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commit: dc849f2aa34abfd239c23d07515ff42917fd8552 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Wed Mar 8 21:35:39 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Wed Mar 8 22:16:21 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dc849f2a |
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|
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sci-biology/blat: Remove old |
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|
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Package-Manager: Portage-2.3.4, Repoman-2.3.2 |
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Closes: https://github.com/gentoo/gentoo/pull/4165 |
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|
| 13 |
sci-biology/blat/blat-34-r1.ebuild | 44 ------- |
| 14 |
sci-biology/blat/blat-34.ebuild | 33 ----- |
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sci-biology/blat/files/34-gentoo.patch | 226 --------------------------------- |
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3 files changed, 303 deletions(-) |
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|
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diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild |
| 19 |
deleted file mode 100644 |
| 20 |
index 52079d22bea..00000000000 |
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--- a/sci-biology/blat/blat-34-r1.ebuild |
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+++ /dev/null |
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@@ -1,44 +0,0 @@ |
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-# Copyright 1999-2011 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
| 26 |
- |
| 27 |
-EAPI=4 |
| 28 |
- |
| 29 |
-inherit eutils toolchain-funcs |
| 30 |
- |
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-MY_PN="${PN}Src" |
| 32 |
- |
| 33 |
-DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" |
| 34 |
-HOMEPAGE="http://www.cse.ucsc.edu/~kent/" |
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-SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" |
| 36 |
- |
| 37 |
-SLOT="0" |
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-LICENSE="blat" |
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-KEYWORDS="~amd64 ~x86 ~x64-macos" |
| 40 |
-IUSE="" |
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- |
| 42 |
-S="${WORKDIR}/${MY_PN}" |
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- |
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-DEPEND="app-arch/unzip" |
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-RDEPEND="" |
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- |
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-src_prepare() { |
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- epatch "${FILESDIR}"/${PV}-gentoo.patch |
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- sed \ |
| 50 |
- -e "1i\CFLAGS=${CFLAGS}" \ |
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- -e "1i\LDFLAGS=${LDFLAGS}" \ |
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- -i inc/common.mk || die |
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- tc-export CC |
| 54 |
-} |
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- |
| 56 |
-src_compile() { |
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- MACHTYPE=$(tc-arch) |
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- [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
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- mkdir -p "${S}/bin/${MACHTYPE}" |
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- emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" |
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-} |
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- |
| 63 |
-src_install() { |
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- MACHTYPE=$(tc-arch) |
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- [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
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- dobin "${S}/bin/${MACHTYPE}/"* |
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-} |
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|
| 69 |
diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild |
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deleted file mode 100644 |
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index 3ec0eb05bdb..00000000000 |
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--- a/sci-biology/blat/blat-34.ebuild |
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+++ /dev/null |
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@@ -1,33 +0,0 @@ |
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-# Copyright 1999-2009 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-inherit toolchain-funcs |
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- |
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-DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" |
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-LICENSE="blat" |
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-HOMEPAGE="http://www.cse.ucsc.edu/~kent/" |
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-SLOT="0" |
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-IUSE="" |
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-KEYWORDS="amd64 x86" |
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- |
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-MY_PN="${PN}Src" |
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-SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" |
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-S="${WORKDIR}/${MY_PN}" |
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- |
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-DEPEND="app-arch/unzip" |
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-RDEPEND="" |
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- |
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-src_compile() { |
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- MACHTYPE=$(tc-arch) |
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- [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
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- sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" |
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- sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk} |
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- mkdir -p "${S}/bin/${MACHTYPE}" |
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- emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" |
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-} |
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- |
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-src_install() { |
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- MACHTYPE=$(tc-arch) |
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- [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
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- dobin "${S}/bin/${MACHTYPE}/"* |
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-} |
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|
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diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch |
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deleted file mode 100644 |
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index 8bdd05bff68..00000000000 |
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--- a/sci-biology/blat/files/34-gentoo.patch |
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+++ /dev/null |
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@@ -1,226 +0,0 @@ |
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- blat/makefile | 2 +- |
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- gfClient/makefile | 2 +- |
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- gfServer/makefile | 2 +- |
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- hg/pslPretty/makefile | 2 +- |
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- hg/pslReps/makefile | 2 +- |
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- hg/pslSort/makefile | 2 +- |
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- inc/common.mk | 11 +++-------- |
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- makefile | 28 ++++++++++++++-------------- |
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- utils/faToNib/makefile | 2 +- |
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- utils/faToTwoBit/makefile | 2 +- |
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- utils/nibFrag/makefile | 2 +- |
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- utils/twoBitInfo/makefile | 2 +- |
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- utils/twoBitToFa/makefile | 2 +- |
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- 13 files changed, 28 insertions(+), 33 deletions(-) |
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- |
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-diff --git a/blat/makefile b/blat/makefile |
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-index b889c7b..739503a 100644 |
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---- a/blat/makefile |
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-+++ b/blat/makefile |
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-@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a |
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- O = blat.o |
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- |
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- blat: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L |
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- ${STRIP} ${BINDIR}/blat${EXE} |
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- |
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- all: |
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-diff --git a/gfClient/makefile b/gfClient/makefile |
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-index c3288de..36e957e 100644 |
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---- a/gfClient/makefile |
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-+++ b/gfClient/makefile |
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-@@ -8,5 +8,5 @@ O = gfClient.o |
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- X = gfClient |
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- |
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- gfClient: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L |
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- ${STRIP} ${BINDIR}/$X${EXE} |
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-diff --git a/gfServer/makefile b/gfServer/makefile |
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-index c06b3a5..f042d22 100644 |
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---- a/gfServer/makefile |
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-+++ b/gfServer/makefile |
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-@@ -8,7 +8,7 @@ O = gfServer.o |
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- X = gfServer |
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- |
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- gfServer: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L |
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- ${STRIP} ${BINDIR}/$X${EXE} |
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- |
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- test: |
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-diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile |
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-index c780b96..cbbcd0d 100644 |
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---- a/hg/pslPretty/makefile |
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-+++ b/hg/pslPretty/makefile |
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-@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a |
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- O = pslPretty.o |
| 173 |
- |
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- pslPretty: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L |
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- |
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- test:: testRna testDnax |
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- |
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-diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile |
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-index 6e8f6d7..2b73b60 100644 |
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---- a/hg/pslReps/makefile |
| 183 |
-+++ b/hg/pslReps/makefile |
| 184 |
-@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a |
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- O = pslReps.o |
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- |
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- pslReps: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L |
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- |
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- lib: |
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- cd ../../lib && ${MAKE} |
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-diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile |
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-index 81fe083..eb63257 100644 |
| 195 |
---- a/hg/pslSort/makefile |
| 196 |
-+++ b/hg/pslSort/makefile |
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-@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a |
| 198 |
- O = pslSort.o |
| 199 |
- |
| 200 |
- pslSort: $O $(MYLIBS) |
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-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L |
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-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L |
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- |
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- |
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- lib: |
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-diff --git a/inc/common.mk b/inc/common.mk |
| 207 |
-index 1823163..3a04e2b 100644 |
| 208 |
---- a/inc/common.mk |
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-+++ b/inc/common.mk |
| 210 |
-@@ -1,20 +1,15 @@ |
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--CC=gcc |
| 212 |
--ifeq (${COPT},) |
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-- COPT=-O |
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--endif |
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--CFLAGS= |
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- HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} |
| 217 |
- HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type |
| 218 |
- HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc |
| 219 |
- |
| 220 |
- # Stronger warning checks, and warnings-->errors, for libraries and CGIs: |
| 221 |
- ifeq (darwin,$(findstring darwin,${OSTYPE})) |
| 222 |
-- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable |
| 223 |
-+ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable |
| 224 |
- else |
| 225 |
- ifeq (solaris,$(findstring solaris,${OSTYPE})) |
| 226 |
- HG_WARN_ERR = -DJK_WARN -Wall |
| 227 |
- else |
| 228 |
-- HG_WARN_ERR = -DJK_WARN -Wall -Werror |
| 229 |
-+ HG_WARN_ERR = -DJK_WARN -Wall |
| 230 |
- endif |
| 231 |
- endif |
| 232 |
- # Apply the stronger checks to all code on our development machine: |
| 233 |
-@@ -37,7 +32,7 @@ ifeq (${BINDIR},) |
| 234 |
- endif |
| 235 |
- MKDIR=mkdir -p |
| 236 |
- ifeq (${STRIP},) |
| 237 |
-- STRIP=strip |
| 238 |
-+ STRIP=true |
| 239 |
- endif |
| 240 |
- CVS=cvs |
| 241 |
- |
| 242 |
-diff --git a/makefile b/makefile |
| 243 |
-index 6f9fddf..dded1cd 100644 |
| 244 |
---- a/makefile |
| 245 |
-+++ b/makefile |
| 246 |
-@@ -1,18 +1,18 @@ |
| 247 |
- all: |
| 248 |
-- cd lib && ${MAKE} |
| 249 |
-- cd jkOwnLib && ${MAKE} |
| 250 |
-- cd blat && $(MAKE) |
| 251 |
-- cd gfClient && $(MAKE) |
| 252 |
-- cd gfServer && $(MAKE) |
| 253 |
-- cd hg/pslPretty && $(MAKE) |
| 254 |
-- cd hg/pslReps && $(MAKE) |
| 255 |
-- cd hg/pslSort && $(MAKE) |
| 256 |
-- cd utils/nibFrag && $(MAKE) |
| 257 |
-- cd utils/faToNib && $(MAKE) |
| 258 |
-- cd utils/faToTwoBit && $(MAKE) |
| 259 |
-- cd utils/twoBitToFa && $(MAKE) |
| 260 |
-- cd utils/twoBitInfo && $(MAKE) |
| 261 |
-- cd webBlat && $(MAKE) |
| 262 |
-+ $(MAKE) -C lib |
| 263 |
-+ $(MAKE) -C jkOwnLib |
| 264 |
-+ $(MAKE) -C blat |
| 265 |
-+ $(MAKE) -C gfClient |
| 266 |
-+ $(MAKE) -C gfServer |
| 267 |
-+ $(MAKE) -C hg/pslPretty |
| 268 |
-+ $(MAKE) -C hg/pslReps |
| 269 |
-+ $(MAKE) -C hg/pslSort |
| 270 |
-+ $(MAKE) -C utils/nibFrag |
| 271 |
-+ $(MAKE) -C utils/faToNib |
| 272 |
-+ $(MAKE) -C utils/faToTwoBit |
| 273 |
-+ $(MAKE) -C utils/twoBitToFa |
| 274 |
-+ $(MAKE) -C utils/twoBitInfo |
| 275 |
-+ $(MAKE) -C webBlat |
| 276 |
- |
| 277 |
- clean: |
| 278 |
- rm -f */*.o */*/*.o |
| 279 |
-diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile |
| 280 |
-index fd0e3eb..63a1593 100644 |
| 281 |
---- a/utils/faToNib/makefile |
| 282 |
-+++ b/utils/faToNib/makefile |
| 283 |
-@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a |
| 284 |
- O = faToNib.o |
| 285 |
- |
| 286 |
- faToNib: $O $(MYLIBS) |
| 287 |
-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L |
| 288 |
-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L |
| 289 |
-diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile |
| 290 |
-index b1b44a9..1e8c1c8 100644 |
| 291 |
---- a/utils/faToTwoBit/makefile |
| 292 |
-+++ b/utils/faToTwoBit/makefile |
| 293 |
-@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a |
| 294 |
- O = faToTwoBit.o |
| 295 |
- |
| 296 |
- faToTwoBit: $O ${MYLIBS} |
| 297 |
-- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L |
| 298 |
-+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L |
| 299 |
- ${STRIP} ${BINDIR}/faToTwoBit${EXE} |
| 300 |
- |
| 301 |
- clean: |
| 302 |
-diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile |
| 303 |
-index 260a6f3..e37b9ab 100755 |
| 304 |
---- a/utils/nibFrag/makefile |
| 305 |
-+++ b/utils/nibFrag/makefile |
| 306 |
-@@ -4,7 +4,7 @@ include ../../inc/common.mk |
| 307 |
- O = nibFrag.o |
| 308 |
- |
| 309 |
- nibFrag: $(O) |
| 310 |
-- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a |
| 311 |
-+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a |
| 312 |
- |
| 313 |
- |
| 314 |
- |
| 315 |
-diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile |
| 316 |
-index 649784f..9434d1c 100644 |
| 317 |
---- a/utils/twoBitInfo/makefile |
| 318 |
-+++ b/utils/twoBitInfo/makefile |
| 319 |
-@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a |
| 320 |
- O = twoBitInfo.o |
| 321 |
- |
| 322 |
- twoBitInfo: $O ${MYLIBS} |
| 323 |
-- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L |
| 324 |
-+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L |
| 325 |
- ${STRIP} ${BINDIR}/twoBitInfo${EXE} |
| 326 |
- |
| 327 |
- clean: |
| 328 |
-diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile |
| 329 |
-index cf979f2..081f3b8 100644 |
| 330 |
---- a/utils/twoBitToFa/makefile |
| 331 |
-+++ b/utils/twoBitToFa/makefile |
| 332 |
-@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a |
| 333 |
- O = twoBitToFa.o |
| 334 |
- |
| 335 |
- twoBitToFa: $O ${MYLIBS} |
| 336 |
-- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L |
| 337 |
-+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L |
| 338 |
- #${STRIP} ${BINDIR}/twoBitToFa${EXE} |
| 339 |
- |
| 340 |
- clean: |
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