* [gentoo-commits] repo/gentoo:master commit in: sci-biology/blat/files/, sci-biology/blat/
@ 2017-03-08 22:16 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-03-08 22:16 UTC (permalink / raw
To: gentoo-commits
commit: eacdfe16dd975d80b8d261c56f20c5843299651b
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 8 21:35:39 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Mar 8 22:16:14 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eacdfe16
sci-biology/blat: Modernise to EAPI 6
Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
sci-biology/blat/blat-34-r2.ebuild | 42 +++++
.../blat/files/blat-34-fix-build-system.patch | 207 +++++++++++++++++++++
2 files changed, 249 insertions(+)
diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild
new file mode 100644
index 00000000000..e10bc367a31
--- /dev/null
+++ b/sci-biology/blat/blat-34-r2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_PN=${PN}Src
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
+
+LICENSE="blat"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="app-arch/unzip"
+
+S=${WORKDIR}/${MY_PN}
+
+PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch )
+
+src_compile() {
+ tc-export AR CC
+
+ export HOME="${S}"
+ export MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+
+ mkdir -p bin/${MACHTYPE} || die
+ default
+}
+
+src_install() {
+ export MACHTYPE=$(tc-arch)
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
+
+ dobin bin/${MACHTYPE}/*
+}
diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch
new file mode 100644
index 00000000000..361149cc121
--- /dev/null
+++ b/sci-biology/blat/files/blat-34-fix-build-system.patch
@@ -0,0 +1,207 @@
+--- a/blat/makefile
++++ b/blat/makefile
+@@ -7,7 +7,7 @@
+ O = blat.o
+
+ blat: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/blat${EXE}
+
+ all:
+--- a/gfClient/makefile
++++ b/gfClient/makefile
+@@ -8,5 +8,5 @@
+ X = gfClient
+
+ gfClient: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/$X${EXE}
+--- a/gfServer/makefile
++++ b/gfServer/makefile
+@@ -8,7 +8,7 @@
+ X = gfServer
+
+ gfServer: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L
+ ${STRIP} ${BINDIR}/$X${EXE}
+
+ test:
+--- a/hg/pslPretty/makefile
++++ b/hg/pslPretty/makefile
+@@ -8,7 +8,7 @@
+ O = pslPretty.o
+
+ pslPretty: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L
+
+ test:: testRna testDnax
+
+--- a/hg/pslReps/makefile
++++ b/hg/pslReps/makefile
+@@ -9,7 +9,7 @@
+ O = pslReps.o
+
+ pslReps: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
+
+ lib:
+ cd ../../lib && ${MAKE}
+--- a/hg/pslSort/makefile
++++ b/hg/pslSort/makefile
+@@ -8,7 +8,7 @@
+ O = pslSort.o
+
+ pslSort: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L
+
+
+ lib:
+--- a/inc/common.mk
++++ b/inc/common.mk
+@@ -1,20 +1,15 @@
+-CC=gcc
+-ifeq (${COPT},)
+- COPT=-O
+-endif
+-CFLAGS=
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+ HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type
+ HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
+
+ # Stronger warning checks, and warnings-->errors, for libraries and CGIs:
+ ifeq (darwin,$(findstring darwin,${OSTYPE}))
+- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable
++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable
+ else
+ ifeq (solaris,$(findstring solaris,${OSTYPE}))
+ HG_WARN_ERR = -DJK_WARN -Wall
+ else
+- HG_WARN_ERR = -DJK_WARN -Wall -Werror
++ HG_WARN_ERR = -DJK_WARN -Wall
+ endif
+ endif
+ # Apply the stronger checks to all code on our development machine:
+@@ -37,7 +32,7 @@
+ endif
+ MKDIR=mkdir -p
+ ifeq (${STRIP},)
+- STRIP=strip
++ STRIP=true
+ endif
+ CVS=cvs
+
+--- a/jkOwnLib/makefile
++++ b/jkOwnLib/makefile
+@@ -9,7 +9,7 @@
+ T = ../lib/$(MACHTYPE)/jkOwnLib.a
+
+ $(T): $(O) ../lib/$(MACHTYPE)
+- ar rcus $(T) $(O)
++ $(AR) rcus $(T) $(O)
+
+ ../lib/$(MACHTYPE):
+ mkdir ../lib/$(MACHTYPE)
+--- a/lib/makefile
++++ b/lib/makefile
+@@ -32,7 +32,7 @@
+
+
+ $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE)
+- ar rcus $(MACHTYPE)/jkweb.a $(O)
++ $(AR) rcus $(MACHTYPE)/jkweb.a $(O)
+
+ $(MACHTYPE):
+ mkdir $(MACHTYPE)
+--- a/makefile
++++ b/makefile
+@@ -1,18 +1,18 @@
+ all:
+- cd lib && ${MAKE}
+- cd jkOwnLib && ${MAKE}
+- cd blat && $(MAKE)
+- cd gfClient && $(MAKE)
+- cd gfServer && $(MAKE)
+- cd hg/pslPretty && $(MAKE)
+- cd hg/pslReps && $(MAKE)
+- cd hg/pslSort && $(MAKE)
+- cd utils/nibFrag && $(MAKE)
+- cd utils/faToNib && $(MAKE)
+- cd utils/faToTwoBit && $(MAKE)
+- cd utils/twoBitToFa && $(MAKE)
+- cd utils/twoBitInfo && $(MAKE)
+- cd webBlat && $(MAKE)
++ $(MAKE) -C lib
++ $(MAKE) -C jkOwnLib
++ $(MAKE) -C blat
++ $(MAKE) -C gfClient
++ $(MAKE) -C gfServer
++ $(MAKE) -C hg/pslPretty
++ $(MAKE) -C hg/pslReps
++ $(MAKE) -C hg/pslSort
++ $(MAKE) -C utils/nibFrag
++ $(MAKE) -C utils/faToNib
++ $(MAKE) -C utils/faToTwoBit
++ $(MAKE) -C utils/twoBitToFa
++ $(MAKE) -C utils/twoBitInfo
++ $(MAKE) -C webBlat
+
+ clean:
+ rm -f */*.o */*/*.o
+--- a/utils/faToNib/makefile
++++ b/utils/faToNib/makefile
+@@ -8,4 +8,4 @@
+ O = faToNib.o
+
+ faToNib: $O $(MYLIBS)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L
+--- a/utils/faToTwoBit/makefile
++++ b/utils/faToTwoBit/makefile
+@@ -7,7 +7,7 @@
+ O = faToTwoBit.o
+
+ faToTwoBit: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L
+ ${STRIP} ${BINDIR}/faToTwoBit${EXE}
+
+ clean:
+--- a/utils/nibFrag/makefile
++++ b/utils/nibFrag/makefile
+@@ -4,7 +4,7 @@
+ O = nibFrag.o
+
+ nibFrag: $(O)
+- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a
+
+
+
+--- a/utils/twoBitInfo/makefile
++++ b/utils/twoBitInfo/makefile
+@@ -7,7 +7,7 @@
+ O = twoBitInfo.o
+
+ twoBitInfo: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L
+ ${STRIP} ${BINDIR}/twoBitInfo${EXE}
+
+ clean:
+--- a/utils/twoBitToFa/makefile
++++ b/utils/twoBitToFa/makefile
+@@ -8,7 +8,7 @@
+ O = twoBitToFa.o
+
+ twoBitToFa: $O ${MYLIBS}
+- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L
+ #${STRIP} ${BINDIR}/twoBitToFa${EXE}
+
+ clean:
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/blat/files/, sci-biology/blat/
@ 2020-07-04 15:24 Sergei Trofimovich
0 siblings, 0 replies; 2+ messages in thread
From: Sergei Trofimovich @ 2020-07-04 15:24 UTC (permalink / raw
To: gentoo-commits
commit: 4550eaf9f23d3579acdf226618f3fb482e675956
Author: David Denoncin <ddenoncin <AT> gmail <DOT> com>
AuthorDate: Sat Jul 4 14:26:35 2020 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sat Jul 4 15:24:04 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4550eaf9
sci-biology/blat: -fno-common fix
Closes: https://bugs.gentoo.org/706450
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: David Denoncin <ddenoncin <AT> gmail.com>
Closes: https://github.com/gentoo/gentoo/pull/16587
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>
sci-biology/blat/blat-34-r2.ebuild | 7 +++++--
sci-biology/blat/files/blat-34-fno-common.patch | 11 +++++++++++
2 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild
index e10bc367a31..b0724635638 100644
--- a/sci-biology/blat/blat-34-r2.ebuild
+++ b/sci-biology/blat/blat-34-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -21,7 +21,10 @@ DEPEND="app-arch/unzip"
S=${WORKDIR}/${MY_PN}
-PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch )
+PATCHES=(
+ "${FILESDIR}"/${PN}-34-fix-build-system.patch
+ "${FILESDIR}"/${PN}-34-fno-common.patch
+)
src_compile() {
tc-export AR CC
diff --git a/sci-biology/blat/files/blat-34-fno-common.patch b/sci-biology/blat/files/blat-34-fno-common.patch
new file mode 100644
index 00000000000..63a49cf8129
--- /dev/null
+++ b/sci-biology/blat/files/blat-34-fno-common.patch
@@ -0,0 +1,11 @@
+--- a/inc/htmshell.h
++++ b/inc/htmshell.h
+@@ -85,7 +85,7 @@ void htmlBadVar(char *varName);
+ void htmlImage(char *fileName, int width, int height);
+ /* Display centered image file. */
+
+-jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */
++extern jmp_buf htmlRecover; /* Error recovery jump. Exposed for cart's use. */
+
+ void htmlVaWarn(char *format, va_list args);
+ /* Write an error message. (Generally you just call warn() or errAbort().
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