* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2016-04-19 20:35 Ian Stakenvicius
0 siblings, 0 replies; 6+ messages in thread
From: Ian Stakenvicius @ 2016-04-19 20:35 UTC (permalink / raw
To: gentoo-commits
commit: cd5113534b40b92c4b055c9a12c52e105e22828a
Author: Ian Stakenvicius <axs <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 19 20:34:54 2016 +0000
Commit: Ian Stakenvicius <axs <AT> gentoo <DOT> org>
CommitDate: Tue Apr 19 20:34:54 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd511353
sci-biology/hmmer: cheamup of 2.3.2 version
* Bumped EAPI
* Merged KEYWORDS between 2.3.2-r1 and 2.3.2-r2
* dropped IUSE="pvm" as package was dropped 5 years ago
* fixed metadata.xml to match
Package-Manager: portage-2.2.26
sci-biology/hmmer/hmmer-2.3.2-r1.ebuild | 51 ----------------------
...hmmer-2.3.2-r2.ebuild => hmmer-2.3.2-r3.ebuild} | 28 ++++++------
sci-biology/hmmer/metadata.xml | 4 --
3 files changed, 15 insertions(+), 68 deletions(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
deleted file mode 100644
index 7b1fbba..0000000
--- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
-HOMEPAGE="http://hmmer.janelia.org/"
-SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ia64 ~ppc ~sparc x86"
-
-DEPEND="pvm? ( sys-cluster/pvm )"
-
-src_compile() {
- ./configure \
- --host=${CHOST} \
- --prefix="${D}"/usr \
- --exec_prefix="${D}"/usr \
- --mandir="${D}"/usr/share/man \
- --enable-lfs \
- $(use_enable pvm) \
- $(use_enable threads) || die
- emake || die
-}
-
-src_install() {
- einstall || die
-
- cd src
- dolib libhmmer.a
- insinto /usr/include/hmmer
- doins *.h
-
- cd ../squid
- dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
- dolib libsquid.a
- insinto /usr/include/hmmer
- doins *.h
-
- cd ..
- dodoc NOTES
- newdoc 00README README
- insinto /usr/share/doc/${PF}
- doins Userguide.pdf
-}
-
-src_test() {
- make check
-}
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
similarity index 69%
rename from sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
rename to sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
index 64fa500..9868ec1 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
@@ -1,45 +1,47 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
+EAPI=6
+
DESCRIPTION="Sequence analysis using profile hidden Markov models"
LICENSE="GPL-2"
HOMEPAGE="http://hmmer.janelia.org/"
SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86"
+IUSE="threads test"
+KEYWORDS="~alpha amd64 ia64 ~ppc ppc64 ~sparc x86"
-DEPEND="pvm? ( sys-cluster/pvm )"
+DEPEND=""
+RDEPEND=""
-src_compile() {
+src_configure() {
econf \
--host=${CHOST} \
--prefix="${D}"/usr \
--exec_prefix="${D}"/usr \
--mandir="${D}"/usr/share/man \
--enable-lfs \
- $(use_enable pvm) \
- $(use_enable threads) || die
- emake || die
+ $(use_enable threads)
}
src_install() {
- einstall || die
+ emake DESTDIR="${D}" install
- cd src
+ pushd src >/dev/null || die
dolib libhmmer.a
insinto /usr/include/hmmer
doins *.h
+ popd >/dev/null || die
- cd ../squid
+ pushd squid >/dev/null || die
dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
dolib libsquid.a
insinto /usr/include/hmmer
doins *.h
+ popd >/dev/null || die
- cd ..
dodoc NOTES
newdoc 00README README
insinto /usr/share/doc/${PF}
@@ -47,5 +49,5 @@ src_install() {
}
src_test() {
- make check
+ emake check
}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index a6a17ef..8417d15 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -5,8 +5,4 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <use>
- <flag name="pvm">Add support for parallel virtual machine
- (<pkg>sys-cluster/pvm</pkg>)</flag>
- </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2017-02-06 21:27 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2017-02-06 21:27 UTC (permalink / raw
To: gentoo-commits
commit: 99b5ad341522b2e3b1a5c99d3fa7029d521f2351
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 6 20:48:01 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Feb 6 21:25:58 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=99b5ad34
sci-biology/hmmer: Only keep amd64 and x86 in KEYWORDS
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3856
sci-biology/hmmer/hmmer-2.3.2-r3.ebuild | 4 ++--
sci-biology/hmmer/hmmer-2.3.2-r4.ebuild | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
index 9868ec1..bd980ed 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
SLOT="0"
IUSE="threads test"
-KEYWORDS="~alpha amd64 ia64 ~ppc ppc64 ~sparc x86"
+KEYWORDS="amd64 x86"
DEPEND=""
RDEPEND=""
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
index 7cecfe6..af2cbfd 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -11,7 +11,7 @@ SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
SLOT="2"
IUSE="altivec test threads"
-KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86"
+KEYWORDS="~amd64 ~x86"
DEPEND="test? ( dev-lang/perl )"
RDEPEND=""
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2017-09-26 5:08 Kent Fredric
0 siblings, 0 replies; 6+ messages in thread
From: Kent Fredric @ 2017-09-26 5:08 UTC (permalink / raw
To: gentoo-commits
commit: 522907f07209b4b34bd3e8c569edbb31058c7917
Author: Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 25 13:22:54 2017 +0000
Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Tue Sep 26 05:07:23 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=522907f0
sci-biology/hmmer: de-stabilize
Sci Team don't want unnecessary stable pacakges, and this is not
necessary.
The stated stable versions are broken on all available perls anyway.
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/hmmer/hmmer-2.3.2-r3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
index f721d4c3a68..0d1a357d4d0 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
@@ -10,7 +10,7 @@ SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
SLOT="0"
IUSE="threads test"
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND=""
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2017-09-26 5:08 Kent Fredric
0 siblings, 0 replies; 6+ messages in thread
From: Kent Fredric @ 2017-09-26 5:08 UTC (permalink / raw
To: gentoo-commits
commit: fe3bbbb5d658bf8673eba70e65f1b6b6de9d7c88
Author: Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 25 13:24:20 2017 +0000
Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Tue Sep 26 05:07:24 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fe3bbbb5
sci-biology/hmmer: Cleanup broken versions re bug #421799
Closes: https://bugs.gentoo.org/421799
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/hmmer/hmmer-2.3.2-r3.ebuild | 52 ---------------------------------
1 file changed, 52 deletions(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
deleted file mode 100644
index 0d1a357d4d0..00000000000
--- a/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
-HOMEPAGE="http://hmmer.janelia.org/"
-SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-IUSE="threads test"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND=""
-
-src_configure() {
- econf \
- --host=${CHOST} \
- --prefix="${D}"/usr \
- --exec_prefix="${D}"/usr \
- --mandir="${D}"/usr/share/man \
- --enable-lfs \
- $(use_enable threads)
-}
-
-src_install() {
- emake DESTDIR="${D}" install
-
- pushd src >/dev/null || die
- dolib libhmmer.a
- insinto /usr/include/hmmer
- doins *.h
- popd >/dev/null || die
-
- pushd squid >/dev/null || die
- dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
- dolib libsquid.a
- insinto /usr/include/hmmer
- doins *.h
- popd >/dev/null || die
-
- dodoc NOTES
- newdoc 00README README
- insinto /usr/share/doc/${PF}
- doins Userguide.pdf
-}
-
-src_test() {
- emake check
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2022-07-07 19:58 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2022-07-07 19:58 UTC (permalink / raw
To: gentoo-commits
commit: 9215238aeb785b45c5c95d9008dcfc76a1ca9507
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 7 19:56:55 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Jul 7 19:56:55 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9215238a
sci-biology/hmmer: update EAPI 6 -> 8 (2.3.2)
Closes: https://bugs.gentoo.org/725306
Signed-off-by: David Seifert <soap <AT> gentoo.org>
...hmmer-2.3.2-r4.ebuild => hmmer-2.3.2-r5.ebuild} | 27 +++++++++++++---------
1 file changed, 16 insertions(+), 11 deletions(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
similarity index 80%
rename from sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
rename to sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
index a58b60f93288..b9f77b9dfce8 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
@@ -1,20 +1,21 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
+
+inherit toolchain-funcs
DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
HOMEPAGE="http://hmmer.org/"
SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
+LICENSE="GPL-2"
SLOT="2"
-IUSE="altivec test threads"
-RESTRICT="!test? ( test )"
KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_ppc_altivec test"
+RESTRICT="!test? ( test )"
-DEPEND="test? ( dev-lang/perl )"
-RDEPEND=""
+BDEPEND="test? ( dev-lang/perl )"
PATCHES=(
"${FILESDIR}/${P}-fix-perl-shebangs.patch"
@@ -28,8 +29,12 @@ src_configure() {
econf \
--enable-lfs \
- $(use_enable altivec) \
- $(use_enable threads)
+ --enable-threads \
+ $(use_enable cpu_flags_ppc_altivec altivec)
+}
+
+src_compile() {
+ emake AR="$(tc-getAR) rcs"
}
src_install() {
@@ -52,14 +57,14 @@ src_install() {
local i
# first rename man pages...
- pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die
+ pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
for i in hmm*.1; do
mv ${i%.1}{,2}.1 || die
done
popd >/dev/null || die
# ... then rename binaries
- pushd "${ED%/}"/usr/bin/ >/dev/null || die
+ pushd "${ED}"/usr/bin/ >/dev/null || die
for i in hmm*; do
mv ${i}{,2} || die
done
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/
@ 2022-11-20 21:23 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2022-11-20 21:23 UTC (permalink / raw
To: gentoo-commits
commit: 41183c48ca86eaaee196abfb18b935f12836f75a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 20 21:23:10 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Nov 20 21:23:10 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=41183c48
sci-biology/hmmer: expose XSI pthread_setconcurrency() prototypes
Closes: https://bugs.gentoo.org/882279
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/hmmer/hmmer-2.3.2-r5.ebuild | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
index b9f77b9dfce8..b305820faff3 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
DESCRIPTION="Sequence analysis using profile hidden Markov models"
HOMEPAGE="http://hmmer.org/"
@@ -23,6 +23,9 @@ PATCHES=(
)
src_configure() {
+ # required to expose pthread_setconcurrency(), #882279
+ append-cppflags -D_XOPEN_SOURCE=500
+
# prevent stray environmental variable
# from causing issues in the test phase
unset TMPDIR
^ permalink raw reply related [flat|nested] 6+ messages in thread
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