sci-biology / fasta

FASTA is a DNA and Protein sequence alignment software package

Official package sites : https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml ·

v36.3.8i :: 0 :: gentoo

Modified
License
fasta
Keywords
~amd64 ~amd64-linux ~ppc ~x64-macos ~x86 ~x86-linux
USE flags
debug

v36.3.8h-r1 :: 0 :: gentoo

Modified
License
fasta
Keywords
~amd64 ~amd64-linux ~ppc ~x64-macos ~x86 ~x86-linux
USE flags
debug

General

debug
Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Backtraces

cpu_flags_x86

sse2
Use the SSE2 instruction set
890417
sci-biology/fasta-36.3.8i fails to compile (DASH-SYSTEM): comp_lib9.c:(.text+0xad6): undefined reference to adler32
938324
sci-biology/fasta-36.3.8i - mm_file.h: error: implicit declaration of function ftello
Repository mirror & CI · gentoo
Merge updates from master
Eli Schwartz · gentoo
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@gentoo.org>
Eli Schwartz · gentoo
sci-biology/fasta: mark as LTO-unsafe
Closes: https://bugs.gentoo.org/862267 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
Eli Schwartz · gentoo
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@gentoo.org>
Repository mirror & CI · gentoo
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Sam James · gentoo
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@gentoo.org>
Repository mirror & CI · gentoo
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David Seifert · gentoo
sci-biology/fasta: fix broken README symlink
Closes: https://bugs.gentoo.org/835634 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
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David Seifert · gentoo
sci-biology/fasta: drop 36.3.5e
Closes: https://bugs.gentoo.org/648618 Closes: https://bugs.gentoo.org/828700 Signed-off-by: David Seifert <soap@gentoo.org>
David Seifert · gentoo
sci-biology/fasta: add 36.3.8h
Bug: https://bugs.gentoo.org/648618 Bug: https://bugs.gentoo.org/828700 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/fasta: eutils->epatch
Package-Manager: Portage-3.0.14-prefix, Repoman-3.0.2 Signed-off-by: Sam James <sam@gentoo.org>
Repository mirror & CI · gentoo
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Fabian Groffen · gentoo
sci-biology/fasta: drop x86-macos
Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Fabian Groffen <grobian@gentoo.org>
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David Seifert · gentoo
*/*: [QA] Remove redundant `|| die` guards
* Since all ebuilds in the tree are EAPI>=4, `|| die` on builtin commands is redundant and dead code. Closes: https://github.com/gentoo/gentoo/pull/13940 Reviewed-by: Ulrich Müller <ulm@gentoo.org> Reviewed-by: Michał Górny <mgorny@gentoo.org> Reviewed-by: Andreas K. Hüttel <dilfridge@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Michał Górny · gentoo
*/*: [QA] Fix trivial cases of MissingTestRestrict
The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
Michael Mair-Keimberger · gentoo
sci-biology/fasta: use HTTPs
Closes: https://github.com/gentoo/gentoo/pull/8513
David Seifert · gentoo
sci-biology/fasta: Remove old
Package-Manager: Portage-2.3.19, Repoman-2.3.6
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed