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Am Mittwoch 15 Dezember 2010 22:38:30 schrieb Justin (jlec) Lecher: |
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> Hi, |
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> |
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> I fixed the last ebuild in the tree, so that all the binary wrappers |
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> should work now. And currently working on the bump. But it seems to not |
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> be that smooth. So don't expect it do appear before Xmas. |
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|
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By now there's even a more recent build agin: 2010_12_13_0000 and I suppose |
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there will be a new release after xmas as well ;). As I'just found a bug and |
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got it fixed upstream (in svn) I'm using their svn-version in a local install |
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at the moment. So the old version of cctbx in portage is no showstopper to me |
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right now and as far as I'm concerned you can take your time to versionbump |
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it. |
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|
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Now to some feedback: |
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I tried emerging sci-libs/cctbx-2010.03.29.2334-r3 but encountered an error |
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(sci-libs/cctbx-2010.03.29.2334-r1 compiles and installs). |
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|
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It looks like something in that update broke clipper somehow as you can see |
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from the relevant parts of the log: |
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|
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|
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* Package: sci-libs/cctbx-2010.03.29.2334-r3 |
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* Repository: gentoo |
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* Maintainer: jlec@g.o sci-chemistry@g.o |
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* USE: amd64 elibc_glibc kernel_linux minimal multilib openmp userland_GNU |
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>>> Unpacking source... |
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>>> Unpacking cctbx-2010.03.29.2334.tar.gz to /var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/work |
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>>> Source unpacked in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r3/work |
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>>> Preparing source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work ... |
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* Applying 2010.03.29.2334-tst_server.py.patch ... |
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[ ok ] |
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* Applying 2010.03.29.2334-boost.patch ... |
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[ ok ] |
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* Applying 2010.03.29.2334-clipper.patch ... |
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[ ok ] |
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* Applying 2010.03.29.2334-flags.patch ... |
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[ ok ] |
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* Applying 2010.03.29.2334-soname.patch ... |
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[ ok ] |
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>>> Source prepared. |
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>>> Configuring source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work ... |
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* configuring with /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/libtbx/configure.py --compiler=gcc --enable-openmp-if- |
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possible=True --scan-boost --use_e |
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nvironment_flags --current_working_directory=/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/work/cctbx_build --build=release fftw3tbx rstbx |
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smtbx mmtbx clipper_adaptbx fable |
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Python: 2.6.5 "/usr/bin/python2.6" |
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Compiler: gcc |
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Build mode: release |
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Warning level: 0 |
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Static libraries: False |
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Static exe: False |
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Scan Boost headers: True |
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Write full flex_fwd.h files: False |
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Build Boost.Python extensions: True |
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Define BOOST_PYTHON_NO_PY_SIGNATURES: False |
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Define BOOST_PYTHON_BOOL_INT_STRICT: True |
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Boost threads enabled: False |
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Enable OpenMP if possible: True |
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Use environment flags: True |
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CXXFLAGS = -march=native -O2 -pipe |
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CFLAGS = -march=native -O2 -pipe |
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CPPFLAGS = |
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LDFLAGS = -Wl,-O1 -Wl,--as-needed |
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[...] |
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g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -Wl,-O1 -Wl,--as-needed -fopenmp |
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cctbx/examples/convert_ccp4_symop_lib.o -Llib -L/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/work |
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/cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper/examples/symtest.cpp:1:29: error: |
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clipper/clipper.h: No such file or directory |
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g++ -o chiltbx/handle_test -Wl,-O1 -Wl,--as-needed -fopenmp |
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chiltbx/handle_test.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/lib |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:1:39: error: |
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clipper/core/clipper_util.h: No such file or directory |
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g++ -o exe_dev/cctbx.find_distances -Wl,-O1 -Wl,--as-needed -fopenmp |
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cctbx/examples/find_distances.o -Llib -L/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/work/cctbx_sources/l |
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ib -lcctbx_sgtbx_asu -lcctbx -lm |
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g++ -o exe_dev/cctbx.getting_started -Wl,-O1 -Wl,--as-needed -fopenmp |
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cctbx/examples/getting_started.o -Llib -L/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/work/cctbx_sources |
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/lib -lcctbx_sgtbx_asu -lcctbx -lm |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper/examples/symtest.cpp:6: error: 'clipper' is not |
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a namespace-name |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper/examples/symtest.cpp:6: error: expected |
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namespace-name before ';' token |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper/examples/symtest.cpp: In function 'int main()': |
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[...] |
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scons: *** [clipper/examples/symtest.o] Error 1 |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp: In function 'void |
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clipper::<unnamed>::show_as_unsigned(const char*, const FloatType&)': |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:39: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:40: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:41: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp: In function 'void |
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clipper::<unnamed>::sanity_check()': |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:54: error: 'itype32' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:55: error: 'uitype32' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:56: error: 'ftype32' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:57: error: 'itype64' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:58: error: 'uitype64' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:59: error: 'ftype64' |
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was not declared in this scope |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:60: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:61: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:64: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:69: error: 'Util' has |
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not been declared |
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/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- |
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r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:73: error: 'sqrt' was |
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not declared in this scope |
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scons: *** [clipper_adaptbx/sanity_check.o] Error 1 |
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scons: building terminated because of errors. |
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* ERROR: sci-libs/cctbx-2010.03.29.2334-r3 failed: |
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* make failed |
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* |
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* Call stack: |
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* ebuild.sh, line 56: Called src_compile |
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* environment, line 4448: Called die |
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* The specific snippet of code: |
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* libtbx.scons ${makeopts_exp} . || die "make failed" |
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* |
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* If you need support, post the output of 'emerge --info =sci- |
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libs/cctbx-2010.03.29.2334-r3', |
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* the complete build log and the output of 'emerge -pqv =sci- |
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libs/cctbx-2010.03.29.2334-r3'. |
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* The complete build log is located at '/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/temp/build.log'. |
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* The ebuild environment file is located at '/var/tmp/portage/sci- |
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libs/cctbx-2010.03.29.2334-r3/temp/environment'. |
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* S: '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r3/work' |
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|
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|
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With regards, |
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|
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Jan Simons |
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|
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Institute of Crystallography |
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RWTH Aachen University |