* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2016-08-06 10:38 Pacho Ramos
0 siblings, 0 replies; 9+ messages in thread
From: Pacho Ramos @ 2016-08-06 10:38 UTC (permalink / raw
To: gentoo-commits
commit: 6bd248214702a04090c2af470a4eaa56ba2a3876
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 6 10:33:36 2016 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat Aug 6 10:33:36 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6bd24821
sci-biology/fasta: Cleanup per bug #146900
Package-Manager: portage-2.3.0
sci-biology/fasta/metadata.xml | 4 ----
1 file changed, 4 deletions(-)
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
index 6c82c02..f76b365 100644
--- a/sci-biology/fasta/metadata.xml
+++ b/sci-biology/fasta/metadata.xml
@@ -1,10 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>je_fro@gentoo.org</email>
- <name>Jeff Gardner</name>
- </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2018-05-21 17:05 Aaron Bauman
0 siblings, 0 replies; 9+ messages in thread
From: Aaron Bauman @ 2018-05-21 17:05 UTC (permalink / raw
To: gentoo-commits
commit: 7d108794dce54cb34c09df68ef26a962c08ad956
Author: Michael Mair-Keimberger <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Mon May 21 10:11:07 2018 +0000
Commit: Aaron Bauman <bman <AT> gentoo <DOT> org>
CommitDate: Mon May 21 17:02:30 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7d108794
sci-biology/fasta: use HTTPs
Closes: https://github.com/gentoo/gentoo/pull/8513
sci-biology/fasta/fasta-36.3.5e.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
index 96494b79aa3..30fda7e9ae0 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils flag-o-matic toolchain-funcs
DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
LICENSE="fasta"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2021-01-06 15:09 Fabian Groffen
0 siblings, 0 replies; 9+ messages in thread
From: Fabian Groffen @ 2021-01-06 15:09 UTC (permalink / raw
To: gentoo-commits
commit: 14b94e0f1f220e1dbd6be0e01ae67b70a68c61d7
Author: Fabian Groffen <grobian <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 6 15:08:50 2021 +0000
Commit: Fabian Groffen <grobian <AT> gentoo <DOT> org>
CommitDate: Wed Jan 6 15:08:50 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=14b94e0f
sci-biology/fasta: drop x86-macos
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Fabian Groffen <grobian <AT> gentoo.org>
sci-biology/fasta/fasta-36.3.5e.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
index 392ee4c7641..6ac8d96b424 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -11,7 +11,7 @@ SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
LICENSE="fasta"
SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="debug cpu_flags_x86_sse2 test"
RESTRICT="!test? ( test )"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2022-03-19 19:33 David Seifert
0 siblings, 0 replies; 9+ messages in thread
From: David Seifert @ 2022-03-19 19:33 UTC (permalink / raw
To: gentoo-commits
commit: b49951fbe7556d78601553909d034080a98e9e5f
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 19:33:05 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 19:33:05 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b49951fb
sci-biology/fasta: fix broken README symlink
Closes: https://bugs.gentoo.org/835634
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/fasta/{fasta-36.3.8h.ebuild => fasta-36.3.8h-r1.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/fasta/fasta-36.3.8h.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
similarity index 95%
rename from sci-biology/fasta/fasta-36.3.8h.ebuild
rename to sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index cbe7a89c0383..1c396edf4586 100644
--- a/sci-biology/fasta/fasta-36.3.8h.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -77,5 +77,5 @@ src_install() {
doins -r conf/. data seq
doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
- dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+ dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2022-03-20 18:51 Sam James
0 siblings, 0 replies; 9+ messages in thread
From: Sam James @ 2022-03-20 18:51 UTC (permalink / raw
To: gentoo-commits
commit: 0e456e888bc1895caf56c1ba4a44980117b6b5c8
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 20 18:49:28 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sun Mar 20 18:50:51 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0e456e88
sci-biology/fasta: [QA] fix tc-get* quoting
This can cause build problems for e.g. 32-bit (gcc -m32 ...)
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/fasta/fasta-36.3.8h-r1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index 1c396edf4586..1cd7ca60dcde 100644
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -27,11 +27,11 @@ src_prepare() {
use debug && append-flags -DDEBUG
- if [[ $(tc-getCC) == *icc* ]]; then
+ if [[ "$(tc-getCC)" == *icc* ]]; then
CC_ALT=icc
ALT="${ALT}_icc"
else
- CC_ALT=$(tc-getCC)
+ CC_ALT="$(tc-getCC)"
use x86 && ALT="32"
use amd64 && ALT="64"
fi
@@ -39,7 +39,7 @@ src_prepare() {
if use cpu_flags_x86_sse2 ; then
ALT="${ALT}_sse2"
append-flags -msse2
- [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+ [[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
fi
export CC_ALT="${CC_ALT}"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2022-07-30 8:35 Sam James
0 siblings, 0 replies; 9+ messages in thread
From: Sam James @ 2022-07-30 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 72d0deddc6e08cd8a897b933a8e1825fd95976a0
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 30 08:34:09 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jul 30 08:34:09 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=72d0dedd
sci-biology/fasta: add github upstream metadata
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/fasta/metadata.xml | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
index ccdff086e20b..be62121d4e2d 100644
--- a/sci-biology/fasta/metadata.xml
+++ b/sci-biology/fasta/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="github">wrpearson/fasta36</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2024-08-22 4:17 Eli Schwartz
0 siblings, 0 replies; 9+ messages in thread
From: Eli Schwartz @ 2024-08-22 4:17 UTC (permalink / raw
To: gentoo-commits
commit: e13c18b293f82931681b74b1973af90217526354
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 22 03:36:08 2024 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Aug 22 04:17:11 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e13c18b2
sci-biology/fasta: remove tcsh as a test dependency, drop IUSE
This has been present since the initial import into cvs:
https://gitweb.gentoo.org/archive/repo/gentoo-2.git/commit/?id=fe5d632c39746b7b396434277896dd0e58e15567
It does not seem to have made any sense at the time -- the compile phase
required running `emake -f ../make/Makefile***` because upstream was one
of those projects that apparently liked having code separate from ways
to build the code (???) and no src_test was defined at all. So having a
test dependency made no real sense as tests were never run!!!
There is an actual test phase today. It manually runs an sh script, and
tcsh still isn't involved anywhere. There are two entirely separate tcsh
scripts in the upstream codebase, though.
Regardless, having this test dependency is nonsensical. So is having
IUSE=test and a matching RESTRICT. None of this gets us *anything*.
Therefore, drop it.
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-biology/fasta/fasta-36.3.8h-r1.ebuild | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index 1cd7ca60dcde..e27b281053b6 100644
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -15,10 +15,7 @@ S="${WORKDIR}/${PN}36-${MY_PV}"
LICENSE="fasta"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2 test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="test? ( app-shells/tcsh )"
+IUSE="debug cpu_flags_x86_sse2"
src_prepare() {
CC_ALT=
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2024-08-22 4:17 Eli Schwartz
0 siblings, 0 replies; 9+ messages in thread
From: Eli Schwartz @ 2024-08-22 4:17 UTC (permalink / raw
To: gentoo-commits
commit: 17f6c86d219f1f04c0cb2852ce1cd810169985a2
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 22 04:14:40 2024 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Aug 22 04:17:11 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17f6c86d
sci-biology/fasta: add 36.3.8i
A 2022 release, how modern. :D Ignore the part where the tag name
contains the date "2020".
It obsoletes the patch as well, which seems good. However it does NOT
fix the LTO issue.
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-biology/fasta/Manifest | 1 +
sci-biology/fasta/fasta-36.3.8i.ebuild | 81 ++++++++++++++++++++++++++++++++++
2 files changed, 82 insertions(+)
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index c0bd97106d3a..8144c91b5e78 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1 +1,2 @@
DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
+DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234
diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild b/sci-biology/fasta/fasta-36.3.8i.ebuild
new file mode 100644
index 000000000000..6363b4b56f2d
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8i.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_14-Nov-2020"
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}36-${MY_PV}"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="debug cpu_flags_x86_sse2"
+
+src_prepare() {
+ CC_ALT=
+ CFLAGS_ALT=
+ ALT=
+
+ use debug && append-flags -DDEBUG
+
+ if [[ "$(tc-getCC)" == *icc* ]]; then
+ CC_ALT=icc
+ ALT="${ALT}_icc"
+ else
+ CC_ALT="$(tc-getCC)"
+ use x86 && ALT="32"
+ use amd64 && ALT="64"
+ fi
+
+ if use cpu_flags_x86_sse2 ; then
+ ALT="${ALT}_sse2"
+ append-flags -msse2
+ [[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
+ fi
+
+ export CC_ALT="${CC_ALT}"
+ export ALT="${ALT}"
+
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862267
+ # https://github.com/wrpearson/fasta36/issues/63
+ filter-lto
+
+ sed \
+ -e 's:-ffast-math::g' \
+ -i make/Makefile* || die
+
+ eapply_user
+}
+
+src_compile() {
+ emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all
+}
+
+src_test() {
+ cd test || die
+ FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+ dobin bin/*
+
+ pushd bin >/dev/null || die
+ local i
+ for i in *36; do
+ dosym ${i} /usr/bin/${i%36}
+ done
+ popd >/dev/null || die
+
+ insinto /usr/share/${PN}
+ doins -r conf/. data seq
+
+ doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+ dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/
@ 2024-08-22 4:17 Eli Schwartz
0 siblings, 0 replies; 9+ messages in thread
From: Eli Schwartz @ 2024-08-22 4:17 UTC (permalink / raw
To: gentoo-commits
commit: d9f0a90cdc4b14c9684749be04f3fd78e1c853d5
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 22 04:12:09 2024 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Aug 22 04:17:11 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d9f0a90c
sci-biology/fasta: mark as LTO-unsafe
Closes: https://bugs.gentoo.org/862267
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-biology/fasta/fasta-36.3.8h-r1.ebuild | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index e27b281053b6..b811765e502e 100644
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -42,6 +42,11 @@ src_prepare() {
export CC_ALT="${CC_ALT}"
export ALT="${ALT}"
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862267
+ # https://github.com/wrpearson/fasta36/issues/63
+ filter-lto
+
eapply "${FILESDIR}"/${P}-ldflags.patch
sed \
^ permalink raw reply related [flat|nested] 9+ messages in thread
end of thread, other threads:[~2024-08-22 4:17 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
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2016-08-06 10:38 Pacho Ramos
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