[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/
commit: 4e3464f740a62b786296d21274e6197b8f3a4bd0
Author: Sam James gentoo org>
AuthorDate: Sat Jul 2 22:33:11 2022 +
Commit: Sam James gentoo org>
CommitDate: Sat Jul 2 22:33:11 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4e3464f7
sci-biology/vcftools: drop 0.1.14
Signed-off-by: Sam James gentoo.org>
sci-biology/vcftools/Manifest | 1 -
.../files/vcftools-0.1.14-buildsystem.patch| 50 --
sci-biology/vcftools/vcftools-0.1.14.ebuild| 39 -
3 files changed, 90 deletions(-)
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
index 411610b28376..36aa8e465e22 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1,2 +1 @@
-DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B
14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5
SHA512
863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7
DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B
5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64
SHA512
c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6
diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
deleted file mode 100644
index 126a709385db..
--- a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-* Add prefix in Makefiles, not the configure script
-* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB,
- as it is more flexible and helps us with LAPACK
-* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS
-
a/configure.ac
-+++ b/configure.ac
-@@ -34,7 +34,7 @@
- [--with-pmdir=DIR],
- [install Perl modules in DIR]),
- [PMDIR=${withval}],
--[PMDIR='${prefix}'/"$pmdir_relative_path"])
-+[PMDIR="$pmdir_relative_path"])
-
- AC_SUBST([PMDIR])
-
-@@ -73,9 +73,9 @@
- [pca=${enableval}],
- [pca=no])
-
--if test "x${pca}" = "xyes" ; then
-- AC_CHECK_LIB(lapack, dgeev_)
--fi
-+AS_IF([test "x${pca}" = "xyes"],[
-+ AC_SEARCH_LIBS([dgeev_], [lapack])
-+])
-
- # Generate output.
- AC_CONFIG_FILES([Makefile
a/src/cpp/Makefile.am
-+++ b/src/cpp/Makefile.am
-@@ -1,6 +1,6 @@
- bin_PROGRAMS = vcftools
-
--vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
-+vcftools_CPPFLAGS = $(ZLIB_CFLAGS)
- vcftools_LDADD = $(ZLIB_LIBS)
-
- vcftools_SOURCES = \
a/src/perl/Makefile.am
-+++ b/src/perl/Makefile.am
-@@ -24,7 +24,7 @@
- vcf-tstv \
- vcf-validator
-
--pmdir = $(PMDIR)
-+pmdir = $(exec_prefix)/$(PMDIR)
-
- dist_pm_DATA = \
- FaSlice.pm \
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild
b/sci-biology/vcftools/vcftools-0.1.14.ebuild
deleted file mode 100644
index 7b386453ae25..
--- a/sci-biology/vcftools/vcftools-0.1.14.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools flag-o-matic perl-functions toolchain-funcs
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/;
-SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz;
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="lapack"
-
-RDEPEND="sys-libs/zlib
- dev-lang/perl:=
- lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" )
-
-src_prepare() {
- default
- eautoreconf
-}
-
-src_configure() {
- perl_set_version
-
- append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
- append-libs $($(tc-getPKG_CONFIG) --libs lapack)
-
- econf \
- $(use_enable lapack pca) \
- --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/
commit: dc7beed7f021c6afe109a71cd67a3cf014538a57
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Sat Feb 19 14:05:07 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Sat Feb 19 14:05:12 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dc7beed7
sci-biology/vcftools: add version 0.1.16
Closes: https://bugs.gentoo.org/833503
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/vcftools/Manifest | 1 +
sci-biology/vcftools/vcftools-0.1.16.ebuild | 37 +
2 files changed, 38 insertions(+)
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
index d54587b1a971..411610b28376 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1 +1,2 @@
DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B
14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5
SHA512
863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7
+DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B
5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64
SHA512
c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6
diff --git a/sci-biology/vcftools/vcftools-0.1.16.ebuild
b/sci-biology/vcftools/vcftools-0.1.16.ebuild
new file mode 100644
index ..b06a81dd0a1a
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.16.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools flag-o-matic perl-functions toolchain-funcs
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/;
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz;
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="lapack"
+
+RDEPEND="sys-libs/zlib
+ dev-lang/perl:=
+ lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ perl_set_version
+
+ append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
+ append-libs $($(tc-getPKG_CONFIG) --libs lapack)
+
+ econf \
+ $(use_enable lapack pca) \
+ --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/
commit: 1618e0bc8341fcb31c9a1b79c21a2a084cf282fd
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 25 10:11:30 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 25 10:11:30 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1618e0bc
sci-biology/vcftools: Add missing RDEPEND on sys-libs/zlib
Package-Manager: portage-2.3.1
sci-biology/vcftools/vcftools-0.1.14.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild
b/sci-biology/vcftools/vcftools-0.1.14.ebuild
index 9281435..be843a9 100644
--- a/sci-biology/vcftools/vcftools-0.1.14.ebuild
+++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild
@@ -15,7 +15,8 @@ SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE="lapack"
-RDEPEND="dev-lang/perl:=
+RDEPEND="sys-libs/zlib
+ dev-lang/perl:=
lapack? ( virtual/lapack )"
DEPEND="${RDEPEND}
virtual/pkgconfig"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/
commit: bdf7251db30941f3912dd646d37fb125fbabf018
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 25 09:24:17 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 25 09:39:01 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bdf7251d
sci-biology/vcftools: Version bump to 0.1.14
Gentoo-bug: 594924
* EAPI=6
* Properly RDEPEND on dev-lang/perl
Package-Manager: portage-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/2407
Signed-off-by: David Seifert gentoo.org>
sci-biology/vcftools/Manifest | 1 +
.../files/vcftools-0.1.14-buildsystem.patch| 50 ++
sci-biology/vcftools/vcftools-0.1.14.ebuild| 39 +
3 files changed, 90 insertions(+)
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
index acbb214..9a014b1 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1 +1,2 @@
+DIST vcftools-0.1.14.tar.gz 342369 SHA256
76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512
863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7
WHIRLPOOL
6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8
DIST vcftools_0.1.12b.tar.gz 631374 SHA256
9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512
803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd
WHIRLPOOL
3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863
diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
new file mode 100644
index ..126a709
--- /dev/null
+++ b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch
@@ -0,0 +1,50 @@
+* Add prefix in Makefiles, not the configure script
+* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB,
+ as it is more flexible and helps us with LAPACK
+* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS
+
+--- a/configure.ac
b/configure.ac
+@@ -34,7 +34,7 @@
+ [--with-pmdir=DIR],
+ [install Perl modules in DIR]),
+ [PMDIR=${withval}],
+-[PMDIR='${prefix}'/"$pmdir_relative_path"])
++[PMDIR="$pmdir_relative_path"])
+
+ AC_SUBST([PMDIR])
+
+@@ -73,9 +73,9 @@
+ [pca=${enableval}],
+ [pca=no])
+
+-if test "x${pca}" = "xyes" ; then
+- AC_CHECK_LIB(lapack, dgeev_)
+-fi
++AS_IF([test "x${pca}" = "xyes"],[
++ AC_SEARCH_LIBS([dgeev_], [lapack])
++])
+
+ # Generate output.
+ AC_CONFIG_FILES([Makefile
+--- a/src/cpp/Makefile.am
b/src/cpp/Makefile.am
+@@ -1,6 +1,6 @@
+ bin_PROGRAMS = vcftools
+
+-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
++vcftools_CPPFLAGS = $(ZLIB_CFLAGS)
+ vcftools_LDADD = $(ZLIB_LIBS)
+
+ vcftools_SOURCES = \
+--- a/src/perl/Makefile.am
b/src/perl/Makefile.am
+@@ -24,7 +24,7 @@
+ vcf-tstv \
+ vcf-validator
+
+-pmdir = $(PMDIR)
++pmdir = $(exec_prefix)/$(PMDIR)
+
+ dist_pm_DATA = \
+ FaSlice.pm \
diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild
b/sci-biology/vcftools/vcftools-0.1.14.ebuild
new file mode 100644
index ..9281435
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools flag-o-matic perl-functions toolchain-funcs
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/;
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz;
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="dev-lang/perl:=
+ lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" )
+
+src_prepare() {
+ default
+ eautoreconf
+}
+
+src_configure() {
+ perl_set_version
+
+ append-flags $($(tc-getPKG_CONFIG) --cflags lapack)
+ append-libs $($(tc-getPKG_CONFIG) --libs lapack)
+
+ econf \
+ $(use_enable lapack pca) \
+ --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}"
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/
commit: e81e21772377c90519cdd2e095b305e1039ecead
Author: David Seifert gentoo org>
AuthorDate: Sun Sep 25 09:26:02 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Sep 25 09:39:05 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e81e2177
sci-biology/vcftools: Remove old ebuild
Package-Manager: portage-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/2407
Signed-off-by: David Seifert gentoo.org>
sci-biology/vcftools/Manifest | 1 -
.../files/vcftools-0.1.12b-buildsystem.patch | 53 --
sci-biology/vcftools/vcftools-0.1.12b.ebuild | 45 --
3 files changed, 99 deletions(-)
diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
index 9a014b1..0e95b82 100644
--- a/sci-biology/vcftools/Manifest
+++ b/sci-biology/vcftools/Manifest
@@ -1,2 +1 @@
DIST vcftools-0.1.14.tar.gz 342369 SHA256
76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512
863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7
WHIRLPOOL
6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8
-DIST vcftools_0.1.12b.tar.gz 631374 SHA256
9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512
803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd
WHIRLPOOL
3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863
diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
deleted file mode 100644
index 8519766..
--- a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile
vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.0 +0200
-+++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200
-@@ -3,8 +3,8 @@
- # ($Revision: 1.1 $)
-
- # Compiler
--CC = gcc
--CPP = g++
-+CC ?= gcc
-+CPP ?= g++
- # Output executable
- EXECUTABLE = vcftools
- # Flag used to turn on compilation of PCA routines
-@@ -12,9 +12,9 @@
- VCFTOOLS_PCA = 0
- endif
- # Compiler flags
--CFLAGS = -O2 -m64
-+CFLAGS ?= -O2 -m64
- #CFLAGS = -Wall -O2 -pg -m64
--CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64
-+CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64
- #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
- # Included libraries (zlib)
- LIB = -lz
-@@ -29,13 +29,13 @@
- # Define flag for PCA routine compilation
- CPPFLAGS += -DVCFTOOLS_PCA
- # Add LAPACK library
-- LIB += -llapack
-+ LIB += `$(PKG_CONFIG) --libs lapack`
- # Add PCA source code
- OBJS+= dgeev.o
- endif
-
- vcftools: $(OBJS)
-- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB)
- ifdef BINDIR
- cp $(CURDIR)/$@ $(BINDIR)/$@
- endif
-@@ -47,8 +47,8 @@
- -include $(OBJS:.o=.d)
-
- %.o: %.cpp
-- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
-- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
-+ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o
-+ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d
-
- # remove compilation products
- clean:
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild
b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
deleted file mode 100644
index ddc214c..
--- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
-HOMEPAGE="http://vcftools.sourceforge.net/;
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="lapack"
-
-RDEPEND="lapack? ( virtual/lapack )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-buildsystem.patch
- tc-export CXX PKG_CONFIG
-}
-
-src_compile() {
- local myconf
- use lapack && myconf="VCFTOOLS_PCA=1"
- emake -C cpp ${myconf}
-}
-
-src_install(){
- perl_set_version
- dobin cpp/${PN}
- insinto ${VENDOR_LIB}
- doins perl/*.pm
- dobin perl/{fill,vcf}-*
- dodoc README.txt
-}
