613 |
- |
9614 |
-EAPI=5 |
9615 |
- |
9616 |
-PYTHON_COMPAT=( python2_7 ) |
9617 |
- |
9618 |
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs |
9619 |
- |
9620 |
-SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
9621 |
- |
9622 |
-#UPDATE="04_03_09" |
9623 |
-#PATCHDATE="090511" |
9624 |
- |
9625 |
-MY_P="${P/-libs}" |
9626 |
- |
9627 |
-PATCH_TOT="0" |
9628 |
- |
9629 |
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries" |
9630 |
-HOMEPAGE="http://www.ccp4.ac.uk/" |
9631 |
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" |
9632 |
-# patch tarball from upstream |
9633 |
- [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
9634 |
-# patches created by us |
9635 |
- [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
9636 |
- |
9637 |
-for i in $(seq $PATCH_TOT); do |
9638 |
- NAME="PATCH${i}[1]" |
9639 |
- SRC_URI="${SRC_URI} |
9640 |
- ${SRC}/${PV}/patches/${!NAME}" |
9641 |
-done |
9642 |
- |
9643 |
-LICENSE="ccp4" |
9644 |
-SLOT="0" |
9645 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
9646 |
-IUSE="minimal" |
9647 |
- |
9648 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
9649 |
- |
9650 |
-RDEPEND=" |
9651 |
- ${PYTHON_DEPS} |
9652 |
- !<sci-chemistry/ccp4-6.1.3 |
9653 |
- !<sci-chemistry/ccp4-apps-${PV}-r10 |
9654 |
- app-shells/tcsh |
9655 |
- dev-lang/tcl:0 |
9656 |
- >=sci-libs/cbflib-0.9.2.2 |
9657 |
- sci-libs/fftw:2.1 |
9658 |
- sci-libs/mmdb:0 |
9659 |
- sci-libs/monomer-db |
9660 |
- sci-libs/ssm |
9661 |
- virtual/jpeg:0= |
9662 |
- virtual/lapack |
9663 |
- virtual/blas" |
9664 |
-DEPEND="${RDEPEND} |
9665 |
- virtual/pkgconfig" |
9666 |
- |
9667 |
-S="${WORKDIR}/${MY_P}" |
9668 |
- |
9669 |
-MAKEOPTS+=" -j1" |
9670 |
- |
9671 |
-pkg_setup() { |
9672 |
- fortran-2_pkg_setup |
9673 |
- python-single-r1_pkg_setup |
9674 |
-} |
9675 |
- |
9676 |
-src_prepare() { |
9677 |
- tc-export PKG_CONFIG RANLIB AR |
9678 |
- |
9679 |
- sed \ |
9680 |
- -e "/^AR/s:ar:$(tc-getAR):g" \ |
9681 |
- -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die |
9682 |
- |
9683 |
- einfo "Applying upstream patches ..." |
9684 |
- for patch in $(seq $PATCH_TOT); do |
9685 |
- base="PATCH${patch}" |
9686 |
- dir=$(eval echo \${${base}[0]}) |
9687 |
- p=$(eval echo \${${base}[1]}) |
9688 |
- pushd "${dir}" >& /dev/null |
9689 |
- ccp_patch "${DISTDIR}/${p}" |
9690 |
- popd >& /dev/null |
9691 |
- done |
9692 |
- einfo "Done." |
9693 |
- echo |
9694 |
- |
9695 |
- [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
9696 |
- |
9697 |
- einfo "Applying Gentoo patches ..." |
9698 |
- # fix buffer overflows wrt bug 339706 |
9699 |
- ccp_patch "${FILESDIR}"/${PV}-overflows.patch |
9700 |
- |
9701 |
- # it tries to create libdir, bindir etc on live system in configure |
9702 |
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
9703 |
- |
9704 |
- # gerror_ gets defined twice on ppc if you're using gfortran/g95 |
9705 |
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch |
9706 |
- |
9707 |
- # make creation of libccif.so smooth |
9708 |
- ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch |
9709 |
- |
9710 |
- # lets try to build libmmdb seperatly |
9711 |
- ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch |
9712 |
- |
9713 |
- # unbundle libjpeg and cbflib |
9714 |
- ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch |
9715 |
- |
9716 |
- # Fix missing DESTIDR |
9717 |
- # not installing during build |
9718 |
- ccp_patch "${FILESDIR}"/${PV}-noinstall.patch |
9719 |
- sed \ |
9720 |
- -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ |
9721 |
- -i configure || die |
9722 |
- |
9723 |
- # Fix upstreams code |
9724 |
- ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch |
9725 |
- |
9726 |
- # use pkg-config to detect BLAS/LAPACK |
9727 |
- ccp_patch "${FILESDIR}"/${PV}-lapack.patch |
9728 |
- |
9729 |
- # proto type changing in version 0.9.2.2 |
9730 |
- ccp_patch "${FILESDIR}"/${PV}-cbf.patch |
9731 |
- |
9732 |
- # proto type changing in version 0.9.2.2 |
9733 |
- ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch |
9734 |
- |
9735 |
- ccp_patch "${FILESDIR}"/${P}-force.patch |
9736 |
- |
9737 |
- ccp_patch "${FILESDIR}"/${P}-format-security.patch |
9738 |
- |
9739 |
- einfo "Done." # done applying Gentoo patches |
9740 |
- echo |
9741 |
- |
9742 |
- # not needed, we have it extra |
9743 |
- rm -rf src/rapper/{libxml2,gc7.0} || die |
9744 |
- |
9745 |
- sed \ |
9746 |
- -e "s:/usr:${EPREFIX}/usr:g" \ |
9747 |
- -e 's:-Wl,-rpath,$CLIB::g' \ |
9748 |
- -e 's: -rpath $CLIB::g' \ |
9749 |
- -e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
9750 |
- -e 's:sleep 1:sleep .2:g' \ |
9751 |
- -i configure || die |
9752 |
- |
9753 |
- gnuconfig_update |
9754 |
- |
9755 |
- for i in lib/DiffractionImage src/rapper src/pisa; do |
9756 |
- pushd ${i} > /dev/null |
9757 |
- sed 's:-g::g' -i configure* || die |
9758 |
- [[ -f configure.in ]] && mv configure.{in,ac} |
9759 |
- eautoreconf |
9760 |
- popd > /dev/null |
9761 |
- done |
9762 |
- |
9763 |
- ## unbundle libssm |
9764 |
- sed -e '/libdir/s:ssm::g' -i Makefile.in || die |
9765 |
- find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die |
9766 |
-} |
9767 |
- |
9768 |
-src_configure() { |
9769 |
- rm -rf lib/DiffractionImage/{jpg,CBFlib} || die |
9770 |
- |
9771 |
- # Build system is broken if we set LDFLAGS |
9772 |
- userldflags="${LDFLAGS}" |
9773 |
- export SHARED_LIB_FLAGS="${LDFLAGS}" |
9774 |
- unset LDFLAGS |
9775 |
- |
9776 |
- # GENTOO_OSNAME can be one of: |
9777 |
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
9778 |
- # linux_compaq_compilers linux_intel_compilers generic Darwin |
9779 |
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
9780 |
- if [[ "$(tc-getFC)" = "ifort" ]]; then |
9781 |
- if use ia64; then |
9782 |
- GENTOO_OSNAME="ia64_linux_intel" |
9783 |
- else |
9784 |
- # Should be valid for x86, maybe amd64 |
9785 |
- GENTOO_OSNAME="linux_intel_compilers" |
9786 |
- fi |
9787 |
- else |
9788 |
- # Should be valid for x86 and amd64, at least |
9789 |
- GENTOO_OSNAME="linux" |
9790 |
- fi |
9791 |
- |
9792 |
- # Sets up env |
9793 |
- ln -s \ |
9794 |
- ccp4.setup-bash \ |
9795 |
- "${S}"/include/ccp4.setup || die |
9796 |
- |
9797 |
- # We agree to the license by emerging this, set in LICENSE |
9798 |
- sed -i \ |
9799 |
- -e "s~^\(^agreed=\).*~\1yes~g" \ |
9800 |
- "${S}"/configure || die |
9801 |
- |
9802 |
- # Fix up variables -- need to reset CCP4_MASTER at install-time |
9803 |
- sed -i \ |
9804 |
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
9805 |
- -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
9806 |
- -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
9807 |
- -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
9808 |
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
9809 |
- "${S}"/include/ccp4.setup* || die |
9810 |
- |
9811 |
- # Set up variables for build |
9812 |
- source "${S}"/include/ccp4.setup-sh |
9813 |
- |
9814 |
- export CC=$(tc-getCC) |
9815 |
- export CXX=$(tc-getCXX) |
9816 |
- export COPTIM=${CFLAGS} |
9817 |
- export CXXOPTIM=${CXXFLAGS} |
9818 |
- # Default to -O2 if FFLAGS is unset |
9819 |
- export FC=$(tc-getFC) |
9820 |
- export FOPTIM=${FFLAGS:- -O2} |
9821 |
- |
9822 |
- export SHARE_LIB="\ |
9823 |
- $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ |
9824 |
- $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" |
9825 |
- |
9826 |
- # Can't use econf, configure rejects unknown options like --prefix |
9827 |
- ./configure \ |
9828 |
- --onlylibs \ |
9829 |
- --with-shared-libs \ |
9830 |
- --with-fftw="${EPREFIX}/usr" \ |
9831 |
- --with-warnings \ |
9832 |
- --disable-cctbx \ |
9833 |
- --disable-clipper \ |
9834 |
- --disable-ssm \ |
9835 |
- --tmpdir="${TMPDIR}" \ |
9836 |
- --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \ |
9837 |
- --libdir="${EPREFIX}/usr/$(get_libdir)" \ |
9838 |
- ${GENTOO_OSNAME} || die "configure failed" |
9839 |
-} |
9840 |
- |
9841 |
-src_compile() { |
9842 |
- emake DESTDIR="${D}" onlylib |
9843 |
-} |
9844 |
- |
9845 |
-src_install() { |
9846 |
- # Set up variables for build |
9847 |
- source "${S}"/include/ccp4.setup-sh |
9848 |
- |
9849 |
- emake \ |
9850 |
- DESTDIR="${D}" \ |
9851 |
- includedir="${EPREFIX}/usr/include" \ |
9852 |
- library_includedir="${EPREFIX}/usr/include" \ |
9853 |
- install |
9854 |
- |
9855 |
- sed \ |
9856 |
- -e "330,1000d" \ |
9857 |
- -i "${S}"/include/ccp4.setup-sh || die |
9858 |
- |
9859 |
- sed \ |
9860 |
- -e "378,1000d" \ |
9861 |
- -i "${S}"/include/ccp4.setup-csh || die |
9862 |
- |
9863 |
- sed \ |
9864 |
- -e "s:-${PV/-r*/}::g" \ |
9865 |
- -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \ |
9866 |
- -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \ |
9867 |
- -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \ |
9868 |
- -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \ |
9869 |
- -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \ |
9870 |
- -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \ |
9871 |
- -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \ |
9872 |
- -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \ |
9873 |
- -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ |
9874 |
- -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ |
9875 |
- -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \ |
9876 |
- -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \ |
9877 |
- -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ |
9878 |
- -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ |
9879 |
- -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
9880 |
- -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
9881 |
- -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
9882 |
- -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ |
9883 |
- -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
9884 |
- -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
9885 |
- -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ |
9886 |
- -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ |
9887 |
- -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
9888 |
- -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ |
9889 |
- -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \ |
9890 |
- -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \ |
9891 |
- -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \ |
9892 |
- -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \ |
9893 |
- -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ |
9894 |
- -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ |
9895 |
- -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
9896 |
- -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ |
9897 |
- -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \ |
9898 |
- -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \ |
9899 |
- -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \ |
9900 |
- -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \ |
9901 |
- -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ |
9902 |
- -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ |
9903 |
- -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \ |
9904 |
- -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \ |
9905 |
- -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \ |
9906 |
- -e '/CLIB=/d' \ |
9907 |
- -e '/CLIB /d' \ |
9908 |
- -e '/CLIBS=/d' \ |
9909 |
- -e '/CLIBS /d' \ |
9910 |
- -e "/alias/d" \ |
9911 |
- -e "/CCP4_HELPDIR/d" \ |
9912 |
- -e "/IMOSFLM_VERSION/d" \ |
9913 |
- -i "${S}"/include/ccp4.setup* || die |
9914 |
- |
9915 |
- # Don't check for updates on every sourcing of /etc/profile |
9916 |
- sed -i \ |
9917 |
- -e "s:\(eval python.*\):#\1:g" \ |
9918 |
- "${S}"/include/ccp4.setup* || die |
9919 |
- |
9920 |
- # Libs |
9921 |
- for file in "${S}"/lib/*; do |
9922 |
- if [[ -d ${file} ]]; then |
9923 |
- continue |
9924 |
- elif [[ -x ${file} ]]; then |
9925 |
- dolib.so ${file} |
9926 |
- else |
9927 |
- insinto /usr/$(get_libdir) |
9928 |
- doins ${file} |
9929 |
- fi |
9930 |
- done |
9931 |
- |
9932 |
- prune_libtool_files |
9933 |
- |
9934 |
- sed \ |
9935 |
- -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ |
9936 |
- -i "${S}"/include/ccp4.setup-sh || die |
9937 |
- |
9938 |
- if ! use minimal; then |
9939 |
- # Setup scripts |
9940 |
- insinto /etc/profile.d |
9941 |
- newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh |
9942 |
- newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh |
9943 |
- |
9944 |
- # Data |
9945 |
- insinto /usr/share/ccp4/data/ |
9946 |
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} |
9947 |
- |
9948 |
- # Environment files, setup scripts, etc. |
9949 |
- rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die |
9950 |
- insinto /usr/share/ccp4/ |
9951 |
- doins -r "${S}"/include |
9952 |
- fi |
9953 |
- |
9954 |
- rm -f "${S}"/include/ccp4.setup* || die |
9955 |
- |
9956 |
- dodoc "${S}"/lib/data/*.doc |
9957 |
- newdoc "${S}"/lib/data/README DATA-README |
9958 |
-} |
9959 |
- |
9960 |
-pkg_postinst() { |
9961 |
- einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" |
9962 |
- einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this." |
9963 |
-} |
9964 |
- |
9965 |
-# Epatch wrapper for bulk patching |
9966 |
-ccp_patch() { |
9967 |
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
9968 |
-} |
9969 |
|
9970 |
diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch |
9971 |
deleted file mode 100644 |
9972 |
index a77d949..0000000 |
9973 |
--- a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch |
9974 |
+++ /dev/null |
9975 |
@@ -1,11 +0,0 @@ |
9976 |
---- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 |
9977 |
-+++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 |
9978 |
-@@ -716,7 +716,7 @@ |
9979 |
- |
9980 |
- #endif /* end of apple xlf support */ |
9981 |
- |
9982 |
--#if ( defined (__linux__) && defined (_CALL_SYSV) ) |
9983 |
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) |
9984 |
- /* linuxppc xlf support */ |
9985 |
- void gerror_ (str, Lstr) |
9986 |
- char *str; |
9987 |
|
9988 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch |
9989 |
deleted file mode 100644 |
9990 |
index 6930fca..0000000 |
9991 |
--- a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch |
9992 |
+++ /dev/null |
9993 |
@@ -1,16 +0,0 @@ |
9994 |
- lib/DiffractionImage/DiffractionImageCBF.cpp | 2 +- |
9995 |
- 1 files changed, 1 insertions(+), 1 deletions(-) |
9996 |
- |
9997 |
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp |
9998 |
-index 69b32b0..3ffee26 100755 |
9999 |
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp |
10000 |
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp |
10001 |
-@@ -62,7 +62,7 @@ namespace DI |
10002 |
- int* tmpimg; |
10003 |
- tmpimg=new int[height*width]; |
10004 |
- test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign, |
10005 |
-- nelements,&nread,0,32,sign,ccbbff,0, |
10006 |
-+ nelements,&nread,0,0,32,sign,ccbbff,0, |
10007 |
- byte_ord.c_str(),2,(size_t) width, |
10008 |
- (size_t) height,1,(size_t) padding); |
10009 |
- for(int i=0;i<height*width;i++) |
10010 |
|
10011 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch |
10012 |
deleted file mode 100644 |
10013 |
index ca18d75..0000000 |
10014 |
--- a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch |
10015 |
+++ /dev/null |
10016 |
@@ -1,33 +0,0 @@ |
10017 |
---- configure 2009-08-04 22:35:34.000000000 +0200 |
10018 |
-+++ configure.new 2009-08-04 22:54:32.000000000 +0200 |
10019 |
-@@ -3136,8 +3136,8 @@ |
10020 |
- fi |
10021 |
- ( touch /tmp/$$.cache_file 2>/dev/null && \ |
10022 |
- cat /dev/null > /tmp/$$.cache_file && \ |
10023 |
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ |
10024 |
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif |
10025 |
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \ |
10026 |
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib |
10027 |
- rm -f /tmp/$$.cache_file |
10028 |
- if [ "X$LIBFOPTIM" != "X" ]; then |
10029 |
- FOPTIM=$FOPTIM_save |
10030 |
---- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200 |
10031 |
-+++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200 |
10032 |
-@@ -5568,7 +5568,7 @@ |
10033 |
- enable_shared_lib=no |
10034 |
- ;; |
10035 |
- |
10036 |
-- i?86-unknown-linux | i?86-pc-linux-gnu ) |
10037 |
-+ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu) |
10038 |
- if test $enable_shared_lib = yes ; then |
10039 |
- |
10040 |
- SO_LOC_VAR='LD_LIBRARY_PATH' |
10041 |
-@@ -5585,7 +5585,7 @@ |
10042 |
- else |
10043 |
- SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`' |
10044 |
- fi |
10045 |
-- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)' |
10046 |
-+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm' |
10047 |
- # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)' |
10048 |
- SHARED_LIB_EXPORTS_CMD='' |
10049 |
- fi |
10050 |
|
10051 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch |
10052 |
deleted file mode 100644 |
10053 |
index b3147ad..0000000 |
10054 |
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch |
10055 |
+++ /dev/null |
10056 |
@@ -1,24 +0,0 @@ |
10057 |
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in |
10058 |
-index c23f488..b32dd1e 100755 |
10059 |
---- a/lib/src/Makefile.in |
10060 |
-+++ b/lib/src/Makefile.in |
10061 |
-@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h $(mmdbsrcdir)/hybrid_36.h |
10062 |
- |
10063 |
- ##### Makefile targets ###### |
10064 |
- |
10065 |
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES) |
10066 |
-+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES) |
10067 |
- # maybe create shared library |
10068 |
- $(SHARE_LIB) |
10069 |
- |
10070 |
-@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS: |
10071 |
- done |
10072 |
- |
10073 |
- install : all install-ccp4HEADERS install-mmdbHEADERS |
10074 |
-- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB) |
10075 |
- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) |
10076 |
- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) |
10077 |
-- $(RANLIB) $(libdir)/$(LMMDB) |
10078 |
- $(RANLIB) $(libdir)/$(LC) |
10079 |
- $(RANLIB) $(libdir)/$(LF) |
10080 |
- $(SHARE_INST) |
10081 |
|
10082 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch |
10083 |
deleted file mode 100644 |
10084 |
index 583697c..0000000 |
10085 |
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch |
10086 |
+++ /dev/null |
10087 |
@@ -1,87 +0,0 @@ |
10088 |
---- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 |
10089 |
-+++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 |
10090 |
-@@ -643,45 +643,45 @@ |
10091 |
- # echo "! Beware -- the $system installation isn't properly tested." ; } |
10092 |
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' |
10093 |
- |
10094 |
--if test -z "$onlylibs" ; then |
10095 |
-- for i in CCP4_SCR BINSORT_SCR; do |
10096 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
10097 |
-- else |
10098 |
-- eval echo "! No directory \$$i and can\'t create it." |
10099 |
-- echo " Check the value of $i." |
10100 |
-- badvar=1 |
10101 |
-- fi |
10102 |
-- done |
10103 |
-- |
10104 |
-- for i in libdir bindir includedir; do |
10105 |
-- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
10106 |
-- else |
10107 |
-- eval echo "! No directory \$$i and can\'t create it." |
10108 |
-- echo " Check the argument of --$i." |
10109 |
-- badvar=1 |
10110 |
-- fi |
10111 |
-- done |
10112 |
-- |
10113 |
-- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
10114 |
-- if test -d $i || mkdir $i; then : |
10115 |
-- else |
10116 |
-- eval echo "! No directory $i and can\'t create it." |
10117 |
-- badvar=1 |
10118 |
-- fi |
10119 |
-- done |
10120 |
--else |
10121 |
-- # Kludge to fool the "Makefile" target in the top-level CCP4 |
10122 |
-- # Makefile into not trying to remake src/Makefile.in |
10123 |
-- for i in $srcdir/src $srcdir/lib/src ; do |
10124 |
-- if test -d $i || mkdir $i; then |
10125 |
-- if ! test -f $i/Makefile.in ; then |
10126 |
-- echo |
10127 |
-- echo "onlylibs: making dummy file $i/Makefile.in" |
10128 |
-- touch $i/Makefile.in |
10129 |
-- fi |
10130 |
-- fi |
10131 |
-- done |
10132 |
--fi |
10133 |
-+#if test -z "$onlylibs" ; then |
10134 |
-+# for i in CCP4_SCR BINSORT_SCR; do |
10135 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
10136 |
-+# else |
10137 |
-+# eval echo "! No directory \$$i and can\'t create it." |
10138 |
-+# echo " Check the value of $i." |
10139 |
-+# badvar=1 |
10140 |
-+# fi |
10141 |
-+# done |
10142 |
-+# |
10143 |
-+# for i in libdir bindir includedir; do |
10144 |
-+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : |
10145 |
-+# else |
10146 |
-+# eval echo "! No directory \$$i and can\'t create it." |
10147 |
-+# echo " Check the argument of --$i." |
10148 |
-+# badvar=1 |
10149 |
-+# fi |
10150 |
-+# done |
10151 |
-+# |
10152 |
-+# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do |
10153 |
-+# if test -d $i || mkdir $i; then : |
10154 |
-+# else |
10155 |
-+# eval echo "! No directory $i and can\'t create it." |
10156 |
-+# badvar=1 |
10157 |
-+# fi |
10158 |
-+# done |
10159 |
-+#else |
10160 |
-+# # Kludge to fool the "Makefile" target in the top-level CCP4 |
10161 |
-+# # Makefile into not trying to remake src/Makefile.in |
10162 |
-+# for i in $srcdir/src $srcdir/lib/src ; do |
10163 |
-+# if test -d $i || mkdir $i; then |
10164 |
-+# if ! test -f $i/Makefile.in ; then |
10165 |
-+# echo |
10166 |
-+# echo "onlylibs: making dummy file $i/Makefile.in" |
10167 |
-+# touch $i/Makefile.in |
10168 |
-+# fi |
10169 |
-+# fi |
10170 |
-+# done |
10171 |
-+#fi |
10172 |
- |
10173 |
- ### sanity checks |
10174 |
- |
10175 |
|
10176 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch |
10177 |
deleted file mode 100644 |
10178 |
index 6e39976..0000000 |
10179 |
--- a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch |
10180 |
+++ /dev/null |
10181 |
@@ -1,22 +0,0 @@ |
10182 |
---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200 |
10183 |
-+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200 |
10184 |
-@@ -363,7 +363,7 @@ |
10185 |
- fi |
10186 |
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\ |
10187 |
- --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\ |
10188 |
-- $(RX_LFLAG) -o $(SHARED_LIB_NAME)' |
10189 |
-+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm' |
10190 |
- SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)' |
10191 |
- fi |
10192 |
- ;; |
10193 |
---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200 |
10194 |
-+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200 |
10195 |
-@@ -1807,7 +1807,7 @@ |
10196 |
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\ |
10197 |
- $(SHARED_LIB_NAME) \\\ |
10198 |
- --whole-archive $L \\\ |
10199 |
-- -o $(SHARED_LIB_NAME)' |
10200 |
-+ -o $(SHARED_LIB_NAME) -lm' |
10201 |
- SHARED_LIB_EXPORTS_CMD='' |
10202 |
- fi |
10203 |
- ;; |
10204 |
|
10205 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch |
10206 |
deleted file mode 100644 |
10207 |
index 8bfa7db..0000000 |
10208 |
--- a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch |
10209 |
+++ /dev/null |
10210 |
@@ -1,140 +0,0 @@ |
10211 |
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c |
10212 |
-index bfda882..f821e04 100755 |
10213 |
---- a/lib/DiffractionImage/Bruker/FRM_LIB.c |
10214 |
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c |
10215 |
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. |
10216 |
- #include "sys/types.h" /* _open, etc. */ |
10217 |
- #include "sys/stat.h" /* _open, etc. */ |
10218 |
- |
10219 |
-+#include <unistd.h> |
10220 |
-+ |
10221 |
- #ifndef _MSC_VER |
10222 |
- int min(int a, int b) |
10223 |
- { |
10224 |
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c |
10225 |
-index 1a933de..1c40c32 100755 |
10226 |
---- a/lib/DiffractionImage/MAR/mar300_header.c |
10227 |
-+++ b/lib/DiffractionImage/MAR/mar300_header.c |
10228 |
-@@ -23,6 +23,9 @@ |
10229 |
- */ |
10230 |
- #include "mar300_header.h" |
10231 |
- |
10232 |
-+#include <sys/types.h> |
10233 |
-+#include <unistd.h> |
10234 |
-+ |
10235 |
- /* |
10236 |
- * Local functions |
10237 |
- */ |
10238 |
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c |
10239 |
-index a8351ea..16d0f7b 100755 |
10240 |
---- a/lib/DiffractionImage/MAR/mar345_header.c |
10241 |
-+++ b/lib/DiffractionImage/MAR/mar345_header.c |
10242 |
-@@ -32,6 +32,9 @@ |
10243 |
- */ |
10244 |
- #include "mar345_header.h" |
10245 |
- |
10246 |
-+#include <sys/types.h> |
10247 |
-+#include <unistd.h> |
10248 |
-+ |
10249 |
- /* |
10250 |
- * Definitions |
10251 |
- */ |
10252 |
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c |
10253 |
-index 07f2741..6364ca4 100755 |
10254 |
---- a/lib/DiffractionImage/MAR/nb_header.c |
10255 |
-+++ b/lib/DiffractionImage/MAR/nb_header.c |
10256 |
-@@ -20,6 +20,8 @@ |
10257 |
- #include <io.h> |
10258 |
- #endif |
10259 |
- |
10260 |
-+#include <sys/types.h> |
10261 |
-+#include <unistd.h> |
10262 |
- /* |
10263 |
- * mar software include files |
10264 |
- */ |
10265 |
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c |
10266 |
-index 443bb8c..0d96b3f 100755 |
10267 |
---- a/lib/DiffractionImage/MAR/swap.c |
10268 |
-+++ b/lib/DiffractionImage/MAR/swap.c |
10269 |
-@@ -10,6 +10,9 @@ |
10270 |
- * |
10271 |
- **********************************************************************/ |
10272 |
- |
10273 |
-+#define _XOPEN_SOURCE |
10274 |
-+#include <unistd.h> |
10275 |
-+ |
10276 |
- void swaplong(); |
10277 |
- void swapshort(); |
10278 |
- |
10279 |
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c |
10280 |
-index 0f6a6b7..a09dc48 100755 |
10281 |
---- a/lib/ccif/f_interface.c |
10282 |
-+++ b/lib/ccif/f_interface.c |
10283 |
-@@ -25,6 +25,7 @@ |
10284 |
- ********************************************************************/ |
10285 |
- |
10286 |
- #include "stdpccts.h" |
10287 |
-+#include <sys/mman.h> |
10288 |
- |
10289 |
- /* This file is terribly organised, and badly needs re-doing. There is probably |
10290 |
- * scope for splitting this into three modules: |
10291 |
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c |
10292 |
-index 8b5d04f..74ee3f7 100755 |
10293 |
---- a/lib/src/ccp4_general_f.c |
10294 |
-+++ b/lib/src/ccp4_general_f.c |
10295 |
-@@ -26,6 +26,7 @@ |
10296 |
- #include <string.h> |
10297 |
- #include <stdlib.h> |
10298 |
- #include <math.h> |
10299 |
-+#include <time.h> |
10300 |
- #include "ccp4_errno.h" |
10301 |
- #include "ccp4_fortran.h" |
10302 |
- #include "ccp4_parser.h" |
10303 |
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c |
10304 |
-index 3e83d4d..bb3e975 100755 |
10305 |
---- a/lib/src/ccp4_program.c |
10306 |
-+++ b/lib/src/ccp4_program.c |
10307 |
-@@ -25,6 +25,7 @@ |
10308 |
- #include <stdio.h> |
10309 |
- #include <stdlib.h> |
10310 |
- #include <string.h> |
10311 |
-+#include <time.h> |
10312 |
- #include "ccp4_program.h" |
10313 |
- #include "ccp4_parser.h" |
10314 |
- #include "ccp4_utils.h" |
10315 |
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c |
10316 |
-index ee8af24..c6fb3cd 100755 |
10317 |
---- a/lib/src/fsplit.c |
10318 |
-+++ b/lib/src/fsplit.c |
10319 |
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; |
10320 |
- #include <string.h> |
10321 |
- #include <sys/types.h> |
10322 |
- #include <sys/stat.h> |
10323 |
-+#include <unistd.h> |
10324 |
- |
10325 |
- /* |
10326 |
- * usage: fsplit [-e efile] ... [file] |
10327 |
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c |
10328 |
-index ea52e96..30dbd56 100755 |
10329 |
---- a/src/clipper_progs/src/pirate/compress42.c |
10330 |
-+++ b/src/clipper_progs/src/pirate/compress42.c |
10331 |
-@@ -142,6 +142,7 @@ |
10332 |
- #include <sys/types.h> |
10333 |
- #include <sys/stat.h> |
10334 |
- #include <errno.h> |
10335 |
-+#include <unistd.h> |
10336 |
- |
10337 |
- #ifdef DIRENT |
10338 |
- # include <dirent.h> |
10339 |
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c |
10340 |
-index e224430..c7b82f4 100755 |
10341 |
---- a/src/mtz2cif_/mtz2cif.c |
10342 |
-+++ b/src/mtz2cif_/mtz2cif.c |
10343 |
-@@ -28,6 +28,7 @@ |
10344 |
- #include "cmtzlib.h" |
10345 |
- #include "ccp4_parser.h" |
10346 |
- #include "ccp4_general.h" |
10347 |
-+#include "ccp4_program.h" |
10348 |
- #include "csymlib.h" |
10349 |
- #include "mtz2cif_lib.h" |
10350 |
- |
10351 |
|
10352 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch |
10353 |
deleted file mode 100644 |
10354 |
index 0463b37..0000000 |
10355 |
--- a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch |
10356 |
+++ /dev/null |
10357 |
@@ -1,597 +0,0 @@ |
10358 |
-diff --git a/configure b/configure |
10359 |
-index 833f483..bcfa62d 100755 |
10360 |
---- a/configure |
10361 |
-+++ b/configure |
10362 |
-@@ -3226,574 +3226,14 @@ else |
10363 |
- echo |
10364 |
- echo "Warning: this option has not been extensively tested!" |
10365 |
- echo "Please report problems to ccp4@×××××××.uk" |
10366 |
-- # Search for vendor LAPACK/BLAS first |
10367 |
-- if test ! "$with_netlib_lapack" ; then |
10368 |
-- # Initialise variables to blank |
10369 |
-- lapackdir= |
10370 |
-- XLAPACK_LIB= |
10371 |
-- # Possible directories to check for vendor or pre-existing LAPACK or |
10372 |
-- # BLAS - add to these if you want to test others |
10373 |
-- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" |
10374 |
-- # Possible library names |
10375 |
-- # These are the names like xxxx where the library will be libxxxx.a |
10376 |
-- # or libxxxx.so |
10377 |
-- echo |
10378 |
-- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" |
10379 |
-- echo "on this system" |
10380 |
-- case $system in |
10381 |
-- linux | linux64 | linux32 ) |
10382 |
-- # linux users will usually have them in /usr/lib but don't call it |
10383 |
-- trylapack="lapack" |
10384 |
-- tryblas="blas" |
10385 |
-- # if code is non_shared then this can lead to problems. both blas and lapack |
10386 |
-- # need to be resolved even if they are not called! |
10387 |
-- if test "$non_shared" = yes; then |
10388 |
-- echo "You are compiling linux non_shared. This sometimes causes problems " |
10389 |
-- echo " so checking for requirements." |
10390 |
-- echo "Checking: try to link library against test program" |
10391 |
-- if test -f testlink.f || test -f testlink ; then |
10392 |
-- rm -f testlink* |
10393 |
-- fi |
10394 |
-- cat > testlink.f <<EOF |
10395 |
-- PROGRAM TESTLINK |
10396 |
--C A bit of scala code to test the linking |
10397 |
-- real bf(3), bnorm |
10398 |
--c |
10399 |
-- integer maxbmt |
10400 |
-- parameter (maxbmt = 2) |
10401 |
-- double precision B(maxbmt,maxbmt), eigval(maxbmt), |
10402 |
-- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) |
10403 |
-- integer m, ia, ix, istat |
10404 |
--c |
10405 |
-- B(1,1) = 1.00 |
10406 |
-- B(1,2) = 1.00 |
10407 |
-- B(2,1) = 1.00 |
10408 |
-- B(2,2) = 1.00 |
10409 |
--c |
10410 |
-- m = maxbmt |
10411 |
-- ia = maxbmt |
10412 |
-- ix = maxbmt |
10413 |
-- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) |
10414 |
-- end |
10415 |
--EOF |
10416 |
-- #firstly test without -lblas |
10417 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" |
10418 |
-- echo $test_compile |
10419 |
-- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then |
10420 |
-- # Compilation was okay |
10421 |
-- echo "... only -llapack needed" |
10422 |
-- XLAPACK_LIB="-llapack" |
10423 |
-- # Set the next two variables so that configure |
10424 |
-- # doesn't try to build netlib libraries |
10425 |
-- LAPACKLIB="lapack" |
10426 |
-- noblas=yes |
10427 |
-- trylapack= |
10428 |
-- tryblas= |
10429 |
-- else |
10430 |
-- echo "more than just -llapack needed...." |
10431 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" |
10432 |
-- echo $test_compile |
10433 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10434 |
-- # Compilation was okay |
10435 |
-- echo "...-llapack and -lblas were needed" |
10436 |
-- XLAPACK_LIB="-llapack -lblas" |
10437 |
-- # Set the next two variables so that configure |
10438 |
-- # doesn't try to build netlib libraries |
10439 |
-- LAPACKLIB="lapack blas" |
10440 |
-- noblas=no |
10441 |
-- trylapack= |
10442 |
-- tryblas= |
10443 |
-- else |
10444 |
-- echo "....could not find either lapack or blas." |
10445 |
-- fi |
10446 |
-- fi |
10447 |
-- fi |
10448 |
-- # add 64 bit libs |
10449 |
-- case $system in |
10450 |
-- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; |
10451 |
-- esac |
10452 |
-- |
10453 |
-- ;; |
10454 |
-- osf1) |
10455 |
-- # OSF1 has dxml (old version) and cxml |
10456 |
-- # which should have both lapack and blas |
10457 |
-- trylapack="dxml cxml" |
10458 |
-- tryblas= |
10459 |
-- trydirs="${trydirs} /usr/shlib" |
10460 |
-- ;; |
10461 |
-- irix) |
10462 |
-- # Additional search paths for IRIX |
10463 |
-- trydirs="${trydirs} /usr/lib32" |
10464 |
-- # SCSL should have both LAPACK and BLAS |
10465 |
-- trylapack="scs" |
10466 |
-- tryblas="blas" |
10467 |
-- ;; |
10468 |
-- irix64) |
10469 |
-- # Additional search paths for IRIX64 |
10470 |
-- trydirs="${trydirs} /usr/lib64" |
10471 |
-- # SCSL should have both LAPACK and BLAS |
10472 |
-- trylapack="scs" |
10473 |
-- tryblas="blas" |
10474 |
-- # Extra compiler flags? |
10475 |
-- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" |
10476 |
-- ;; |
10477 |
-- aix) |
10478 |
-- # Additional search paths for AIX |
10479 |
-- trydirs="${trydirs}" |
10480 |
-- # AIX might have ESSL library - blas only I think |
10481 |
-- trylapack= |
10482 |
-- tryblas="essl" |
10483 |
-- ;; |
10484 |
-- hpux) |
10485 |
-- # Additional search paths for HPUX |
10486 |
-- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" |
10487 |
-- # HPUX should have both LAPACK (part of mlib) and BLAS |
10488 |
-- trylapack="lapack" |
10489 |
-- tryblas="blas" |
10490 |
-- # Extra compiler flags? |
10491 |
-- # +U77 required for ETIME function - this is already in XFFLAGS |
10492 |
-- #XLAPACKFLAGS="+U77" |
10493 |
-- ;; |
10494 |
-- |
10495 |
-- sunos | sunos64) |
10496 |
-- # Sun has libraries with BLAS and LAPACK invoked using |
10497 |
-- # -xlic_lib=sunperf |
10498 |
-- trylapack= |
10499 |
-- tryblas= |
10500 |
-- echo "SunOs can use the Sun Performance Library (if installed)" |
10501 |
-- echo "which has both BLAS and LAPACK 3.0" |
10502 |
-- echo |
10503 |
-- echo "Looking for a valid library to use..." |
10504 |
-- echo |
10505 |
-- # Loop over the possible library names |
10506 |
-- try_libs="sunperf" |
10507 |
-- for testlib in $try_libs |
10508 |
-- do |
10509 |
-- if test ! "$XLAPACK_LIB" ; then |
10510 |
-- # Try running a test compile to see if this a valid library |
10511 |
-- if test -f testlink.f || test -f testlink ; then |
10512 |
-- rm -f testlink* |
10513 |
-- fi |
10514 |
-- cat > testlink.f <<EOF |
10515 |
--c Test fortran program to link against library |
10516 |
-- PROGRAM TESTLINK |
10517 |
-- IMPLICIT NONE |
10518 |
-- INTEGER A |
10519 |
-- A = 1 |
10520 |
-- STOP |
10521 |
-- END |
10522 |
--EOF |
10523 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" |
10524 |
-- echo $test_compile |
10525 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10526 |
-- # Compilation was okay |
10527 |
-- echo "... -xlic_lib=$testlib is okay" |
10528 |
-- XLAPACK_LIB="-dalign -xlic_lib=$testlib" |
10529 |
-- # Set the next two variables so that configure |
10530 |
-- # doesn't try to build netlib libraries |
10531 |
-- LAPACKLIB="$testlib" |
10532 |
-- noblas=yes |
10533 |
-- else |
10534 |
-- # Compilation failed |
10535 |
-- echo "... cannot use -xlic_lib=$testlib" |
10536 |
-- fi |
10537 |
-- # End of test for testlib |
10538 |
-- fi |
10539 |
-- # End of loop over possible lib names |
10540 |
-- done |
10541 |
-- # Report if no suitable library was found |
10542 |
-- if test ! "$XLAPACK_LIB" ; then |
10543 |
-- echo |
10544 |
-- echo "No suitable LAPACK library was found." |
10545 |
-- echo "This may be because the Sun Performance Library is not" |
10546 |
-- echo "installed on your system" |
10547 |
-- echo "Contact your system administrator or Sun vendor" |
10548 |
-- fi |
10549 |
-- ;; |
10550 |
-- Darwin | Darwin32 | Darwin64 ) |
10551 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
10552 |
-- # -framework vecLib |
10553 |
-- echo "Darwin can use the vecLib Library (if installed)" |
10554 |
-- echo "which has both BLAS and LAPACK 3.0" |
10555 |
-- echo |
10556 |
-- # This is a special case so try running a test compile |
10557 |
-- echo "Checking: try to link library against test program" |
10558 |
-- if test -f testlink.f || test -f testlink ; then |
10559 |
-- rm -f testlink* |
10560 |
-- fi |
10561 |
-- cat > testlink.f <<EOF |
10562 |
--c Test fortran program to link against library |
10563 |
-- PROGRAM TESTLINK |
10564 |
-- IMPLICIT NONE |
10565 |
-- INTEGER A |
10566 |
-- A = 1 |
10567 |
-- STOP |
10568 |
-- END |
10569 |
--EOF |
10570 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" |
10571 |
-- echo $test_compile |
10572 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10573 |
-- # Compilation was okay |
10574 |
-- echo "... -framework vecLib is okay" |
10575 |
-- XLAPACK_LIB="-framework vecLib" |
10576 |
-- # Set the next two variables so that configure |
10577 |
-- # doesn't try to build netlib libraries |
10578 |
-- LAPACKLIB="vecLib" |
10579 |
-- noblas=yes |
10580 |
-- else |
10581 |
--#alternative linking for vecLib libraries |
10582 |
-- case `uname -sr` in |
10583 |
-- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; |
10584 |
-- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; |
10585 |
-- esac |
10586 |
-- |
10587 |
-- echo $test_compile |
10588 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10589 |
-- # Compilation was okay |
10590 |
-- echo "... -framework vecLib is okay" |
10591 |
-- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" |
10592 |
-- # Set the next two variables so that configure |
10593 |
-- # doesn't try to build netlib libraries |
10594 |
-- LAPACKLIB="-Wl,-framework -Wl,vecLib" |
10595 |
-- noblas=yes |
10596 |
-- else |
10597 |
-- # Compilation failed |
10598 |
-- echo "... cannot use -framework vecLib" |
10599 |
-- echo |
10600 |
-- fi |
10601 |
-- fi |
10602 |
-- trylapack= |
10603 |
-- tryblas= |
10604 |
--# try the fink installation |
10605 |
-- trydirs="${trydirs} /sw" |
10606 |
-- ;; |
10607 |
-- Darwin_ibm_compilers ) |
10608 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
10609 |
-- # -framework vecLib |
10610 |
-- echo "Darwin can use the vecLib Library (if installed)" |
10611 |
-- echo "which has both BLAS and LAPACK 3.0" |
10612 |
-- echo |
10613 |
-- # This is a special case so try running a test compile |
10614 |
-- echo "Checking: try to link library against test program" |
10615 |
-- if test -f testlink.f || test -f testlink ; then |
10616 |
-- rm -f testlink* |
10617 |
-- fi |
10618 |
-- cat > testlink.f <<EOF |
10619 |
--c Test fortran program to link against library |
10620 |
-- PROGRAM TESTLINK |
10621 |
-- IMPLICIT NONE |
10622 |
-- INTEGER A |
10623 |
-- A = 1 |
10624 |
-- STOP |
10625 |
-- END |
10626 |
--EOF |
10627 |
-- case `uname -sr` in |
10628 |
-- Darwin\ 8* ) |
10629 |
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" |
10630 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" |
10631 |
-- ;; |
10632 |
-- Darwin\ 7* ) |
10633 |
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" |
10634 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" |
10635 |
-- ;; |
10636 |
-- *) |
10637 |
-- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" |
10638 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" |
10639 |
-- esac |
10640 |
-- echo $test_compile |
10641 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10642 |
-- # Compilation was okay |
10643 |
-- echo "... -framework vecLib is okay" |
10644 |
-- # Set the next two variables so that configure |
10645 |
-- # doesn't try to build netlib libraries |
10646 |
-- LAPACKLIB="vecLib" |
10647 |
-- noblas=yes |
10648 |
-- else |
10649 |
-- # Compilation failed |
10650 |
-- XLAPACK_LIB="" |
10651 |
-- echo "... cannot use -framework vecLib" |
10652 |
-- echo |
10653 |
-- fi |
10654 |
-- trylapack= |
10655 |
-- tryblas= |
10656 |
--# try the fink installation |
10657 |
-- trydirs="${trydirs} /sw" |
10658 |
-- ;; |
10659 |
-- |
10660 |
-- Darwin_intel_compilers) |
10661 |
-- # Darwin has libraries with BLAS and LAPACK invoked using |
10662 |
-- # -F vecLib |
10663 |
-- echo "Darwin can use the vecLib Library (if installed)" |
10664 |
-- echo "which has both BLAS and LAPACK 3.0" |
10665 |
-- echo |
10666 |
-- # This is a special case so try running a test compile |
10667 |
-- echo "Checking: try to link library against test program" |
10668 |
-- if test -f testlink.f || test -f testlink ; then |
10669 |
-- rm -f testlink* |
10670 |
-- fi |
10671 |
-- cat > testlink.f <<EOF |
10672 |
--c Test fortran program to link against library |
10673 |
-- PROGRAM TESTLINK |
10674 |
-- IMPLICIT NONE |
10675 |
-- INTEGER A |
10676 |
-- A = 1 |
10677 |
-- STOP |
10678 |
-- END |
10679 |
--EOF |
10680 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" |
10681 |
-- echo $test_compile |
10682 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10683 |
-- # Compilation was okay |
10684 |
-- # doesn't try to build netlib libraries |
10685 |
-- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" |
10686 |
-- LAPACKLIB="vecLib" |
10687 |
-- noblas=yes |
10688 |
-- else |
10689 |
-- # Compilation failed |
10690 |
-- echo "... cannot use -framework vecLib" |
10691 |
-- echo |
10692 |
-- fi |
10693 |
-- trylapack= |
10694 |
-- tryblas= |
10695 |
--# try the fink installation |
10696 |
-- trydirs="${trydirs} /sw" |
10697 |
-- ;; |
10698 |
-- |
10699 |
--# linux_ia64_sgi_altix) |
10700 |
--# SGI Japan |
10701 |
-- ia64_linux_intel) |
10702 |
-- # Additional search paths for Linux/IA64 |
10703 |
-- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" |
10704 |
-- # SCSL and MKL should have both LAPACK and BLAS |
10705 |
-- trylapack="mkl_lapack scs lapack" |
10706 |
-- tryblas="mkl scs blas" |
10707 |
-- ;; |
10708 |
-- linux_ibm_compilers ) |
10709 |
-- trylapack="lapack" |
10710 |
-- tryblas="blas" |
10711 |
-- ;; |
10712 |
-- linux64_ibm_compilers ) |
10713 |
-- trydirs="/usr/lib64 ${trydirs}" |
10714 |
-- trylapack="lapack" |
10715 |
-- tryblas="blas" |
10716 |
-- ;; |
10717 |
-- linux_intel_compilers ) |
10718 |
-- trydirs="/usr/lib64 ${trydirs}" |
10719 |
-- trylapack="mkl_lapack lapack" |
10720 |
-- tryblas="mkl blas" |
10721 |
-- ;; |
10722 |
-- *) |
10723 |
-- echo "The guesses for this system may not be correct - please" |
10724 |
-- echo "e-mail ccp4@×××××××.uk if you have any extra information" |
10725 |
-- echo |
10726 |
-- # Default guess is just libblas |
10727 |
-- trylapack="lapack" |
10728 |
-- tryblas="blas" |
10729 |
-- ;; |
10730 |
-- esac |
10731 |
-- # |
10732 |
-- # Search for LAPACK libraries |
10733 |
-- # |
10734 |
-- # Write out what the guesses are |
10735 |
-- if test "$trylapack" ; then |
10736 |
-- echo "Possible LAPACK library names for this system:" |
10737 |
-- for libname in $trylapack |
10738 |
-- do |
10739 |
-- echo " lib$libname" |
10740 |
-- done |
10741 |
-- # Possible library name extensions |
10742 |
-- tryexts="a so dylib" |
10743 |
-- # Now loop over all the possibilities and see if anything |
10744 |
-- # turns up |
10745 |
-- echo |
10746 |
-- echo "Searching for libraries with LAPACK and BLAS:" |
10747 |
-- for testdir in $trydirs |
10748 |
-- do |
10749 |
-- for testlib in $trylapack |
10750 |
-- do |
10751 |
-- for ext in $tryexts |
10752 |
-- do |
10753 |
-- if test ! "$LAPACKLIB"; then |
10754 |
-- if test -s "$testdir/lib$testlib.$ext" ; then |
10755 |
-- echo "...found LAPACK library: $testdir/lib$testlib.$ext" |
10756 |
-- # Now try and link to a test program |
10757 |
-- # This is really for IRIX where libraries can be |
10758 |
-- # o32 or n32 |
10759 |
-- echo " Testing: try to link library against test program" |
10760 |
-- if test -f testlink.f || test -f testlink ; then |
10761 |
-- rm -f testlink* |
10762 |
-- fi |
10763 |
-- cat > testlink.f <<EOF |
10764 |
--c Test fortran program to link against library |
10765 |
-- PROGRAM TESTLINK |
10766 |
-- IMPLICIT NONE |
10767 |
-- INTEGER A |
10768 |
-- A = 1 |
10769 |
-- STOP |
10770 |
-- END |
10771 |
--EOF |
10772 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
10773 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
10774 |
-- echo $test_compile |
10775 |
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then |
10776 |
-- have_lapack=yes |
10777 |
-- else |
10778 |
--# cover clapack option |
10779 |
-- echo $test_ccompile |
10780 |
-- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then |
10781 |
-- have_lapack=yes |
10782 |
-- fi |
10783 |
-- fi |
10784 |
-- if test x$have_lapack = xyes ; then |
10785 |
-- # This one is okay |
10786 |
-- LAPACKLIB="$testlib" |
10787 |
-- LAPACKDIR="$testdir" |
10788 |
-- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" |
10789 |
-- # |
10790 |
-- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" |
10791 |
-- # |
10792 |
-- # Test to see if we need BLAS too |
10793 |
-- # Do this by trying to compile a test program |
10794 |
-- # Use the LSAME test for now |
10795 |
-- echo |
10796 |
-- echo " * Checking whether we need a separate BLAS library *" |
10797 |
-- echo " Testing: try linking library against test program" |
10798 |
-- cd lib/lapack/test |
10799 |
-- if test -f testlsame ; then |
10800 |
-- rm -f testsame testlsame.o |
10801 |
-- fi |
10802 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" |
10803 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" |
10804 |
-- echo $test_compile |
10805 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then |
10806 |
-- have_blas=yes |
10807 |
-- else |
10808 |
--#cblas route |
10809 |
-- echo $test_ccompile |
10810 |
-- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then |
10811 |
-- have_blas=yes |
10812 |
-- fi |
10813 |
-- fi |
10814 |
-- if test x$have_blas = xyes ; then |
10815 |
-- echo "Test program okay - additional separate BLAS not required" |
10816 |
-- noblas=yes |
10817 |
-- else |
10818 |
-- echo "Test program failed - need a separate BLAS library" |
10819 |
-- fi |
10820 |
-- cd ../../.. |
10821 |
-- else |
10822 |
-- # Keep looking |
10823 |
-- echo " link failed - cannot use lib$testlib" |
10824 |
-- fi |
10825 |
-- fi |
10826 |
-- fi |
10827 |
-- done |
10828 |
-- done |
10829 |
-- if test ! "$LAPACKLIB"; then |
10830 |
-- echo "...nothing in $testdir" |
10831 |
-- fi |
10832 |
-- done |
10833 |
-- fi |
10834 |
-- |
10835 |
-- # If LAPACKLIB hasn't been set at this point then no LAPACK library |
10836 |
-- # was found |
10837 |
-- if test ! "$LAPACKLIB" ; then |
10838 |
-- echo |
10839 |
-- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" |
10840 |
-- make_lapack=lapacklib |
10841 |
-- fi |
10842 |
-- # Look for possible BLAS |
10843 |
-- if test ! "$noblas" ; then |
10844 |
-- if test "$tryblas" ; then |
10845 |
-- echo |
10846 |
-- echo "Possible BLAS library names for this system:" |
10847 |
-- for libname in $tryblas |
10848 |
-- do |
10849 |
-- echo " lib$libname" |
10850 |
-- done |
10851 |
-- # Possible library name extensions |
10852 |
-- tryexts="a so" |
10853 |
-- # Now loop over all the possibilities and see if anything |
10854 |
-- # turns up |
10855 |
-- echo |
10856 |
-- echo "Searching for libraries with BLAS:" |
10857 |
-- for testdir in $trydirs |
10858 |
-- do |
10859 |
-- for testlib in $tryblas |
10860 |
-- do |
10861 |
-- for ext in $tryexts |
10862 |
-- do |
10863 |
-- if test ! "$BLASLIB"; then |
10864 |
-- if test -s "$testdir/lib$testlib.$ext" ; then |
10865 |
-- echo "...found BLAS library: $testdir/lib$testlib.$ext" |
10866 |
-- # Now try and link to a test program |
10867 |
-- # This is really for IRIX where libraries can be |
10868 |
-- # o32 or n32 |
10869 |
-- echo " Testing: try to link library against test program" |
10870 |
-- if test -f testlink.f || test -f testlink ; then |
10871 |
-- rm -f testlink* |
10872 |
-- fi |
10873 |
-- cat > testlink.f <<EOF |
10874 |
--c Test fortran program to link against library |
10875 |
-- PROGRAM TESTLINK |
10876 |
-- IMPLICIT NONE |
10877 |
-- INTEGER A |
10878 |
-- A = 1 |
10879 |
-- STOP |
10880 |
-- END |
10881 |
--EOF |
10882 |
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" |
10883 |
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" |
10884 |
-- echo $test_compile |
10885 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then |
10886 |
-- have_blas=yes |
10887 |
-- else |
10888 |
-- echo $test_ccompile |
10889 |
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then |
10890 |
-- have_blas=yes |
10891 |
-- fi |
10892 |
-- fi |
10893 |
-- if test x$have_blas = xyes ; then |
10894 |
-- # This one is okay |
10895 |
-- BLASLIB="$testlib" |
10896 |
-- BLASDIR="$testdir" |
10897 |
-- BLASEXT="$ext" |
10898 |
-- echo "Link ok - using lib$BLASLIB from $BLASDIR" |
10899 |
-- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" |
10900 |
-- else |
10901 |
-- # Keep looking |
10902 |
-- echo " link failed - cannot use lib$testlib" |
10903 |
-- fi |
10904 |
-- fi |
10905 |
-- fi |
10906 |
-- done |
10907 |
-- done |
10908 |
-- if test ! "$BLASLIB"; then |
10909 |
-- echo "...nothing in $testdir" |
10910 |
-- fi |
10911 |
-- done |
10912 |
-- fi |
10913 |
-- # Do we need to build BLAS too? |
10914 |
-- if test ! "$BLASLIB" ; then |
10915 |
-- echo |
10916 |
-- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" |
10917 |
-- echo "This may result in poorer performance of the LAPACK routines" |
10918 |
-- make_blas=blaslib |
10919 |
-- BLASLIB=blas |
10920 |
-- BLASDIR="$srcdir/lib/lapack" |
10921 |
-- BLASEXT="a" |
10922 |
-- fi |
10923 |
-- fi |
10924 |
-+ # gentoo is clever |
10925 |
-+ make_blas= |
10926 |
-+ make_lapack= |
10927 |
-+ BLASLIB=$(${PKG_CONFIG} --libs lapack) |
10928 |
-+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) |
10929 |
-+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" |
10930 |
-+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" |
10931 |
- # Otherwise force building of NetLib BLAS and LAPACK libs |
10932 |
-- else |
10933 |
-- echo |
10934 |
-- echo "! Force building of NetLib BLAS and LAPACK..." |
10935 |
-- make_blas=blaslib |
10936 |
-- make_lapack=lapacklib |
10937 |
-- BLASLIB=blas |
10938 |
-- BLASDIR="$srcdir/lib/lapack" |
10939 |
-- BLASEXT="a" |
10940 |
-- fi |
10941 |
- # need to know if we the lapack library was linked using the C or |
10942 |
- # fortran linker |
10943 |
- if test -f testlink.f || test -f testlink || test -f testlink.c ; then |
10944 |
-@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} |
10945 |
- INSTALL_DATA = ${INSTALL_DATA} |
10946 |
- libdir = $libdir |
10947 |
- # |
10948 |
--BLASLIB = lib${BLASLIB}.${BLASEXT} |
10949 |
--LAPACKLIB = liblapack.a |
10950 |
-+BLASLIB = ${BLASLIB} |
10951 |
-+LAPACKLIB = ${LAPACKLIB} |
10952 |
- # |
10953 |
- # These variables define targets in the main Makefile |
10954 |
- blaslib = ${make_blas} |
10955 |
|
10956 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch |
10957 |
deleted file mode 100644 |
10958 |
index 24a0a2d..0000000 |
10959 |
--- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch |
10960 |
+++ /dev/null |
10961 |
@@ -1,230 +0,0 @@ |
10962 |
---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100 |
10963 |
-+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100 |
10964 |
-@@ -172,9 +172,8 @@ |
10965 |
- |
10966 |
- ##### Makefile targets ###### |
10967 |
- |
10968 |
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES) |
10969 |
-+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES) |
10970 |
- # maybe create shared library |
10971 |
-- $(SHARE_LIB) |
10972 |
- |
10973 |
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) |
10974 |
- $(AR) $(LC) $? |
10975 |
-@@ -186,6 +185,27 @@ |
10976 |
- $(AR) $(LF) $(FINTERFACEOBJS) |
10977 |
- $(RANLIB) $@ |
10978 |
- |
10979 |
-+LMMDB_SO : |
10980 |
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \ |
10981 |
-+ $(MMDBOBJS) && \ |
10982 |
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \ |
10983 |
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so |
10984 |
-+ |
10985 |
-+LC_SO : |
10986 |
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \ |
10987 |
-+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \ |
10988 |
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \ |
10989 |
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so |
10990 |
-+ |
10991 |
-+LF_SO : |
10992 |
-+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \ |
10993 |
-+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \ |
10994 |
-+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \ |
10995 |
-+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \ |
10996 |
-+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \ |
10997 |
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \ |
10998 |
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so |
10999 |
-+ |
11000 |
- # cmtz library only |
11001 |
- |
11002 |
- cmtz: $(LCMTZ) |
11003 |
-@@ -339,9 +356,7 @@ |
11004 |
- fi |
11005 |
- cd parser.dir && \ |
11006 |
- for i in `pwd`/*.$F; do \ |
11007 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11008 |
-- && $(AR) ../$(LF) *.o |
11009 |
-- rm -f parser.dir/*.o |
11010 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11011 |
- parser : parser.o |
11012 |
- $(RANLIB) $(LF) |
11013 |
- |
11014 |
-@@ -351,9 +366,7 @@ |
11015 |
- echo ' END' >> ccplib.dir/ccplib.$F |
11016 |
- cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \ |
11017 |
- for i in `pwd`/*.$F; do \ |
11018 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11019 |
-- && $(AR) ../$(LF) *.o |
11020 |
-- rm -f ccplib.dir/*.o |
11021 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11022 |
- ccplib : ccplib.o |
11023 |
- $(RANLIB) $(LF) |
11024 |
- |
11025 |
-@@ -364,9 +377,7 @@ |
11026 |
- @$(SETFLAGS) ; \ |
11027 |
- cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \ |
11028 |
- for i in `pwd`/*.$F; do \ |
11029 |
-- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\ |
11030 |
-- && $(AR) ../$(LF) *.o |
11031 |
-- rm -f lgglib.dir/*.o |
11032 |
-+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done |
11033 |
- lgglib : lgglib.o |
11034 |
- $(RANLIB) $(LF) |
11035 |
- |
11036 |
-@@ -376,9 +387,7 @@ |
11037 |
- echo ' END' >> plot84lib.dir/plot84lib.$F |
11038 |
- cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \ |
11039 |
- for i in `pwd`/*.$F; do \ |
11040 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11041 |
-- && $(AR) ../$(LF) *.o |
11042 |
-- rm -f plot84lib.dir/*.o |
11043 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11044 |
- plot84lib : plot84lib.o |
11045 |
- $(RANLIB) $(LF) |
11046 |
- |
11047 |
-@@ -388,9 +397,7 @@ |
11048 |
- echo ' END' >> libhtml.dir/libhtml.$F |
11049 |
- cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \ |
11050 |
- for i in `pwd`/*.$F; do \ |
11051 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11052 |
-- && $(AR) ../$(LF) *.o |
11053 |
-- rm -f libhtml.dir/*.o |
11054 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11055 |
- libhtml : libhtml.o |
11056 |
- $(RANLIB) $(LF) |
11057 |
- |
11058 |
-@@ -400,9 +407,7 @@ |
11059 |
- echo ' END' >> pxxml.dir/pxxml.$F |
11060 |
- cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \ |
11061 |
- for i in `pwd`/*.$F; do \ |
11062 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11063 |
-- && $(AR) ../$(LF) *.o |
11064 |
-- rm -f pxxml.dir/*.o |
11065 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11066 |
- pxxml : pxxml.o |
11067 |
- $(RANLIB) $(LF) |
11068 |
- |
11069 |
-@@ -412,9 +417,7 @@ |
11070 |
- echo ' END' >> rwbrook.dir/rwbrook.$F |
11071 |
- cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \ |
11072 |
- for i in `pwd`/*.$F; do \ |
11073 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11074 |
-- && $(AR) ../$(LF) *.o |
11075 |
-- rm -f rwbrook.dir/*.o |
11076 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11077 |
- rwbrook : rwbrook.o |
11078 |
- $(RANLIB) $(LF) |
11079 |
- |
11080 |
-@@ -424,9 +427,7 @@ |
11081 |
- echo ' END' >> cciflib.dir/cciflib.$F |
11082 |
- cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \ |
11083 |
- for i in `pwd`/*.$F; do \ |
11084 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\ |
11085 |
-- && $(AR) ../$(LF) *.o |
11086 |
-- rm -f cciflib.dir/*.o |
11087 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done |
11088 |
- cciflib : cciflib.o |
11089 |
- $(RANLIB) $(LF) |
11090 |
- |
11091 |
-@@ -440,9 +441,7 @@ |
11092 |
- && $(AR) ../$(LF) *.o ; else \ |
11093 |
- cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \ |
11094 |
- for i in `pwd`/*.$F; do \ |
11095 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\ |
11096 |
-- && $(AR) ../$(LF) *.o ; fi |
11097 |
-- rm -f harvlib.dir/*.o |
11098 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi |
11099 |
- harvlib : harvlib.o |
11100 |
- $(RANLIB) $(LF) |
11101 |
- |
11102 |
-@@ -452,9 +451,7 @@ |
11103 |
- echo ' END' >> keyparse.dir/keyparse.$F |
11104 |
- cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \ |
11105 |
- for i in `pwd`/*.$F; do \ |
11106 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11107 |
-- && $(AR) ../$(LF) *.o |
11108 |
-- rm -f keyparse.dir/*.o |
11109 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11110 |
- keyparse : keyparse.o |
11111 |
- $(RANLIB) $(LF) |
11112 |
- |
11113 |
-@@ -464,9 +461,7 @@ |
11114 |
- echo ' END' >> dna_output.dir/dna_output.$F |
11115 |
- cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \ |
11116 |
- for i in `pwd`/*.$F; do \ |
11117 |
-- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11118 |
-- && $(AR) ../$(LF) *.o |
11119 |
-- rm -f dna_output.dir/*.o |
11120 |
-+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11121 |
- dna_output : dna_output.o |
11122 |
- $(RANLIB) $(LF) |
11123 |
- |
11124 |
-@@ -474,10 +469,9 @@ |
11125 |
- # for ipdisp. May be useful but could be moved. |
11126 |
- $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h |
11127 |
- $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c |
11128 |
-- $(AR) $(LF) pack_c.o && rm pack_c.o |
11129 |
-+ $(AR) $(LF) pack_c.o |
11130 |
- $(LF)(pack_f.o): $(srcdir)/pack_f.f |
11131 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \ |
11132 |
-- && rm pack_f.o |
11133 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o |
11134 |
- pack: $(LF)(pack_c.o) $(LF)(pack_f.o) |
11135 |
- $(RANLIB) $(LF) |
11136 |
- |
11137 |
-@@ -488,9 +482,7 @@ |
11138 |
- echo ' END' >> sorting_main.dir/sorting_main.$F |
11139 |
- cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \ |
11140 |
- for i in `pwd`/*.$F; do \ |
11141 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11142 |
-- && $(AR) ../$(LF) *.o |
11143 |
-- rm -f sorting_main.dir/*.o |
11144 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11145 |
- sorting_main : sorting_main.o |
11146 |
- $(RANLIB) $(LF) |
11147 |
- |
11148 |
-@@ -500,9 +492,7 @@ |
11149 |
- echo ' END' >> plotsubs.dir/plotsubs.$F |
11150 |
- cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \ |
11151 |
- for i in `pwd`/*.$F; do \ |
11152 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11153 |
-- && $(AR) ../$(LF) *.o |
11154 |
-- rm -f plotsubs.dir/*.o |
11155 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11156 |
- plotsubs : plotsubs.o |
11157 |
- $(RANLIB) $(LF) |
11158 |
- |
11159 |
-@@ -512,9 +502,7 @@ |
11160 |
- echo ' END' >> modlib.dir/modlib.$F |
11161 |
- cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \ |
11162 |
- for i in `pwd`/*.$F; do \ |
11163 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11164 |
-- && $(AR) ../$(LF) *.o |
11165 |
-- rm -f modlib.dir/*.o |
11166 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11167 |
- modlib : modlib.o |
11168 |
- $(RANLIB) $(LF) |
11169 |
- |
11170 |
-@@ -524,9 +512,7 @@ |
11171 |
- echo ' END' >> fftlib.dir/fftlib.$F |
11172 |
- cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \ |
11173 |
- for i in `pwd`/*.$F; do \ |
11174 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \ |
11175 |
-- && $(AR) ../$(LF) *.o |
11176 |
-- rm -f fftlib.dir/*.o |
11177 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11178 |
- fftlib : fftlib.o |
11179 |
- $(RANLIB) $(LF) |
11180 |
- |
11181 |
-@@ -541,9 +527,7 @@ |
11182 |
- echo ' END' >> unix.dir/unix.f |
11183 |
- cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \ |
11184 |
- for i in `pwd`/*.$F; do \ |
11185 |
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ |
11186 |
-- && $(AR) ../$(LF) *.o |
11187 |
-- rm -f unix.dir/*.o |
11188 |
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done |
11189 |
- unix : unix.o |
11190 |
- $(RANLIB) $(LF) |
11191 |
- |
11192 |
|
11193 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch |
11194 |
deleted file mode 100644 |
11195 |
index 6a0cb5b..0000000 |
11196 |
--- a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch |
11197 |
+++ /dev/null |
11198 |
@@ -1,87 +0,0 @@ |
11199 |
- include/ccp4.setup-bash | 8 -------- |
11200 |
- include/ccp4.setup-csh | 11 ----------- |
11201 |
- include/ccp4.setup-sh | 8 -------- |
11202 |
- include/ccp4.setup-zsh | 10 ---------- |
11203 |
- 4 files changed, 37 deletions(-) |
11204 |
- |
11205 |
-diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash |
11206 |
-index 3a67791..80aef23 100755 |
11207 |
---- a/include/ccp4.setup-bash |
11208 |
-+++ b/include/ccp4.setup-bash |
11209 |
-@@ -185,14 +185,6 @@ else |
11210 |
- fi |
11211 |
- fi |
11212 |
- |
11213 |
--#Python path for the subprocess fixed module |
11214 |
-- |
11215 |
--if [ $ccp4_first_in_path -eq 1 ]; then |
11216 |
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} |
11217 |
--else |
11218 |
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python |
11219 |
--fi |
11220 |
-- |
11221 |
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### |
11222 |
- setenv PLOT_COMMAND 'lp -s -dmicrolaser' |
11223 |
- setenv PRINT_COMMAND 'lp -s -denscript' |
11224 |
-diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh |
11225 |
-index 10d3ab8..72cc479 100755 |
11226 |
---- a/include/ccp4.setup-csh |
11227 |
-+++ b/include/ccp4.setup-csh |
11228 |
-@@ -177,17 +177,6 @@ else |
11229 |
- endif |
11230 |
- endif |
11231 |
- |
11232 |
--#Python path for the subprocess fixed module |
11233 |
--if (${?PYTHONPATH}) then |
11234 |
-- if ($ccp4_first_in_path) then |
11235 |
-- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} |
11236 |
-- else |
11237 |
-- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python |
11238 |
-- endif |
11239 |
--else |
11240 |
-- setenv PYTHONPATH ${CCP4}/share/python |
11241 |
--endif |
11242 |
-- |
11243 |
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### |
11244 |
- setenv PLOT_COMMAND 'lp -s -dmicrolaser' |
11245 |
- setenv PRINT_COMMAND 'lp -s -denscript' |
11246 |
-diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh |
11247 |
-index 2298bba..44643ab 100755 |
11248 |
---- a/include/ccp4.setup-sh |
11249 |
-+++ b/include/ccp4.setup-sh |
11250 |
-@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg |
11251 |
- |
11252 |
- ################### EXPERIENCED USERS STOP HERE ##################### |
11253 |
- |
11254 |
--#Python path for the subprocess fixed module |
11255 |
-- |
11256 |
--if test $ccp4_first_in_path -eq 1; then |
11257 |
-- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} |
11258 |
--else |
11259 |
-- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python |
11260 |
--fi |
11261 |
-- |
11262 |
- ################### THE REST SHOULDN'T NEED EDITING ##################### |
11263 |
- |
11264 |
- ### dbCCP4i database handler setup ### |
11265 |
-diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh |
11266 |
-index 660b35b..e453db9 100755 |
11267 |
---- a/include/ccp4.setup-zsh |
11268 |
-+++ b/include/ccp4.setup-zsh |
11269 |
-@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN |
11270 |
- CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary |
11271 |
- export CLASSPATH |
11272 |
- |
11273 |
--#Python path for the subprocess fixed module |
11274 |
-- |
11275 |
--if ($ccp4_first_in_path) then |
11276 |
-- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} |
11277 |
-- export PYTHONPATH |
11278 |
--else |
11279 |
-- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python |
11280 |
-- export PYTHONPATH |
11281 |
--fi |
11282 |
-- |
11283 |
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### |
11284 |
- export PLOT_COMMAND='lpr' |
11285 |
- export PRINT_COMMAND='lpr' |
11286 |
|
11287 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch |
11288 |
deleted file mode 100644 |
11289 |
index c1479f2..0000000 |
11290 |
--- a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch |
11291 |
+++ /dev/null |
11292 |
@@ -1,142 +0,0 @@ |
11293 |
-diff --git a/Makefile.in b/Makefile.in |
11294 |
-index ac552fe..fab1a87 100755 |
11295 |
---- a/Makefile.in |
11296 |
-+++ b/Makefile.in |
11297 |
-@@ -30,8 +30,7 @@ lapacklib : FORCE |
11298 |
- |
11299 |
- cciflib : FORCE |
11300 |
- if test -n "$(ccifdir)"; then cd $(ccifdir); \ |
11301 |
-- $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \ |
11302 |
-- $(MAKE) install |
11303 |
-+ $(MAKE) $(MFLAGS) $(MVARS); else true; fi |
11304 |
- |
11305 |
- cctbx: FORCE |
11306 |
- if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \ |
11307 |
-@@ -40,8 +39,7 @@ cctbx: FORCE |
11308 |
- libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg |
11309 |
- |
11310 |
- libccp4: FORCE |
11311 |
-- cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \ |
11312 |
-- $(MAKE) install |
11313 |
-+ cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) |
11314 |
- |
11315 |
- share : FORCE |
11316 |
- cd share; $(MAKE) $(MFLAGS) $(MVARS) |
11317 |
-@@ -51,18 +49,15 @@ ccp4i : FORCE |
11318 |
- |
11319 |
- clipper: FORCE fftw |
11320 |
- if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \ |
11321 |
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ |
11322 |
-- $(MAKE) install |
11323 |
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi |
11324 |
- |
11325 |
- diffractionImg: |
11326 |
- if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \ |
11327 |
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ |
11328 |
-- $(MAKE) install |
11329 |
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi |
11330 |
- |
11331 |
- ssm: |
11332 |
- if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \ |
11333 |
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ |
11334 |
-- $(MAKE) install |
11335 |
-+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi |
11336 |
- |
11337 |
- fftw: FORCE |
11338 |
- if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \ |
11339 |
-@@ -79,7 +74,7 @@ unsupported : FORCE libdir |
11340 |
- $(MAKE) $(MFLAGS) $(MVARS); else true; fi |
11341 |
- |
11342 |
- datadir : FORCE libdir |
11343 |
-- cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) |
11344 |
-+ cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat |
11345 |
- |
11346 |
- xwindir : FORCE libdir |
11347 |
- if test -f x-windows/Makefile; then cd x-windows; \ |
11348 |
-diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in |
11349 |
-index 975f1d9..75eda9f 100755 |
11350 |
---- a/lib/ccif/Makefile.in |
11351 |
-+++ b/lib/ccif/Makefile.in |
11352 |
-@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk |
11353 |
- # |
11354 |
- |
11355 |
- install : all |
11356 |
-- $(INSTALL_DATA) `pwd`/$L $(libdir)/$L |
11357 |
-- $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB) |
11358 |
-- $(RANLIB) $(libdir)/$L |
11359 |
-+ $(RANLIB) $L |
11360 |
-+ $(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L |
11361 |
-+ $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB) |
11362 |
- if (test -f $(SHARED_LIB_NAME)); then \ |
11363 |
-- $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \ |
11364 |
-+ $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \ |
11365 |
- fi |
11366 |
- |
11367 |
- uninstall : |
11368 |
-diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in |
11369 |
-index cc25c5c..017502d 100755 |
11370 |
---- a/lib/data/Makefile.in |
11371 |
-+++ b/lib/data/Makefile.in |
11372 |
-@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii |
11373 |
- |
11374 |
- install : all |
11375 |
- -rm -f font84.dat |
11376 |
-- test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii . |
11377 |
-- ./fontpack |
11378 |
-- $(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat |
11379 |
-+ test -f font84.ascii || $(LNS) $(DESTDIR)/$(srcdir)/font84.ascii . |
11380 |
-+ LD_LIBRARY_PATH="../src:../ccif" ./fontpack |
11381 |
-+ $(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat |
11382 |
- |
11383 |
- uninstall : |
11384 |
- -rm -f $(libdir)/font84.dat |
11385 |
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in |
11386 |
-index b32dd1e..6aa107d 100755 |
11387 |
---- a/lib/src/Makefile.in |
11388 |
-+++ b/lib/src/Makefile.in |
11389 |
-@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f $(LF) |
11390 |
- # |
11391 |
- |
11392 |
- install-ccp4HEADERS: $(ccp4_HEADERS) |
11393 |
-- if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi |
11394 |
-+ if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi |
11395 |
- @list='$(ccp4_HEADERS)'; for p in $$list; do \ |
11396 |
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ |
11397 |
- f="`echo $$p | sed -e 's|^.*/||'`"; \ |
11398 |
-@@ -716,11 +716,11 @@ uninstall-mmdbHEADERS: |
11399 |
- rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \ |
11400 |
- done |
11401 |
- |
11402 |
--install : all install-ccp4HEADERS install-mmdbHEADERS |
11403 |
-- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) |
11404 |
-- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) |
11405 |
-- $(RANLIB) $(libdir)/$(LC) |
11406 |
-- $(RANLIB) $(libdir)/$(LF) |
11407 |
-+install : all install-ccp4HEADERS |
11408 |
-+ $(RANLIB) $(LC) |
11409 |
-+ $(RANLIB) $(LF) |
11410 |
-+ $(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC) |
11411 |
-+ $(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF) |
11412 |
- $(SHARE_INST) |
11413 |
- |
11414 |
- uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS |
11415 |
-diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in |
11416 |
-index 27d3aa2..0a14fe5 100755 |
11417 |
---- a/lib/ssm/Makefile.in |
11418 |
-+++ b/lib/ssm/Makefile.in |
11419 |
-@@ -375,12 +375,12 @@ distclean-libtool: |
11420 |
- uninstall-info-am: |
11421 |
- install-library_includeHEADERS: $(library_include_HEADERS) |
11422 |
- @$(NORMAL_INSTALL) |
11423 |
-- test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)" |
11424 |
-+ test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm" |
11425 |
- @list='$(library_include_HEADERS)'; for p in $$list; do \ |
11426 |
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ |
11427 |
- f=$(am__strip_dir) \ |
11428 |
-- echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \ |
11429 |
-- $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \ |
11430 |
-+ echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \ |
11431 |
-+ $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \ |
11432 |
- done |
11433 |
- |
11434 |
- uninstall-library_includeHEADERS: |
11435 |
|
11436 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch b/sci-libs/ccp4-libs/files/6.1.3-overflows.patch |
11437 |
deleted file mode 100644 |
11438 |
index 0e3c941..0000000 |
11439 |
--- a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch |
11440 |
+++ /dev/null |
11441 |
@@ -1,35 +0,0 @@ |
11442 |
-Fix overflows and array subscript above array bounds |
11443 |
- |
11444 |
-http://bugs.gentoo.org/show_bug.cgi?id=339706 |
11445 |
- |
11446 |
---- ccp4-6.1.3/lib/ccif/f_interface.c |
11447 |
-+++ ccp4-6.1.3/lib/ccif/f_interface.c |
11448 |
-@@ -926,7 +926,7 @@ |
11449 |
- #endif |
11450 |
- |
11451 |
- { |
11452 |
-- char logname_c[81]; |
11453 |
-+ char logname_c[MAXFLEN]; |
11454 |
- size_t Length; |
11455 |
- int unit; |
11456 |
- CIF_FILE_LIST file_list_entry; |
11457 |
-@@ -4064,7 +4064,7 @@ |
11458 |
- #endif |
11459 |
- |
11460 |
- { |
11461 |
-- char lognam_c[81], *blknam_c; |
11462 |
-+ char lognam_c[MAXFLEN], *blknam_c; |
11463 |
- size_t loglen, blklen; |
11464 |
- int i, j, new; |
11465 |
- |
11466 |
---- ccp4-6.1.3/lib/src/ccp4_diskio_f.c |
11467 |
-+++ ccp4-6.1.3/lib/src/ccp4_diskio_f.c |
11468 |
-@@ -705,7 +705,7 @@ |
11469 |
- log_name = strdup("diskio.dft"); |
11470 |
- if (!(file_name = getenv(log_name))) |
11471 |
- file_name = log_name; |
11472 |
-- for ( *istrm = 1; *istrm == MAXFILES; *istrm++) |
11473 |
-+ for ( *istrm = 1; *istrm < MAXFILES; *istrm++) |
11474 |
- if (!strcmp(file_name,_ioChannels[*istrm]->iobj->name)) break; |
11475 |
- } |
11476 |
- if (*istrm != MAXFILES) { |
11477 |
|
11478 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch |
11479 |
deleted file mode 100644 |
11480 |
index 4271d5b..0000000 |
11481 |
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch |
11482 |
+++ /dev/null |
11483 |
@@ -1,367 +0,0 @@ |
11484 |
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp |
11485 |
-index 69b32b0..602e35f 100755 |
11486 |
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp |
11487 |
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp |
11488 |
-@@ -6,10 +6,10 @@ |
11489 |
- // images. |
11490 |
- |
11491 |
- #include "DiffractionImage.h" |
11492 |
--#include "cbf.h" |
11493 |
--#include "cbf_simple.h" |
11494 |
--#include "cbf_string.h" |
11495 |
--#include "cbf_byte_offset.h" |
11496 |
-+#include <cbflib/cbf.h> |
11497 |
-+#include <cbflib/cbf_simple.h> |
11498 |
-+#include <cbflib/cbf_string.h> |
11499 |
-+#include <cbflib/cbf_byte_offset.h> |
11500 |
- |
11501 |
- |
11502 |
- using namespace std; |
11503 |
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am |
11504 |
-index fedb7ac..89a048e 100755 |
11505 |
---- a/lib/DiffractionImage/MAR/Makefile.am |
11506 |
-+++ b/lib/DiffractionImage/MAR/Makefile.am |
11507 |
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu |
11508 |
- |
11509 |
- noinst_LTLIBRARIES = libmar.la |
11510 |
- |
11511 |
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include |
11512 |
-+AM_CPPFLAGS = |
11513 |
- |
11514 |
- libmar_la_SOURCES = mar300_header.c \ |
11515 |
- mar345_header.c \ |
11516 |
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ |
11517 |
- utils.c \ |
11518 |
- pck.c |
11519 |
- |
11520 |
--libmar_la_LDFLAGS = -static |
11521 |
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c |
11522 |
-index d3f4212..2c37108 100755 |
11523 |
---- a/lib/DiffractionImage/MAR/marcif.c |
11524 |
-+++ b/lib/DiffractionImage/MAR/marcif.c |
11525 |
-@@ -31,8 +31,7 @@ |
11526 |
- #include "marcif_header.h" |
11527 |
- #include "mar345_header.h" |
11528 |
- |
11529 |
--#include <cbf.h> |
11530 |
--#include <img.h> |
11531 |
-+#include <cbflib/cbf.h> |
11532 |
- |
11533 |
- #define printe(x) printf("%s: %s: %s\n",prg,f,x) |
11534 |
- #undef cbf_failnez |
11535 |
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am |
11536 |
-index 189a1d7..6652576 100755 |
11537 |
---- a/lib/DiffractionImage/Makefile.am |
11538 |
-+++ b/lib/DiffractionImage/Makefile.am |
11539 |
-@@ -1,7 +1,9 @@ |
11540 |
- AUTOMAKE_OPTIONS = gnu |
11541 |
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg |
11542 |
-+SUBDIRS = Bruker MAR Rigaku |
11543 |
- |
11544 |
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg |
11545 |
-+SYSLIBS = -ljpeg -lcbf |
11546 |
-+ |
11547 |
-+AM_CPPFLAGS =-I./MAR |
11548 |
- lib_LTLIBRARIES = libDiffImage.la |
11549 |
- |
11550 |
- if WANT_PYTHONMOD |
11551 |
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ |
11552 |
- Profile.cpp \ |
11553 |
- Peak.cpp \ |
11554 |
- dps_peaksearch_cn.c |
11555 |
--libDiffImage_la_LDFLAGS = -static |
11556 |
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) |
11557 |
-+libDiffImage_la_LIBADD = $(SYSLIBS) \ |
11558 |
-+ ./MAR/libmar.la ./Bruker/libbruker.la \ |
11559 |
-+ ./Rigaku/librigaku.la |
11560 |
- |
11561 |
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ |
11562 |
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ |
11563 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11564 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11565 |
-+ ./Rigaku/librigaku.la |
11566 |
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp |
11567 |
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11568 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11569 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11570 |
-- --no-whole-archive -rpath '$(libdir)' |
11571 |
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11572 |
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ |
11573 |
-+ libDiffImage.la \ |
11574 |
-+ ./Bruker/libbruker.la \ |
11575 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11576 |
- |
11577 |
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
11578 |
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ |
11579 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11580 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11581 |
-+ ./Rigaku/librigaku.la |
11582 |
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp |
11583 |
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11584 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11585 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11586 |
-- --no-whole-archive -rpath '$(libdir)' |
11587 |
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11588 |
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ |
11589 |
-+ ./Bruker/libbruker.la \ |
11590 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11591 |
- |
11592 |
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
11593 |
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ |
11594 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11595 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11596 |
-+ ./Rigaku/librigaku.la |
11597 |
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp |
11598 |
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11599 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11600 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11601 |
-- --no-whole-archive -rpath '$(libdir)' |
11602 |
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11603 |
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ |
11604 |
-+ ./Bruker/libbruker.la $(SYSLIBS) \ |
11605 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11606 |
- |
11607 |
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg |
11608 |
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
11609 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11610 |
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
11611 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
11612 |
- automask_SOURCES = automask.cpp |
11613 |
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
11614 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11615 |
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS) |
11616 |
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ |
11617 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11618 |
- diffdump_SOURCES = diffdump.cpp |
11619 |
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
11620 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11621 |
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) |
11622 |
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
11623 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
11624 |
- printpeaks_SOURCES = printpeaks.cpp |
11625 |
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
11626 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11627 |
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) |
11628 |
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
11629 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
11630 |
- diff2jpeg_SOURCES = diff2jpeg.cpp |
11631 |
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) |
11632 |
- |
11633 |
- install-data-local: |
11634 |
- @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} |
11635 |
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure |
11636 |
-index 3fb5784..fdf9683 100755 |
11637 |
---- a/lib/DiffractionImage/configure |
11638 |
-+++ b/lib/DiffractionImage/configure |
11639 |
-@@ -21768,7 +21768,7 @@ _ACEOF |
11640 |
- fi |
11641 |
- |
11642 |
- |
11643 |
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" |
11644 |
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " |
11645 |
- |
11646 |
- |
11647 |
- cat >confcache <<\_ACEOF |
11648 |
-@@ -22407,12 +22407,9 @@ do |
11649 |
- case $ac_config_target in |
11650 |
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; |
11651 |
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; |
11652 |
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; |
11653 |
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; |
11654 |
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; |
11655 |
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; |
11656 |
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; |
11657 |
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; |
11658 |
- |
11659 |
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 |
11660 |
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;} |
11661 |
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in |
11662 |
-index 7f54b4b..16efc64 100755 |
11663 |
---- a/lib/DiffractionImage/configure.in |
11664 |
-+++ b/lib/DiffractionImage/configure.in |
11665 |
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then |
11666 |
- HAVE_PYTHON=1 |
11667 |
- CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" |
11668 |
- ]) |
11669 |
-+ PYLIB="-lpython${PYTHON_VER}" |
11670 |
-+ AC_SUBST(PYLIB) |
11671 |
- fi |
11672 |
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) |
11673 |
- |
11674 |
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) |
11675 |
- AC_CHECK_LIB([m], [sqrt]) |
11676 |
- |
11677 |
- AC_CONFIG_FILES([Makefile |
11678 |
-- CBFlib/Makefile |
11679 |
-- CBFlib/src/Makefile |
11680 |
- MAR/Makefile |
11681 |
- Rigaku/Makefile |
11682 |
-- Bruker/Makefile |
11683 |
-- jpg/Makefile]) |
11684 |
-+ Bruker/Makefile]) |
11685 |
- |
11686 |
- AC_OUTPUT |
11687 |
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am |
11688 |
-index e9554e1..a3ba33d 100755 |
11689 |
---- a/lib/ssm/Makefile.am |
11690 |
-+++ b/lib/ssm/Makefile.am |
11691 |
-@@ -1,7 +1,11 @@ |
11692 |
-+ACLOCAL_AMFLAGS = -I macros |
11693 |
- #libtool |
11694 |
- lib_LTLIBRARIES = libssm.la |
11695 |
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) |
11696 |
-+libssm_la_CFLAGS = @MMDB_CFLAGS@ |
11697 |
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ |
11698 |
- ssm_align.cpp ss_graph.cpp |
11699 |
-+libssm_la_LIBADD = @MMDB_LIBS@ |
11700 |
- |
11701 |
- #non libtool |
11702 |
- #lib_LIBRARIES = libssm.a |
11703 |
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp |
11704 |
- |
11705 |
- bin_PROGRAMS = superpose |
11706 |
- |
11707 |
--INCLUDES = $(MMDB_CXXFLAGS) |
11708 |
-- |
11709 |
--AM_LDFLAGS = $(MMDB_LIBS) |
11710 |
-+INCLUDES = @MMDB_CFLAGS@ |
11711 |
- |
11712 |
- EXTRA_DIST = macros/mmdb.m4 |
11713 |
- |
11714 |
--superpose_LDADD = libssm.la |
11715 |
-+superpose_LDADD = libssm.la @MMDB_LIBS@ |
11716 |
- |
11717 |
- libssm_a_AR = $(AR) $(AR_FLAGS) |
11718 |
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac |
11719 |
-index 783cb46..d637d11 100755 |
11720 |
---- a/lib/ssm/configure.ac |
11721 |
-+++ b/lib/ssm/configure.ac |
11722 |
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, |
11723 |
- [ac_cv_enable_debug=no ] ) |
11724 |
- |
11725 |
- dnl Optional: Check for MMDB. |
11726 |
--AM_PATH_MMDB(, |
11727 |
-- [ if test "x$mmdb_prefix" != x ; then |
11728 |
-- if test "x$ac_MMDB_CXXFLAGS" != x ; then |
11729 |
-- case "$ac_MMDB_CXXFLAGS" in |
11730 |
-- *src/mmdb ) |
11731 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` |
11732 |
-- ;; |
11733 |
-- *include/mmdb ) |
11734 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` |
11735 |
-- ;; |
11736 |
-- *) |
11737 |
-- esac |
11738 |
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" |
11739 |
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` |
11740 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
11741 |
-- else |
11742 |
-- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" |
11743 |
-- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" |
11744 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
11745 |
-- fi |
11746 |
-- else |
11747 |
-- AC_MSG_WARN([mmdb not found]) |
11748 |
-- fi |
11749 |
-- ] |
11750 |
--) |
11751 |
-+ |
11752 |
-+PKG_CHECK_MODULES([MMDB],[mmdb]) |
11753 |
-+AC_SUBST([MMDB_CFLAGS]) |
11754 |
-+AC_SUBST([MMDB_LIBS]) |
11755 |
- |
11756 |
- # Checks for typedefs, structures, and compiler characteristics. |
11757 |
- # |
11758 |
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) |
11759 |
- # test for function in m |
11760 |
- AC_CHECK_LIB([m], [sqrt]) |
11761 |
- |
11762 |
-+ |
11763 |
- AC_SUBST(AR_FLAGS) |
11764 |
- AC_SUBST(superpose_LDFLAGS) |
11765 |
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) |
11766 |
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am |
11767 |
-index 094fd6b..922a131 100755 |
11768 |
---- a/src/pisa/Makefile.am |
11769 |
-+++ b/src/pisa/Makefile.am |
11770 |
-@@ -1,3 +1,4 @@ |
11771 |
-+ACLOCAL_AMFLAGS = -I macros |
11772 |
- SUBDIRS = molref pisastore sbase |
11773 |
- |
11774 |
- pkgdatadir = $(datadir)/pisa |
11775 |
-@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp |
11776 |
- |
11777 |
- bin_PROGRAMS = pisa |
11778 |
- |
11779 |
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) |
11780 |
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) |
11781 |
- |
11782 |
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) |
11783 |
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ |
11784 |
- |
11785 |
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in |
11786 |
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac |
11787 |
-index 81afdda..4f99df6 100755 |
11788 |
---- a/src/pisa/configure.ac |
11789 |
-+++ b/src/pisa/configure.ac |
11790 |
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) |
11791 |
- AC_CHECK_LIB([m], [sqrt]) |
11792 |
- |
11793 |
- dnl Optional: Check for MMDB. |
11794 |
--AM_PATH_MMDB(, |
11795 |
-- [ if test "x$mmdb_prefix" != x ; then |
11796 |
-- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then |
11797 |
-- case "$ac_MMDB_CXXFLAGS" in |
11798 |
-- *src/mmdb ) |
11799 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` |
11800 |
-- ;; |
11801 |
-- *include/mmdb ) |
11802 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` |
11803 |
-- ;; |
11804 |
-- *) |
11805 |
-- esac |
11806 |
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" |
11807 |
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` |
11808 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
11809 |
-- else |
11810 |
-- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" |
11811 |
-- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" |
11812 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
11813 |
-- fi |
11814 |
-- else |
11815 |
-- AC_MSG_ERROR([mmdb not found]) |
11816 |
-- fi |
11817 |
-- ] |
11818 |
--) |
11819 |
-+PKG_CHECK_MODULES([MMDB],[mmdb]) |
11820 |
-+AC_SUBST([MMDB_CFLAGS]) |
11821 |
-+AC_SUBST([MMDB_LIBS]) |
11822 |
- |
11823 |
- ac_saved_CXXFLAGS=$CXXFLAGS |
11824 |
- ac_saved_LIBS=$LIBS |
11825 |
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" |
11826 |
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" |
11827 |
- LIBS="$MMDB_LIBS $LIBS" |
11828 |
- AM_PATH_SSM(, |
11829 |
- [ if test "x$ssm_prefix" != x ; then |
11830 |
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am |
11831 |
-index e78b10d..486b931 100755 |
11832 |
---- a/src/rapper/Makefile.am |
11833 |
-+++ b/src/rapper/Makefile.am |
11834 |
-@@ -1,3 +1,3 @@ |
11835 |
--SUBDIRS = libxml2 gc7.0 LOOP data |
11836 |
-+SUBDIRS = LOOP data |
11837 |
- |
11838 |
- EXTRA_DIST = |
11839 |
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac |
11840 |
-index 5e4ef69..11b63ec 100755 |
11841 |
---- a/src/rapper/configure.ac |
11842 |
-+++ b/src/rapper/configure.ac |
11843 |
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) |
11844 |
- |
11845 |
- AC_SUBST(rapper_LDFLAGS) |
11846 |
- |
11847 |
--AC_CONFIG_SUBDIRS([gc7.0 libxml2]) |
11848 |
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) |
11849 |
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) |
11850 |
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) |
11851 |
|
11852 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch |
11853 |
deleted file mode 100644 |
11854 |
index c787df9..0000000 |
11855 |
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch |
11856 |
+++ /dev/null |
11857 |
@@ -1,395 +0,0 @@ |
11858 |
- lib/DiffractionImage/DiffractionImageCBF.cpp | 8 ++-- |
11859 |
- lib/DiffractionImage/MAR/Makefile.am | 3 +- |
11860 |
- lib/DiffractionImage/MAR/marcif.c | 3 +- |
11861 |
- lib/DiffractionImage/Makefile.am | 68 +++++++++++++++----------- |
11862 |
- lib/DiffractionImage/configure | 5 +-- |
11863 |
- lib/DiffractionImage/configure.in | 7 +-- |
11864 |
- lib/src/Makefile.in | 2 +- |
11865 |
- lib/ssm/Makefile.am | 10 ++-- |
11866 |
- lib/ssm/configure.ac | 30 ++--------- |
11867 |
- src/pisa/Makefile.am | 5 +- |
11868 |
- src/pisa/configure.ac | 30 ++---------- |
11869 |
- src/rapper/Makefile.am | 2 +- |
11870 |
- src/rapper/configure.ac | 2 +- |
11871 |
- 13 files changed, 70 insertions(+), 105 deletions(-) |
11872 |
- |
11873 |
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp |
11874 |
-index 69b32b0..602e35f 100755 |
11875 |
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp |
11876 |
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp |
11877 |
-@@ -6,10 +6,10 @@ |
11878 |
- // images. |
11879 |
- |
11880 |
- #include "DiffractionImage.h" |
11881 |
--#include "cbf.h" |
11882 |
--#include "cbf_simple.h" |
11883 |
--#include "cbf_string.h" |
11884 |
--#include "cbf_byte_offset.h" |
11885 |
-+#include <cbflib/cbf.h> |
11886 |
-+#include <cbflib/cbf_simple.h> |
11887 |
-+#include <cbflib/cbf_string.h> |
11888 |
-+#include <cbflib/cbf_byte_offset.h> |
11889 |
- |
11890 |
- |
11891 |
- using namespace std; |
11892 |
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am |
11893 |
-index fedb7ac..89a048e 100755 |
11894 |
---- a/lib/DiffractionImage/MAR/Makefile.am |
11895 |
-+++ b/lib/DiffractionImage/MAR/Makefile.am |
11896 |
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu |
11897 |
- |
11898 |
- noinst_LTLIBRARIES = libmar.la |
11899 |
- |
11900 |
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include |
11901 |
-+AM_CPPFLAGS = |
11902 |
- |
11903 |
- libmar_la_SOURCES = mar300_header.c \ |
11904 |
- mar345_header.c \ |
11905 |
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ |
11906 |
- utils.c \ |
11907 |
- pck.c |
11908 |
- |
11909 |
--libmar_la_LDFLAGS = -static |
11910 |
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c |
11911 |
-index d3f4212..2c37108 100755 |
11912 |
---- a/lib/DiffractionImage/MAR/marcif.c |
11913 |
-+++ b/lib/DiffractionImage/MAR/marcif.c |
11914 |
-@@ -31,8 +31,7 @@ |
11915 |
- #include "marcif_header.h" |
11916 |
- #include "mar345_header.h" |
11917 |
- |
11918 |
--#include <cbf.h> |
11919 |
--#include <img.h> |
11920 |
-+#include <cbflib/cbf.h> |
11921 |
- |
11922 |
- #define printe(x) printf("%s: %s: %s\n",prg,f,x) |
11923 |
- #undef cbf_failnez |
11924 |
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am |
11925 |
-index 189a1d7..6652576 100755 |
11926 |
---- a/lib/DiffractionImage/Makefile.am |
11927 |
-+++ b/lib/DiffractionImage/Makefile.am |
11928 |
-@@ -1,7 +1,9 @@ |
11929 |
- AUTOMAKE_OPTIONS = gnu |
11930 |
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg |
11931 |
-+SUBDIRS = Bruker MAR Rigaku |
11932 |
- |
11933 |
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg |
11934 |
-+SYSLIBS = -ljpeg -lcbf |
11935 |
-+ |
11936 |
-+AM_CPPFLAGS =-I./MAR |
11937 |
- lib_LTLIBRARIES = libDiffImage.la |
11938 |
- |
11939 |
- if WANT_PYTHONMOD |
11940 |
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ |
11941 |
- Profile.cpp \ |
11942 |
- Peak.cpp \ |
11943 |
- dps_peaksearch_cn.c |
11944 |
--libDiffImage_la_LDFLAGS = -static |
11945 |
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) |
11946 |
-+libDiffImage_la_LIBADD = $(SYSLIBS) \ |
11947 |
-+ ./MAR/libmar.la ./Bruker/libbruker.la \ |
11948 |
-+ ./Rigaku/librigaku.la |
11949 |
- |
11950 |
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ |
11951 |
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ |
11952 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11953 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11954 |
-+ ./Rigaku/librigaku.la |
11955 |
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp |
11956 |
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11957 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11958 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11959 |
-- --no-whole-archive -rpath '$(libdir)' |
11960 |
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11961 |
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ |
11962 |
-+ libDiffImage.la \ |
11963 |
-+ ./Bruker/libbruker.la \ |
11964 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11965 |
- |
11966 |
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
11967 |
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ |
11968 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11969 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11970 |
-+ ./Rigaku/librigaku.la |
11971 |
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp |
11972 |
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11973 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11974 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11975 |
-- --no-whole-archive -rpath '$(libdir)' |
11976 |
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11977 |
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ |
11978 |
-+ ./Bruker/libbruker.la \ |
11979 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11980 |
- |
11981 |
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
11982 |
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ |
11983 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
11984 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11985 |
-+ ./Rigaku/librigaku.la |
11986 |
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp |
11987 |
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
11988 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
11989 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
11990 |
-- --no-whole-archive -rpath '$(libdir)' |
11991 |
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) |
11992 |
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ |
11993 |
-+ ./Bruker/libbruker.la $(SYSLIBS) \ |
11994 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
11995 |
- |
11996 |
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg |
11997 |
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
11998 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
11999 |
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
12000 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
12001 |
- automask_SOURCES = automask.cpp |
12002 |
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12003 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12004 |
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS) |
12005 |
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ |
12006 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
12007 |
- diffdump_SOURCES = diffdump.cpp |
12008 |
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12009 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12010 |
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) |
12011 |
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
12012 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
12013 |
- printpeaks_SOURCES = printpeaks.cpp |
12014 |
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12015 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12016 |
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) |
12017 |
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ |
12018 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) |
12019 |
- diff2jpeg_SOURCES = diff2jpeg.cpp |
12020 |
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) |
12021 |
- |
12022 |
- install-data-local: |
12023 |
- @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} |
12024 |
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure |
12025 |
-index 3fb5784..fdf9683 100755 |
12026 |
---- a/lib/DiffractionImage/configure |
12027 |
-+++ b/lib/DiffractionImage/configure |
12028 |
-@@ -21768,7 +21768,7 @@ _ACEOF |
12029 |
- fi |
12030 |
- |
12031 |
- |
12032 |
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" |
12033 |
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " |
12034 |
- |
12035 |
- |
12036 |
- cat >confcache <<\_ACEOF |
12037 |
-@@ -22407,12 +22407,9 @@ do |
12038 |
- case $ac_config_target in |
12039 |
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; |
12040 |
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; |
12041 |
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; |
12042 |
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; |
12043 |
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; |
12044 |
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; |
12045 |
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; |
12046 |
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; |
12047 |
- |
12048 |
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 |
12049 |
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;} |
12050 |
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in |
12051 |
-index 7f54b4b..16efc64 100755 |
12052 |
---- a/lib/DiffractionImage/configure.in |
12053 |
-+++ b/lib/DiffractionImage/configure.in |
12054 |
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then |
12055 |
- HAVE_PYTHON=1 |
12056 |
- CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" |
12057 |
- ]) |
12058 |
-+ PYLIB="-lpython${PYTHON_VER}" |
12059 |
-+ AC_SUBST(PYLIB) |
12060 |
- fi |
12061 |
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) |
12062 |
- |
12063 |
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) |
12064 |
- AC_CHECK_LIB([m], [sqrt]) |
12065 |
- |
12066 |
- AC_CONFIG_FILES([Makefile |
12067 |
-- CBFlib/Makefile |
12068 |
-- CBFlib/src/Makefile |
12069 |
- MAR/Makefile |
12070 |
- Rigaku/Makefile |
12071 |
-- Bruker/Makefile |
12072 |
-- jpg/Makefile]) |
12073 |
-+ Bruker/Makefile]) |
12074 |
- |
12075 |
- AC_OUTPUT |
12076 |
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in |
12077 |
-index c23f488..9579b3b 100755 |
12078 |
---- a/lib/src/Makefile.in |
12079 |
-+++ b/lib/src/Makefile.in |
12080 |
-@@ -659,7 +659,7 @@ csymlib.o: $(srcdir)/csymlib.c $(srcdir)/csymlib.h |
12081 |
- csymlib_f.o: $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h |
12082 |
- ccp4_unitcell.o: $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h |
12083 |
- ccp4_unitcell_f.o: $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h |
12084 |
--hybrid_36_f.o: $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h |
12085 |
-+hybrid_36_f.o: $(srcdir)/hybrid_36_f.c |
12086 |
- cvecmat.o: $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h |
12087 |
- cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c $(srcdir)/mtzdata.h |
12088 |
- cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c |
12089 |
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am |
12090 |
-index e9554e1..a3ba33d 100755 |
12091 |
---- a/lib/ssm/Makefile.am |
12092 |
-+++ b/lib/ssm/Makefile.am |
12093 |
-@@ -1,7 +1,11 @@ |
12094 |
-+ACLOCAL_AMFLAGS = -I macros |
12095 |
- #libtool |
12096 |
- lib_LTLIBRARIES = libssm.la |
12097 |
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) |
12098 |
-+libssm_la_CFLAGS = @MMDB_CFLAGS@ |
12099 |
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ |
12100 |
- ssm_align.cpp ss_graph.cpp |
12101 |
-+libssm_la_LIBADD = @MMDB_LIBS@ |
12102 |
- |
12103 |
- #non libtool |
12104 |
- #lib_LIBRARIES = libssm.a |
12105 |
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp |
12106 |
- |
12107 |
- bin_PROGRAMS = superpose |
12108 |
- |
12109 |
--INCLUDES = $(MMDB_CXXFLAGS) |
12110 |
-- |
12111 |
--AM_LDFLAGS = $(MMDB_LIBS) |
12112 |
-+INCLUDES = @MMDB_CFLAGS@ |
12113 |
- |
12114 |
- EXTRA_DIST = macros/mmdb.m4 |
12115 |
- |
12116 |
--superpose_LDADD = libssm.la |
12117 |
-+superpose_LDADD = libssm.la @MMDB_LIBS@ |
12118 |
- |
12119 |
- libssm_a_AR = $(AR) $(AR_FLAGS) |
12120 |
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac |
12121 |
-index 783cb46..d637d11 100755 |
12122 |
---- a/lib/ssm/configure.ac |
12123 |
-+++ b/lib/ssm/configure.ac |
12124 |
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, |
12125 |
- [ac_cv_enable_debug=no ] ) |
12126 |
- |
12127 |
- dnl Optional: Check for MMDB. |
12128 |
--AM_PATH_MMDB(, |
12129 |
-- [ if test "x$mmdb_prefix" != x ; then |
12130 |
-- if test "x$ac_MMDB_CXXFLAGS" != x ; then |
12131 |
-- case "$ac_MMDB_CXXFLAGS" in |
12132 |
-- *src/mmdb ) |
12133 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` |
12134 |
-- ;; |
12135 |
-- *include/mmdb ) |
12136 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` |
12137 |
-- ;; |
12138 |
-- *) |
12139 |
-- esac |
12140 |
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" |
12141 |
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` |
12142 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
12143 |
-- else |
12144 |
-- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" |
12145 |
-- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" |
12146 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
12147 |
-- fi |
12148 |
-- else |
12149 |
-- AC_MSG_WARN([mmdb not found]) |
12150 |
-- fi |
12151 |
-- ] |
12152 |
--) |
12153 |
-+ |
12154 |
-+PKG_CHECK_MODULES([MMDB],[mmdb]) |
12155 |
-+AC_SUBST([MMDB_CFLAGS]) |
12156 |
-+AC_SUBST([MMDB_LIBS]) |
12157 |
- |
12158 |
- # Checks for typedefs, structures, and compiler characteristics. |
12159 |
- # |
12160 |
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) |
12161 |
- # test for function in m |
12162 |
- AC_CHECK_LIB([m], [sqrt]) |
12163 |
- |
12164 |
-+ |
12165 |
- AC_SUBST(AR_FLAGS) |
12166 |
- AC_SUBST(superpose_LDFLAGS) |
12167 |
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) |
12168 |
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am |
12169 |
-index 094fd6b..922a131 100755 |
12170 |
---- a/src/pisa/Makefile.am |
12171 |
-+++ b/src/pisa/Makefile.am |
12172 |
-@@ -1,3 +1,4 @@ |
12173 |
-+ACLOCAL_AMFLAGS = -I macros |
12174 |
- SUBDIRS = molref pisastore sbase |
12175 |
- |
12176 |
- pkgdatadir = $(datadir)/pisa |
12177 |
-@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp |
12178 |
- |
12179 |
- bin_PROGRAMS = pisa |
12180 |
- |
12181 |
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) |
12182 |
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) |
12183 |
- |
12184 |
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) |
12185 |
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ |
12186 |
- |
12187 |
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in |
12188 |
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac |
12189 |
-index 81afdda..4f99df6 100755 |
12190 |
---- a/src/pisa/configure.ac |
12191 |
-+++ b/src/pisa/configure.ac |
12192 |
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) |
12193 |
- AC_CHECK_LIB([m], [sqrt]) |
12194 |
- |
12195 |
- dnl Optional: Check for MMDB. |
12196 |
--AM_PATH_MMDB(, |
12197 |
-- [ if test "x$mmdb_prefix" != x ; then |
12198 |
-- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then |
12199 |
-- case "$ac_MMDB_CXXFLAGS" in |
12200 |
-- *src/mmdb ) |
12201 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` |
12202 |
-- ;; |
12203 |
-- *include/mmdb ) |
12204 |
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` |
12205 |
-- ;; |
12206 |
-- *) |
12207 |
-- esac |
12208 |
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" |
12209 |
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` |
12210 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
12211 |
-- else |
12212 |
-- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" |
12213 |
-- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" |
12214 |
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) |
12215 |
-- fi |
12216 |
-- else |
12217 |
-- AC_MSG_ERROR([mmdb not found]) |
12218 |
-- fi |
12219 |
-- ] |
12220 |
--) |
12221 |
-+PKG_CHECK_MODULES([MMDB],[mmdb]) |
12222 |
-+AC_SUBST([MMDB_CFLAGS]) |
12223 |
-+AC_SUBST([MMDB_LIBS]) |
12224 |
- |
12225 |
- ac_saved_CXXFLAGS=$CXXFLAGS |
12226 |
- ac_saved_LIBS=$LIBS |
12227 |
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" |
12228 |
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" |
12229 |
- LIBS="$MMDB_LIBS $LIBS" |
12230 |
- AM_PATH_SSM(, |
12231 |
- [ if test "x$ssm_prefix" != x ; then |
12232 |
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am |
12233 |
-index e78b10d..486b931 100755 |
12234 |
---- a/src/rapper/Makefile.am |
12235 |
-+++ b/src/rapper/Makefile.am |
12236 |
-@@ -1,3 +1,3 @@ |
12237 |
--SUBDIRS = libxml2 gc7.0 LOOP data |
12238 |
-+SUBDIRS = LOOP data |
12239 |
- |
12240 |
- EXTRA_DIST = |
12241 |
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac |
12242 |
-index 5e4ef69..11b63ec 100755 |
12243 |
---- a/src/rapper/configure.ac |
12244 |
-+++ b/src/rapper/configure.ac |
12245 |
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) |
12246 |
- |
12247 |
- AC_SUBST(rapper_LDFLAGS) |
12248 |
- |
12249 |
--AC_CONFIG_SUBDIRS([gc7.0 libxml2]) |
12250 |
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) |
12251 |
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) |
12252 |
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) |
12253 |
|
12254 |
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch |
12255 |
deleted file mode 100644 |
12256 |
index 9697832..0000000 |
12257 |
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch |
12258 |
+++ /dev/null |
12259 |
@@ -1,203 +0,0 @@ |
12260 |
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp |
12261 |
-index 69b32b0..602e35f 100755 |
12262 |
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp |
12263 |
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp |
12264 |
-@@ -6,10 +6,10 @@ |
12265 |
- // images. |
12266 |
- |
12267 |
- #include "DiffractionImage.h" |
12268 |
--#include "cbf.h" |
12269 |
--#include "cbf_simple.h" |
12270 |
--#include "cbf_string.h" |
12271 |
--#include "cbf_byte_offset.h" |
12272 |
-+#include <cbflib/cbf.h> |
12273 |
-+#include <cbflib/cbf_simple.h> |
12274 |
-+#include <cbflib/cbf_string.h> |
12275 |
-+#include <cbflib/cbf_byte_offset.h> |
12276 |
- |
12277 |
- |
12278 |
- using namespace std; |
12279 |
-diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in |
12280 |
-index 4264696..00c4d8d 100755 |
12281 |
---- a/lib/DiffractionImage/MAR/Makefile.in |
12282 |
-+++ b/lib/DiffractionImage/MAR/Makefile.in |
12283 |
-@@ -174,7 +174,7 @@ top_builddir = @top_builddir@ |
12284 |
- top_srcdir = @top_srcdir@ |
12285 |
- AUTOMAKE_OPTIONS = gnu |
12286 |
- noinst_LTLIBRARIES = libmar.la |
12287 |
--AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include |
12288 |
-+AM_CPPFLAGS = |
12289 |
- libmar_la_SOURCES = mar300_header.c \ |
12290 |
- mar345_header.c \ |
12291 |
- marcif.c \ |
12292 |
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c |
12293 |
-index d3f4212..2c37108 100755 |
12294 |
---- a/lib/DiffractionImage/MAR/marcif.c |
12295 |
-+++ b/lib/DiffractionImage/MAR/marcif.c |
12296 |
-@@ -31,8 +31,7 @@ |
12297 |
- #include "marcif_header.h" |
12298 |
- #include "mar345_header.h" |
12299 |
- |
12300 |
--#include <cbf.h> |
12301 |
--#include <img.h> |
12302 |
-+#include <cbflib/cbf.h> |
12303 |
- |
12304 |
- #define printe(x) printf("%s: %s: %s\n",prg,f,x) |
12305 |
- #undef cbf_failnez |
12306 |
-diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in |
12307 |
-index 8197956..807cf25 100755 |
12308 |
---- a/lib/DiffractionImage/Makefile.in |
12309 |
-+++ b/lib/DiffractionImage/Makefile.in |
12310 |
-@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS) |
12311 |
- am_automask_OBJECTS = automask.$(OBJEXT) |
12312 |
- automask_OBJECTS = $(am_automask_OBJECTS) |
12313 |
- automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ |
12314 |
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ |
12315 |
-- ./jpg/libjpeg.la |
12316 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
12317 |
- am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT) |
12318 |
- diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS) |
12319 |
- diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ |
12320 |
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ |
12321 |
-- ./jpg/libjpeg.la |
12322 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
12323 |
- am_diffdump_OBJECTS = diffdump.$(OBJEXT) |
12324 |
- diffdump_OBJECTS = $(am_diffdump_OBJECTS) |
12325 |
- diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ |
12326 |
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ |
12327 |
-- ./jpg/libjpeg.la |
12328 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
12329 |
- am_printpeaks_OBJECTS = printpeaks.$(OBJEXT) |
12330 |
- printpeaks_OBJECTS = $(am_printpeaks_OBJECTS) |
12331 |
- printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ |
12332 |
-- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ |
12333 |
-- ./jpg/libjpeg.la |
12334 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la |
12335 |
- DEFAULT_INCLUDES = -I.@am__isrc@ |
12336 |
- depcomp = $(SHELL) $(top_srcdir)/depcomp |
12337 |
- am__depfiles_maybe = depfiles |
12338 |
-@@ -284,8 +280,8 @@ target_alias = @target_alias@ |
12339 |
- top_builddir = @top_builddir@ |
12340 |
- top_srcdir = @top_srcdir@ |
12341 |
- AUTOMAKE_OPTIONS = gnu |
12342 |
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg |
12343 |
--AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg |
12344 |
-+SUBDIRS = Bruker MAR Rigaku |
12345 |
-+AM_CPPFLAGS = -I./MAR |
12346 |
- lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \ |
12347 |
- $(am__append_3) |
12348 |
- libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ |
12349 |
-@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ |
12350 |
- dps_peaksearch_cn.c |
12351 |
- |
12352 |
- libDiffImage_la_LDFLAGS = -static |
12353 |
--libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
12354 |
-+libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \ |
12355 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
12356 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12357 |
-+ ./Rigaku/librigaku.la |
12358 |
- |
12359 |
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp |
12360 |
- libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
12361 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
12362 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
12363 |
-+ -lcbf ./Bruker/libbruker.la \ |
12364 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ |
12365 |
- --no-whole-archive -rpath '$(libdir)' |
12366 |
- |
12367 |
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
12368 |
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ |
12369 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
12370 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12371 |
-+ ./Rigaku/librigaku.la |
12372 |
- |
12373 |
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp |
12374 |
- lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
12375 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
12376 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
12377 |
-+ -lcbf ./Bruker/libbruker.la \ |
12378 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ |
12379 |
- --no-whole-archive -rpath '$(libdir)' |
12380 |
- |
12381 |
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ |
12382 |
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ |
12383 |
- ./Bruker/libbruker.la ./MAR/libmar.la \ |
12384 |
-- ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12385 |
-+ ./Rigaku/librigaku.la |
12386 |
- |
12387 |
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp |
12388 |
- libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ |
12389 |
-- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ |
12390 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ |
12391 |
-+ -lcbf ./Bruker/libbruker.la \ |
12392 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ |
12393 |
- --no-whole-archive -rpath '$(libdir)' |
12394 |
- |
12395 |
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12396 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12397 |
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ |
12398 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg |
12399 |
- |
12400 |
- automask_SOURCES = automask.cpp |
12401 |
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12402 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12403 |
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ |
12404 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg |
12405 |
- |
12406 |
- diffdump_SOURCES = diffdump.cpp |
12407 |
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12408 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12409 |
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ |
12410 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg |
12411 |
- |
12412 |
- printpeaks_SOURCES = printpeaks.cpp |
12413 |
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ |
12414 |
-- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la |
12415 |
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ |
12416 |
-+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg |
12417 |
- |
12418 |
- diff2jpeg_SOURCES = diff2jpeg.cpp |
12419 |
- all: all-recursive |
12420 |
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure |
12421 |
-index 3fb5784..fdf9683 100755 |
12422 |
---- a/lib/DiffractionImage/configure |
12423 |
-+++ b/lib/DiffractionImage/configure |
12424 |
-@@ -21768,7 +21768,7 @@ _ACEOF |
12425 |
- fi |
12426 |
- |
12427 |
- |
12428 |
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" |
12429 |
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " |
12430 |
- |
12431 |
- |
12432 |
- cat >confcache <<\_ACEOF |
12433 |
-@@ -22407,12 +22407,9 @@ do |
12434 |
- case $ac_config_target in |
12435 |
- "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; |
12436 |
- "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; |
12437 |
-- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; |
12438 |
-- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; |
12439 |
- "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; |
12440 |
- "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; |
12441 |
- "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; |
12442 |
-- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; |
12443 |
- |
12444 |
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 |
12445 |
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;} |
12446 |
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in |
12447 |
-index 7f54b4b..69b10e1 100755 |
12448 |
---- a/lib/DiffractionImage/configure.in |
12449 |
-+++ b/lib/DiffractionImage/configure.in |
12450 |
-@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) |
12451 |
- AC_CHECK_LIB([m], [sqrt]) |
12452 |
- |
12453 |
- AC_CONFIG_FILES([Makefile |
12454 |
-- CBFlib/Makefile |
12455 |
-- CBFlib/src/Makefile |
12456 |
- MAR/Makefile |
12457 |
- Rigaku/Makefile |
12458 |
-- Bruker/Makefile |
12459 |
-- jpg/Makefile]) |
12460 |
-+ Bruker/Makefile]) |
12461 |
- |
12462 |
- AC_OUTPUT |
12463 |
|
12464 |
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch |
12465 |
deleted file mode 100644 |
12466 |
index 367d53e..0000000 |
12467 |
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch |
12468 |
+++ /dev/null |
12469 |
@@ -1,16 +0,0 @@ |
12470 |
- Makefile.in | 2 +- |
12471 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
12472 |
- |
12473 |
-diff --git a/Makefile.in b/Makefile.in |
12474 |
-index 60033eb..13ddbd0 100755 |
12475 |
---- a/Makefile.in |
12476 |
-+++ b/Makefile.in |
12477 |
-@@ -53,7 +53,7 @@ clipper: FORCE fftw |
12478 |
- |
12479 |
- diffractionImg: |
12480 |
- if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \ |
12481 |
-- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi |
12482 |
-+ $(MAKE) $(MFLAGS) $(MVARS); fi |
12483 |
- |
12484 |
- ssm: |
12485 |
- if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \ |
12486 |
|
12487 |
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch |
12488 |
deleted file mode 100644 |
12489 |
index caf62bb..0000000 |
12490 |
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch |
12491 |
+++ /dev/null |
12492 |
@@ -1,16 +0,0 @@ |
12493 |
- lib/DiffractionImage/DiffractionImagePythonInterface.cpp | 2 +- |
12494 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
12495 |
- |
12496 |
-diff --git a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp |
12497 |
-index f729fc5..4c24e82 100755 |
12498 |
---- a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp |
12499 |
-+++ b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp |
12500 |
-@@ -867,7 +867,7 @@ SWIG_Python_AddErrorMsg(const char* mesg) |
12501 |
- Py_DECREF(old_str); |
12502 |
- Py_DECREF(value); |
12503 |
- } else { |
12504 |
-- PyErr_Format(PyExc_RuntimeError, mesg); |
12505 |
-+ PyErr_Format(PyExc_RuntimeError, "%s", mesg); |
12506 |
- } |
12507 |
- } |
12508 |
- |
12509 |
|
12510 |
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml |
12511 |
deleted file mode 100644 |
12512 |
index c0432fe..0000000 |
12513 |
--- a/sci-libs/ccp4-libs/metadata.xml |
12514 |
+++ /dev/null |
12515 |
@@ -1,9 +0,0 @@ |
12516 |
-<?xml version="1.0" encoding="UTF-8"?> |
12517 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
12518 |
-<pkgmetadata> |
12519 |
- <herd>sci-chemistry</herd> |
12520 |
- <maintainer> |
12521 |
- <email>jlec@g.o</email> |
12522 |
- <name>Justin Lecher (jlec)</name> |
12523 |
- </maintainer> |
12524 |
-</pkgmetadata> |
12525 |
|
12526 |
diff --git a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild b/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild |
12527 |
deleted file mode 100644 |
12528 |
index 1757c69..0000000 |
12529 |
--- a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild |
12530 |
+++ /dev/null |
12531 |
@@ -1,58 +0,0 @@ |
12532 |
-# Copyright 1999-2013 Gentoo Foundation |
12533 |
-# Distributed under the terms of the GNU General Public License v2 |
12534 |
-# $Id$ |
12535 |
- |
12536 |
-EAPI=4 |
12537 |
- |
12538 |
-AUTOTOOLS_AUTORECONF=true |
12539 |
- |
12540 |
-inherit autotools-utils eutils flag-o-matic |
12541 |
- |
12542 |
-MY_PV=${PV/_p/-} |
12543 |
-MY_P="${PN}-${MY_PV}" |
12544 |
- |
12545 |
-DESCRIPTION="Object-oriented libraries for crystallographic data and crystallographic computation" |
12546 |
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html" |
12547 |
-SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/${MY_P}-ac.tar.gz" |
12548 |
- |
12549 |
-LICENSE="LGPL-2.1" |
12550 |
-SLOT="0" |
12551 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
12552 |
-IUSE="debug static-libs" |
12553 |
- |
12554 |
-RDEPEND=" |
12555 |
- sci-libs/ccp4-libs |
12556 |
- sci-libs/fftw |
12557 |
- sci-libs/mmdb" |
12558 |
-DEPEND="${RDEPEND}" |
12559 |
- |
12560 |
-S="${WORKDIR}"/${PN}-2.1 |
12561 |
- |
12562 |
-PATCHES=( |
12563 |
- "${FILESDIR}"/20091215-missing-var.patch |
12564 |
- "${FILESDIR}"/${PV}-makefile.patch |
12565 |
- "${FILESDIR}"/${P}-outofsourcebuild.patch |
12566 |
- ) |
12567 |
- |
12568 |
-src_configure() { |
12569 |
- # Recommended on ccp4bb/coot ML to fix crashes when calculating maps |
12570 |
- # on 64-bit systems |
12571 |
- append-flags -fno-strict-aliasing |
12572 |
- |
12573 |
- local myeconfargs=( |
12574 |
- --enable-ccp4 |
12575 |
- --enable-cif |
12576 |
- --enable-cns |
12577 |
- --enable-contrib |
12578 |
- --enable-minimol |
12579 |
- --enable-mmdb |
12580 |
- --enable-phs |
12581 |
- --with-mmdb="${EPREFIX}/usr" |
12582 |
- $(use_enable debug) |
12583 |
- ) |
12584 |
- autotools-utils_src_configure |
12585 |
-} |
12586 |
- |
12587 |
-src_test() { |
12588 |
- emake -C "${AUTOTOOLS_BUILD_DIR}"/examples check |
12589 |
-} |
12590 |
|
12591 |
diff --git a/sci-libs/coot-data/coot-data-2-r1.ebuild b/sci-libs/coot-data/coot-data-2-r1.ebuild |
12592 |
deleted file mode 100644 |
12593 |
index 1640d46..0000000 |
12594 |
--- a/sci-libs/coot-data/coot-data-2-r1.ebuild |
12595 |
+++ /dev/null |
12596 |
@@ -1,33 +0,0 @@ |
12597 |
-# Copyright 1999-2013 Gentoo Foundation |
12598 |
-# Distributed under the terms of the GNU General Public License v2 |
12599 |
-# $Id$ |
12600 |
- |
12601 |
-EAPI=5 |
12602 |
- |
12603 |
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit" |
12604 |
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/" |
12605 |
-#SRC_URI="http://lmb.bioch.ox.ac.uk/coot/software/dependencies/reference-structures.tar.gz" |
12606 |
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz" |
12607 |
- |
12608 |
-LICENSE="GPL-3" |
12609 |
-SLOT="0" |
12610 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12611 |
-IUSE="" |
12612 |
- |
12613 |
-RESTRICT="binchecks strip" |
12614 |
- |
12615 |
-S="${WORKDIR}" |
12616 |
- |
12617 |
-src_install() { |
12618 |
- insinto /usr/share/coot |
12619 |
- doins -r reference-structures |
12620 |
- |
12621 |
- # Coot looks in the wrong spot for the monomer library |
12622 |
- # Listens to ccp4's CCP4_LIB rather than CLIBD_MON |
12623 |
- cat >> "${T}"/coot <<- EOF |
12624 |
- COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/" |
12625 |
- COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/" |
12626 |
- EOF |
12627 |
- |
12628 |
- newenvd "${T}"/coot 20coot |
12629 |
-} |
12630 |
|
12631 |
diff --git a/sci-libs/coot-data/coot-data-2.ebuild b/sci-libs/coot-data/coot-data-2.ebuild |
12632 |
deleted file mode 100644 |
12633 |
index 2b7d331..0000000 |
12634 |
--- a/sci-libs/coot-data/coot-data-2.ebuild |
12635 |
+++ /dev/null |
12636 |
@@ -1,33 +0,0 @@ |
12637 |
-# Copyright 1999-2011 Gentoo Foundation |
12638 |
-# Distributed under the terms of the GNU General Public License v2 |
12639 |
-# $Id$ |
12640 |
- |
12641 |
-EAPI="3" |
12642 |
- |
12643 |
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit" |
12644 |
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/" |
12645 |
-#SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz" |
12646 |
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz" |
12647 |
- |
12648 |
-LICENSE="GPL-3" |
12649 |
-SLOT="0" |
12650 |
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12651 |
-IUSE="" |
12652 |
- |
12653 |
-RESTRICT="binchecks strip" |
12654 |
- |
12655 |
-S="${WORKDIR}" |
12656 |
- |
12657 |
-src_install() { |
12658 |
- insinto /usr/share/coot |
12659 |
- doins -r reference-structures || die |
12660 |
- |
12661 |
- # Coot looks in the wrong spot for the monomer library |
12662 |
- # Listens to ccp4's CCP4_LIB rather than CLIBD_MON |
12663 |
- cat >> "${T}"/coot <<- EOF |
12664 |
- COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/" |
12665 |
- COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/" |
12666 |
- EOF |
12667 |
- |
12668 |
- newenvd "${T}"/coot 20coot || die |
12669 |
-} |
12670 |
|
12671 |
diff --git a/sci-libs/mmdb/mmdb-1.24.ebuild b/sci-libs/mmdb/mmdb-1.24.ebuild |
12672 |
deleted file mode 100644 |
12673 |
index f44a3ae..0000000 |
12674 |
--- a/sci-libs/mmdb/mmdb-1.24.ebuild |
12675 |
+++ /dev/null |
12676 |
@@ -1,45 +0,0 @@ |
12677 |
-# Copyright 1999-2015 Gentoo Foundation |
12678 |
-# Distributed under the terms of the GNU General Public License v2 |
12679 |
-# $Id$ |
12680 |
- |
12681 |
-EAPI=4 |
12682 |
- |
12683 |
-inherit autotools-utils |
12684 |
- |
12685 |
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" |
12686 |
-HOMEPAGE="https://launchpad.net/mmdb/" |
12687 |
-SRC_URI=" |
12688 |
- http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz |
12689 |
- https://launchpad.net/mmdb/1.23/${PV}/+download/${P}.tar.gz" |
12690 |
- |
12691 |
-LICENSE="GPL-2 LGPL-3" |
12692 |
-SLOT="0" |
12693 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12694 |
-IUSE="static-libs" |
12695 |
- |
12696 |
-DEPEND="!<sci-libs/ccp4-libs-6.1.3" |
12697 |
-RDEPEND="" |
12698 |
- |
12699 |
-src_install() { |
12700 |
- autotools-utils_src_install |
12701 |
- |
12702 |
- # create missing mmdb.pc |
12703 |
- cat >> "${T}"/mmdb.pc <<- EOF |
12704 |
- prefix=${EPREFIX}/usr |
12705 |
- exec_prefix=${EPREFIX}/usr |
12706 |
- libdir=${EPREFIX}/usr/$(get_libdir) |
12707 |
- includedir=${EPREFIX}/usr/include/mmdb |
12708 |
- |
12709 |
- Name: ${PN} |
12710 |
- Description: Macromolecular coordinate library |
12711 |
- Version: ${PV} |
12712 |
- Requires: |
12713 |
- Conflicts: |
12714 |
- Libs: -L"${EPREFIX}/usr/$(get_libdir)" -lmmdb |
12715 |
- Cflags: -I"${EPREFIX}/usr/include/mmdb" |
12716 |
- |
12717 |
- EOF |
12718 |
- |
12719 |
- insinto /usr/$(get_libdir)/pkgconfig |
12720 |
- doins "${T}"/mmdb.pc |
12721 |
-} |
12722 |
|
12723 |
diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild |
12724 |
index 8cae49d..6389827 100644 |
12725 |
--- a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild |
12726 |
+++ b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild |
12727 |
@@ -15,7 +15,4 @@ SLOT="0" |
12728 |
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12729 |
IUSE="static-libs" |
12730 |
|
12731 |
-DEPEND="!<sci-libs/ccp4-libs-6.1.3" |
12732 |
-RDEPEND="" |
12733 |
- |
12734 |
PATCHES=( "${FILESDIR}"/${P}-include-path.patch ) |
12735 |
|
12736 |
diff --git a/sci-libs/mmdb/mmdb-1.25.5.ebuild b/sci-libs/mmdb/mmdb-1.25.5.ebuild |
12737 |
deleted file mode 100644 |
12738 |
index 9be8cec..0000000 |
12739 |
--- a/sci-libs/mmdb/mmdb-1.25.5.ebuild |
12740 |
+++ /dev/null |
12741 |
@@ -1,19 +0,0 @@ |
12742 |
-# Copyright 1999-2014 Gentoo Foundation |
12743 |
-# Distributed under the terms of the GNU General Public License v2 |
12744 |
-# $Id$ |
12745 |
- |
12746 |
-EAPI=5 |
12747 |
- |
12748 |
-inherit autotools-utils |
12749 |
- |
12750 |
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" |
12751 |
-HOMEPAGE="https://launchpad.net/mmdb/" |
12752 |
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz" |
12753 |
- |
12754 |
-LICENSE="GPL-2 LGPL-3" |
12755 |
-SLOT="0" |
12756 |
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12757 |
-IUSE="static-libs" |
12758 |
- |
12759 |
-DEPEND="!<sci-libs/ccp4-libs-6.1.3" |
12760 |
-RDEPEND="" |
12761 |
|
12762 |
diff --git a/sci-libs/monomer-db/monomer-db-0.090729.ebuild b/sci-libs/monomer-db/monomer-db-0.090729.ebuild |
12763 |
deleted file mode 100644 |
12764 |
index 6513cbc..0000000 |
12765 |
--- a/sci-libs/monomer-db/monomer-db-0.090729.ebuild |
12766 |
+++ /dev/null |
12767 |
@@ -1,31 +0,0 @@ |
12768 |
-# Copyright 1999-2015 Gentoo Foundation |
12769 |
-# Distributed under the terms of the GNU General Public License v2 |
12770 |
-# $Id$ |
12771 |
- |
12772 |
-EAPI=5 |
12773 |
- |
12774 |
-DESCRIPTION="Monomer library used for macromolecular structure building and refinement" |
12775 |
-HOMEPAGE="http://www.ccp4.ac.uk/" |
12776 |
-# SRC_URI="http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz" |
12777 |
-SRC_URI="https://dev.gentoo.org/~jlec/science-dist/${P}.tar.gz" |
12778 |
- |
12779 |
-LICENSE="ccp4" |
12780 |
-SLOT="0" |
12781 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
12782 |
-IUSE="" |
12783 |
- |
12784 |
-RDEPEND="!<sci-chemistry/ccp4-6.1.3" |
12785 |
-DEPEND="${RDEPEND}" |
12786 |
- |
12787 |
-RESTRICT="binchecks strip" |
12788 |
- |
12789 |
-S="${WORKDIR}"/dic |
12790 |
- |
12791 |
-src_install() { |
12792 |
- insinto /usr/share/ccp4/data/monomers/ |
12793 |
- for i in {a..z} {1..9} *list *.cif *.txt; do |
12794 |
- doins -r ${i} |
12795 |
- done |
12796 |
- docinto html |
12797 |
- dodoc *.html |
12798 |
-} |
12799 |
|
12800 |
diff --git a/sci-libs/ssm/ssm-1.1.ebuild b/sci-libs/ssm/ssm-1.1.ebuild |
12801 |
deleted file mode 100644 |
12802 |
index d247077..0000000 |
12803 |
--- a/sci-libs/ssm/ssm-1.1.ebuild |
12804 |
+++ /dev/null |
12805 |
@@ -1,31 +0,0 @@ |
12806 |
-# Copyright 1999-2014 Gentoo Foundation |
12807 |
-# Distributed under the terms of the GNU General Public License v2 |
12808 |
-# $Id$ |
12809 |
- |
12810 |
-EAPI=5 |
12811 |
- |
12812 |
-inherit autotools eutils |
12813 |
- |
12814 |
-DESCRIPTION="A macromolecular coordinate superposition library" |
12815 |
-HOMEPAGE="https://launchpad.net/ssm" |
12816 |
-SRC_URI="https://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz" |
12817 |
- |
12818 |
-LICENSE="LGPL-2.1" |
12819 |
-SLOT="0" |
12820 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" |
12821 |
-IUSE="static-libs" |
12822 |
- |
12823 |
-DEPEND=">=sci-libs/mmdb-1.23:0" |
12824 |
-RDEPEND="${DEPEND} |
12825 |
- !<sci-libs/ccp4-libs-6.1.3-r10" |
12826 |
- |
12827 |
-src_prepare() { |
12828 |
- epatch \ |
12829 |
- "${FILESDIR}"/${P}-mmdb.patch \ |
12830 |
- "${FILESDIR}"/${P}-pc.patch |
12831 |
- eautoreconf |
12832 |
-} |
12833 |
- |
12834 |
-src_configure() { |
12835 |
- econf $(use_enable static-libs static) |
12836 |
-} |
12837 |
|
12838 |
diff --git a/sys-apps/coreutils/coreutils-8.20.ebuild b/sys-apps/coreutils/coreutils-8.20.ebuild |
12839 |
index 48946b2..9643476 100644 |
12840 |
--- a/sys-apps/coreutils/coreutils-8.20.ebuild |
12841 |
+++ b/sys-apps/coreutils/coreutils-8.20.ebuild |
12842 |
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12843 |
!sys-apps/mktemp |
12844 |
!<app-forensics/tct-1.18-r1 |
12845 |
!<net-fs/netatalk-2.0.3-r4 |
12846 |
- !<sci-chemistry/ccp4-6.1.1" |
12847 |
+" |
12848 |
DEPEND="${RDEPEND} |
12849 |
static? ( ${LIB_DEPEND} ) |
12850 |
app-arch/xz-utils" |
12851 |
|
12852 |
diff --git a/sys-apps/coreutils/coreutils-8.21.ebuild b/sys-apps/coreutils/coreutils-8.21.ebuild |
12853 |
index 92fccdf..fdaa4c2 100644 |
12854 |
--- a/sys-apps/coreutils/coreutils-8.21.ebuild |
12855 |
+++ b/sys-apps/coreutils/coreutils-8.21.ebuild |
12856 |
@@ -36,7 +36,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12857 |
!sys-apps/mktemp |
12858 |
!<app-forensics/tct-1.18-r1 |
12859 |
!<net-fs/netatalk-2.0.3-r4 |
12860 |
- !<sci-chemistry/ccp4-6.1.1" |
12861 |
+" |
12862 |
DEPEND="${RDEPEND} |
12863 |
static? ( ${LIB_DEPEND} ) |
12864 |
app-arch/xz-utils" |
12865 |
|
12866 |
diff --git a/sys-apps/coreutils/coreutils-8.22-r1.ebuild b/sys-apps/coreutils/coreutils-8.22-r1.ebuild |
12867 |
index 940d49e..78fcad4 100644 |
12868 |
--- a/sys-apps/coreutils/coreutils-8.22-r1.ebuild |
12869 |
+++ b/sys-apps/coreutils/coreutils-8.22-r1.ebuild |
12870 |
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12871 |
!sys-apps/mktemp |
12872 |
!<app-forensics/tct-1.18-r1 |
12873 |
!<net-fs/netatalk-2.0.3-r4 |
12874 |
- !<sci-chemistry/ccp4-6.1.1" |
12875 |
+" |
12876 |
DEPEND="${RDEPEND} |
12877 |
static? ( ${LIB_DEPEND} ) |
12878 |
app-arch/xz-utils" |
12879 |
|
12880 |
diff --git a/sys-apps/coreutils/coreutils-8.22.ebuild b/sys-apps/coreutils/coreutils-8.22.ebuild |
12881 |
index 5f3370c..d570dee 100644 |
12882 |
--- a/sys-apps/coreutils/coreutils-8.22.ebuild |
12883 |
+++ b/sys-apps/coreutils/coreutils-8.22.ebuild |
12884 |
@@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12885 |
!sys-apps/mktemp |
12886 |
!<app-forensics/tct-1.18-r1 |
12887 |
!<net-fs/netatalk-2.0.3-r4 |
12888 |
- !<sci-chemistry/ccp4-6.1.1" |
12889 |
+" |
12890 |
DEPEND="${RDEPEND} |
12891 |
static? ( ${LIB_DEPEND} ) |
12892 |
app-arch/xz-utils" |
12893 |
|
12894 |
diff --git a/sys-apps/coreutils/coreutils-8.23.ebuild b/sys-apps/coreutils/coreutils-8.23.ebuild |
12895 |
index 9d7ebab..bfb0c9b 100644 |
12896 |
--- a/sys-apps/coreutils/coreutils-8.23.ebuild |
12897 |
+++ b/sys-apps/coreutils/coreutils-8.23.ebuild |
12898 |
@@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12899 |
!sys-apps/mktemp |
12900 |
!<app-forensics/tct-1.18-r1 |
12901 |
!<net-fs/netatalk-2.0.3-r4 |
12902 |
- !<sci-chemistry/ccp4-6.1.1" |
12903 |
+" |
12904 |
DEPEND="${RDEPEND} |
12905 |
static? ( ${LIB_DEPEND} ) |
12906 |
app-arch/xz-utils" |
12907 |
|
12908 |
diff --git a/sys-apps/coreutils/coreutils-8.24.ebuild b/sys-apps/coreutils/coreutils-8.24.ebuild |
12909 |
index f5f6bd0..5b88e1c 100644 |
12910 |
--- a/sys-apps/coreutils/coreutils-8.24.ebuild |
12911 |
+++ b/sys-apps/coreutils/coreutils-8.24.ebuild |
12912 |
@@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) |
12913 |
!sys-apps/mktemp |
12914 |
!<app-forensics/tct-1.18-r1 |
12915 |
!<net-fs/netatalk-2.0.3-r4 |
12916 |
- !<sci-chemistry/ccp4-6.1.1" |
12917 |
+" |
12918 |
DEPEND="${RDEPEND} |
12919 |
static? ( ${LIB_DEPEND} ) |
12920 |
app-arch/xz-utils" |
12921 |
|
12922 |
diff --git a/x11-libs/libxdl_view/Manifest b/x11-libs/libxdl_view/Manifest |
12923 |
deleted file mode 100644 |
12924 |
index 8f5dc9d..0000000 |
12925 |
--- a/x11-libs/libxdl_view/Manifest |
12926 |
+++ /dev/null |
12927 |
@@ -1 +0,0 @@ |
12928 |
-DIST libxdl_view-4.2.tar.gz 857566 SHA256 826adc9c6d6706ffc6f9b52e6f7871e3ebf397837010a75daa971812f162d0b3 SHA512 1ea461cc27e53e94b89cdeef9fc435342d66f618f52a6bb936ff2c7ee63fbc89ecbbecfb4da0209ec8969f09b422af3690408dc61470299ce23e3cf84b202266 WHIRLPOOL 212c7e9f09c804bf58445a116ad75d343f6cd8e393e88ed2b2fcd4f311bd59f8a803c7fbf2d3c3a799cc7e88a9ba55f6e148c07a4956b8c6f22a0398f4b8e91f |
12929 |
|
12930 |
diff --git a/x11-libs/libxdl_view/files/4.2-as-needed.patch b/x11-libs/libxdl_view/files/4.2-as-needed.patch |
12931 |
deleted file mode 100644 |
12932 |
index a59d199..0000000 |
12933 |
--- a/x11-libs/libxdl_view/files/4.2-as-needed.patch |
12934 |
+++ /dev/null |
12935 |
@@ -1,16 +0,0 @@ |
12936 |
-diff --git a/Makefile.am b/Makefile.am |
12937 |
-index 347bb21..cbb04db 100644 |
12938 |
---- a/Makefile.am |
12939 |
-+++ b/Makefile.am |
12940 |
-@@ -19,7 +19,11 @@ lib_LTLIBRARIES = libxdl_view.la libxdl_viewextra.la |
12941 |
- ## The initial value of this was a mistake! |
12942 |
- ## See the libtool doc. |
12943 |
- libxdl_view_la_LDFLAGS = -version-info 2:0:0 |
12944 |
-+libxdl_view_la_LIBADD = -lX11 -lXt -lm |
12945 |
-+ |
12946 |
- libxdl_viewextra_la_LDFLAGS = -version-info 0:0:0 |
12947 |
-+libxdl_viewextra_la_DEPENDENCIES = libxdl_view.la |
12948 |
-+libxdl_viewextra_la_LIBADD = -lm -lxdl_view -ljwc_c |
12949 |
- |
12950 |
- EXTRA_DIST = doc/xdl_view_icon.gif doc/xdl_view_top.gif \ |
12951 |
- doc/xdl_view_top.html doc/xdl_view_updates.html \ |
12952 |
|
12953 |
diff --git a/x11-libs/libxdl_view/files/4.2-impl-dec.patch b/x11-libs/libxdl_view/files/4.2-impl-dec.patch |
12954 |
deleted file mode 100644 |
12955 |
index 4181437..0000000 |
12956 |
--- a/x11-libs/libxdl_view/files/4.2-impl-dec.patch |
12957 |
+++ /dev/null |
12958 |
@@ -1,13 +0,0 @@ |
12959 |
-diff --git a/Makefile.am b/Makefile.am |
12960 |
-index 347bb21..aa41ba3 100644 |
12961 |
---- a/Makefile.am |
12962 |
-+++ b/Makefile.am |
12963 |
-@@ -3,6 +3,8 @@ |
12964 |
- |
12965 |
- ## Process this file with automake. |
12966 |
- |
12967 |
-+CFLAGS += -std=c99 -L.libs |
12968 |
-+ |
12969 |
- libxdl_view_la_SOURCES = xdl_base_fr.c xdl_blank_obj.c xdl_image.c \ |
12970 |
- xdl_bg.c xdl_img_rd.c xdl_film_img.c xdl_io_window.c \ |
12971 |
- xdl_menu_area.c xdl_text_tab.c xdl_panel_itm.c \ |
12972 |
|
12973 |
diff --git a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild b/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild |
12974 |
deleted file mode 100644 |
12975 |
index 6a99007..0000000 |
12976 |
--- a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild |
12977 |
+++ /dev/null |
12978 |
@@ -1,32 +0,0 @@ |
12979 |
-# Copyright 1999-2012 Gentoo Foundation |
12980 |
-# Distributed under the terms of the GNU General Public License v2 |
12981 |
-# $Id$ |
12982 |
- |
12983 |
-EAPI=4 |
12984 |
- |
12985 |
-AUTOTOOLS_AUTORECONF=yes |
12986 |
- |
12987 |
-inherit autotools-utils |
12988 |
- |
12989 |
-DESCRIPTION="An X-Windows Based Toolkit" |
12990 |
-HOMEPAGE="http://www.ccp4.ac.uk/dist/x-windows/xdl_view/doc/xdl_view_top.html" |
12991 |
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" |
12992 |
- |
12993 |
-LICENSE="GPL-2" |
12994 |
-SLOT="0" |
12995 |
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
12996 |
-IUSE="static-libs" |
12997 |
- |
12998 |
-RDEPEND=" |
12999 |
- dev-libs/libjwc_c |
13000 |
- x11-libs/libXt" |
13001 |
-DEPEND="${RDEPEND}" |
13002 |
- |
13003 |
-PATCHES=( |
13004 |
- "${FILESDIR}"/${PV}-impl-dec.patch |
13005 |
- "${FILESDIR}"/${PV}-as-needed.patch ) |
13006 |
- |
13007 |
-src_prepare() { |
13008 |
- rm missing || die |
13009 |
- autotools-utils_src_prepare |
13010 |
-} |
13011 |
|
13012 |
diff --git a/x11-libs/libxdl_view/metadata.xml b/x11-libs/libxdl_view/metadata.xml |
13013 |
deleted file mode 100644 |
13014 |
index d747d72..0000000 |
13015 |
--- a/x11-libs/libxdl_view/metadata.xml |
13016 |
+++ /dev/null |
13017 |
@@ -1,8 +0,0 @@ |
13018 |
-<?xml version="1.0" encoding="UTF-8"?> |
13019 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
13020 |
-<pkgmetadata> |
13021 |
- <herd>sci</herd> |
13022 |
- <maintainer> |
13023 |
- <email>sci@g.o</email> |
13024 |
- </maintainer> |
13025 |
-</pkgmetadata> |