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Changelog
Latest Commits
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Commits on 2024-04-18
sci-biology/treeviewx: Stabilize 0.5.1.20100823_p4 amd64, #930203
19e91b6
Sam James
committed on 2024-04-18 22:53:28 UTC
sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild
sci-biology/treeviewx: add github upstream metadata
0498aaf
Pacho Ramos
committed on 2024-04-18 17:03:21 UTC
sci-biology/treeviewx/metadata.xml
sci-biology/treeviewx: Update icon cache
4fb0fe2
Pacho Ramos
committed on 2024-04-18 17:03:21 UTC
sci-biology/treeviewx/treeviewx-0.5.1.20100823_p4.ebuild
Commits on 2024-04-11
sci-biology/newick-utils: update EAPI 7 -> 8
02ca13e
Eli Schwartz
authored
and
Sam James
committed on 2024-04-11 16:28:09 UTC
sci-biology/newick-utils/newick-utils-1.6-r2.ebuild
sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
sci-biology/newick-utils: update HOMEPAGE, SRC_URI to archive.org
f3d0fd2
Eli Schwartz
authored
and
Sam James
committed on 2024-04-11 16:28:08 UTC
sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
sci-biology/newick-utils: mark as LTO-unsafe
9344d5b
Eli Schwartz
authored
and
Sam James
committed on 2024-04-11 16:28:08 UTC
sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
Commits on 2024-04-07
dev-libs/igraph: add 0.10.11
ba7de57
David Seifert
committed on 2024-04-07 14:02:29 UTC
dev-libs/igraph/igraph-0.10.11.ebuild
dev-libs/igraph/Manifest
sci-biology/kallisto: update EAPI 7 -> 8
aee8ccb
Eli Schwartz
authored
and
Sam James
committed on 2024-04-07 06:16:10 UTC
sci-biology/kallisto/kallisto-0.46.2-r1.ebuild
sci-biology/kallisto/kallisto-0.46.2.ebuild
sci-biology/kallisto: port to catch2 version 3
14bc51e
Eli Schwartz
authored
and
Sam James
committed on 2024-04-07 06:16:09 UTC
sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
sci-biology/kallisto/kallisto-0.46.2.ebuild
Commits on 2024-04-01
sci-libs/dcmtk: update LTO comment (fixed upstream in git!)
1df72e0
Sam James
committed on 2024-04-01 05:29:25 UTC
sci-libs/dcmtk/dcmtk-3.6.8.ebuild
Commits on 2024-03-30
sci-biology/emboss: avoid file collision with dev-texlive/texlive-latexextra
92cb387
David Seifert
committed on 2024-03-30 19:36:42 UTC
sci-biology/emboss/emboss-6.6.0-r3.ebuild
sci-biology/emboss/emboss-6.6.0-r2.ebuild
Commits on 2024-03-26
sci-biology/bcftools: add 1.19
9e53125
David Seifert
committed on 2024-03-26 11:06:22 UTC
sci-biology/bcftools/bcftools-1.19.ebuild
sci-biology/bcftools/Manifest
sci-biology/samtools: add 1.19.2
0663dbd
David Seifert
committed on 2024-03-26 11:06:21 UTC
sci-biology/samtools/samtools-1.19.2.ebuild
sci-biology/samtools/Manifest
sci-libs/htslib: add 1.19.1
ca01346
David Seifert
committed on 2024-03-26 11:06:20 UTC
sci-libs/htslib/htslib-1.19.1.ebuild
sci-libs/htslib/Manifest
Commits on 2024-03-22
sci-biology/mothur: uncomment patch...
2186e8d
Sam James
committed on 2024-03-22 08:49:27 UTC
sci-biology/mothur/mothur-1.48.0.ebuild
sci-biology/mothur: add 1.48.0
4aa71fb
Sam James
committed on 2024-03-22 08:43:28 UTC
sci-biology/mothur/files/mothur-1.48.0-build.patch
sci-biology/mothur/mothur-1.48.0.ebuild
sci-biology/mothur/Manifest
sci-biology/mothur/metadata.xml
sci-libs/libmuscle: update EAPI 6 -> 8
9b5a5fd
Eli Schwartz
authored
and
Sam James
committed on 2024-03-22 05:31:48 UTC
sci-libs/libmuscle/libmuscle-3.7-r4.ebuild
sci-libs/libmuscle/libmuscle-3.7-r3.ebuild
sci-libs/libmuscle: mark as LTO-unsafe, strict-aliasing unsafe
cc2f57c
Eli Schwartz
authored
and
Sam James
committed on 2024-03-22 05:31:47 UTC
sci-libs/libmuscle/libmuscle-3.7-r3.ebuild
Commits on 2024-03-21
sci-biology/qrna: add 2.0.4
c19c464
Eli Schwartz
authored
and
Sam James
committed on 2024-03-21 05:57:37 UTC
sci-biology/qrna/files/qrna-2.0.4-ldflags.patch
sci-biology/qrna/qrna-2.0.4.ebuild
sci-biology/qrna/Manifest
Commits on 2024-03-20
sci-biology/t-coffee: mark as LTO-unsafe, strict-aliasing unsafe
86e4c6c
Eli Schwartz
authored
and
Sam James
committed on 2024-03-20 23:46:18 UTC
sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
sci-biology/muscle: fix variable order
6c084e5
Sam James
committed on 2024-03-20 06:20:22 UTC
sci-biology/muscle/muscle-5.1.0.ebuild
sci-biology/muscle: drop unused flag-o-matic from 5.1.0
8ab389e
Sam James
committed on 2024-03-20 06:20:02 UTC
sci-biology/muscle/muscle-5.1.0.ebuild
sci-biology/muscle: add 5.1.0
676077c
Eli Schwartz
authored
and
Sam James
committed on 2024-03-20 06:17:03 UTC
sci-biology/muscle/files/0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch
sci-biology/muscle/muscle-5.1.0.ebuild
sci-biology/muscle/Manifest
sci-biology/muscle: mark as LTO-unsafe, strict-aliasing unsafe
c33c578
Eli Schwartz
authored
and
Sam James
committed on 2024-03-20 06:17:03 UTC
sci-biology/muscle/muscle-3.8.31.ebuild
Commits on 2024-03-18
acct-user/foldingathome: update EAPI 7 -> 8
00a93eb
Conrad Kostecki
committed on 2024-03-18 19:47:52 UTC
acct-user/foldingathome/foldingathome-0-r2.ebuild
acct-user/foldingathome/foldingathome-0-r1.ebuild
acct-group/foldingathome: update EAPI 7 -> 8
92015d1
Conrad Kostecki
committed on 2024-03-18 19:46:05 UTC
acct-group/foldingathome/foldingathome-0-r2.ebuild
acct-group/foldingathome/foldingathome-0-r1.ebuild
Commits on 2024-03-12
sci-biology/glimmerhmm: update EAPI 7 -> 8
1286481
Sam James
committed on 2024-03-12 06:22:02 UTC
sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
sci-biology/glimmerhmm: fix SRC_URI
a708698
Sam James
committed on 2024-03-12 06:16:20 UTC
sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
sci-biology/glimmerhmm: add 3.0.4
b7276d0
Eli Schwartz
authored
and
Sam James
committed on 2024-03-12 06:14:32 UTC
sci-biology/glimmerhmm/files/3.0.4-gentoo.patch
sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
sci-biology/glimmerhmm/Manifest
sci-biology/glimmerhmm: patch sources to fix LTO
224d5e9
Eli Schwartz
authored
and
Sam James
committed on 2024-03-12 06:14:20 UTC
sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch
sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
Commits on 2024-03-11
sci-libs/dcmtk: add 3.6.8
e208639
Sam James
committed on 2024-03-11 16:55:19 UTC
sci-libs/dcmtk/dcmtk-3.6.8.ebuild
sci-libs/dcmtk/files/dcmtk-3.6.8-docdir.patch
sci-libs/dcmtk/Manifest
sci-libs/dcmtk: add github upstream metadata
8eedd72
Sam James
committed on 2024-03-11 16:55:18 UTC
sci-libs/dcmtk/metadata.xml
dev-libs/igraph: drop old
76e4b9a
Eli Schwartz
authored
and
Sam James
committed on 2024-03-11 14:22:52 UTC
dev-libs/igraph/igraph-0.10.4.ebuild
dev-libs/igraph: mark as LTO-unsafe, strict-aliasing unsafe
cccba67
Eli Schwartz
authored
and
Sam James
committed on 2024-03-11 14:22:51 UTC
dev-libs/igraph/igraph-0.10.4-r1.ebuild
dev-libs/igraph: add 0.10.10
37bd133
Eli Schwartz
authored
and
Sam James
committed on 2024-03-11 14:22:51 UTC
dev-libs/igraph/files/808c083fbe661207ee8f0fcd3be5096b5dc17d0d.patch
dev-libs/igraph/igraph-0.10.10.ebuild
dev-libs/igraph/Manifest
Commits on 2024-03-08
sci-biology/abyss: mark as LTO-unsafe
490ada2
Eli Schwartz
authored
and
Sam James
committed on 2024-03-08 11:09:00 UTC
sci-biology/abyss/abyss-2.3.4.ebuild
sci-biology/abyss: remove useless sed
d0b8036
Eli Schwartz
authored
and
Sam James
committed on 2024-03-08 11:09:00 UTC
sci-biology/abyss/abyss-2.3.4.ebuild
Commits on 2024-03-06
sci-libs/profnet: mark as LTO-unsafe
e884307
Eli Schwartz
authored
and
Sam James
committed on 2024-03-06 03:36:17 UTC
sci-libs/profnet/profnet-1.0.22.ebuild
Commits on 2024-03-04
sci-libs/dcmtk: Apply musl-1.2.4 largefile workaround
95a575a
Andreas K. Hüttel
committed on 2024-03-04 00:02:12 UTC
sci-libs/dcmtk/dcmtk-3.6.7-r1.ebuild
Commits on 2024-02-29
sci-biology/bwa: mark as LTO-unsafe
8479cf1
Eli Schwartz
authored
and
Sam James
committed on 2024-02-29 04:47:16 UTC
sci-biology/bwa/bwa-0.7.17.ebuild
sci-biology/exonerate: mark LTO-unsafe
f90551a
Eli Schwartz
authored
and
Sam James
committed on 2024-02-29 02:18:39 UTC
sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
Commits on 2024-01-17
Move {sys-devel → dev-build}/cons
f13cf85
Michał Górny
committed on 2024-01-17 17:14:48 UTC
dev-build/cons/Manifest
dev-build/cons/cons-2.3.0-r1.ebuild
dev-build/cons/metadata.xml
profiles/updates/1Q-2024
sci-biology/emboss/emboss-6.6.0-r2.ebuild
sys-devel/cons/Manifest
sys-devel/cons/cons-2.3.0-r1.ebuild
sys-devel/cons/metadata.xml
Commits on 2024-01-15
Move {sys-devel → dev-build}/autoconf-archive
e92da57
Michał Górny
committed on 2024-01-15 15:58:23 UTC
dev-build/autoconf-archive/Manifest
dev-build/autoconf-archive/autoconf-archive-2023.02.20.ebuild
dev-build/autoconf-archive/metadata.xml
app-admin/metalog/metalog-20220214.ebuild
app-admin/metalog/metalog-20230719.ebuild
app-admin/rsyslog/rsyslog-8.2308.0.ebuild
app-admin/rsyslog/rsyslog-8.2310.0.ebuild
app-admin/rsyslog/rsyslog-8.2312.0.ebuild
app-crypt/tpm2-openssl/tpm2-openssl-1.2.0.ebuild
app-crypt/tpm2-pkcs11/tpm2-pkcs11-1.9.0.ebuild
app-crypt/tpm2-tools/tpm2-tools-5.5.ebuild
app-emulation/spice/spice-0.15.1-r1.ebuild
app-i18n/ibus-pinyin/ibus-pinyin-1.5.0-r5.ebuild
app-i18n/ibus-pinyin/ibus-pinyin-1.5.0-r6.ebuild
app-i18n/im-chooser/im-chooser-1.7.3.ebuild
app-i18n/imsettings/imsettings-1.8.2-r1.ebuild
app-i18n/pyzy/pyzy-0.1.0-r3.ebuild
app-misc/abook/abook-0.6.1-r4.ebuild
app-misc/fdutils/fdutils-5.6_p2.ebuild
app-misc/lcd4linux/lcd4linux-0.11.0_pre20170527-r7.ebuild
app-misc/rdfind/rdfind-1.5.0-r1.ebuild
app-misc/rdfind/rdfind-1.6.0.ebuild
dev-lang/python/python-3.10.13.ebuild
sys-devel/autoconf-archive/Manifest
sys-devel/autoconf-archive/autoconf-archive-2023.02.20.ebuild
sys-devel/autoconf-archive/metadata.xml
...
Commits on 2024-01-12
Move {app-doc → app-text}/doxygen
f7fdfda
Michał Górny
committed on 2024-01-12 14:36:00 UTC
app-text/doxygen/Manifest
app-text/doxygen/doxygen-1.10.0.ebuild
app-text/doxygen/doxygen-1.9.6.ebuild
app-text/doxygen/doxygen-1.9.7-r1.ebuild
app-text/doxygen/doxygen-1.9.8.ebuild
app-text/doxygen/doxygen-9999.ebuild
app-text/doxygen/files/doxygen-1.9.1-do_not_force_libcxx.patch
app-text/doxygen/files/doxygen-1.9.1-ignore-bad-encoding.patch
app-text/doxygen/files/doxygen-1.9.4-link_with_pthread.patch
app-text/doxygen/files/doxygen-1.9.7-musl-1.2.4.patch
app-text/doxygen/files/doxygen-1.9.8-spdlog-link.patch
app-text/doxygen/files/doxygen-1.9.8-suppress-unused-option-libcxx.patch
app-text/doxygen/files/doxygen-1.9.8-unbundle-sqlite.patch
app-text/doxygen/metadata.xml
app-admin/clsync/clsync-0.4.5.ebuild
app-admin/clsync/clsync-9999.ebuild
app-antivirus/clamav/clamav-1.0.3.ebuild
app-antivirus/clamav/clamav-1.1.0.ebuild
app-antivirus/clamav/clamav-1.1.3.ebuild
app-antivirus/clamav/clamav-1.2.1.ebuild
app-arch/rpm/rpm-4.18.0.ebuild
app-arch/rpm/rpm-4.18.1.ebuild
app-arch/rpm/rpm-4.19.1.ebuild
app-backup/dar/dar-2.7.13.ebuild
app-crypt/gpgme/gpgme-1.22.0.ebuild
app-crypt/gpgme/gpgme-1.23.1-r1.ebuild
app-crypt/gpgme/gpgme-1.23.1.ebuild
app-crypt/gpgme/gpgme-1.23.2.ebuild
app-crypt/qca/qca-2.3.7.ebuild
app-crypt/qca/qca-2.3.8.ebuild
app-crypt/tpm2-tss/tpm2-tss-4.0.1.ebuild
app-emulation/open-vm-tools/open-vm-tools-12.2.0.ebuild
app-emulation/open-vm-tools/open-vm-tools-12.2.5.ebuild
app-forensics/sleuthkit/sleuthkit-4.11.1-r1.ebuild
app-doc/doxygen/Manifest
app-doc/doxygen/doxygen-1.10.0.ebuild
app-doc/doxygen/doxygen-1.9.6.ebuild
app-doc/doxygen/doxygen-1.9.7-r1.ebuild
app-doc/doxygen/doxygen-1.9.8.ebuild
app-doc/doxygen/doxygen-9999.ebuild
app-doc/doxygen/files/doxygen-1.9.1-do_not_force_libcxx.patch
app-doc/doxygen/files/doxygen-1.9.1-ignore-bad-encoding.patch
app-doc/doxygen/files/doxygen-1.9.4-link_with_pthread.patch
app-doc/doxygen/files/doxygen-1.9.7-musl-1.2.4.patch
app-doc/doxygen/files/doxygen-1.9.8-spdlog-link.patch
app-doc/doxygen/files/doxygen-1.9.8-suppress-unused-option-libcxx.patch
app-doc/doxygen/files/doxygen-1.9.8-unbundle-sqlite.patch
app-doc/doxygen/metadata.xml
...
Move {app-doc → app-text}/doxygen
f7fdfda
Michał Górny
committed on 2024-01-12 14:36:00 UTC
app-text/doxygen/Manifest
app-text/doxygen/doxygen-1.10.0.ebuild
app-text/doxygen/doxygen-1.9.6.ebuild
app-text/doxygen/doxygen-1.9.7-r1.ebuild
app-text/doxygen/doxygen-1.9.8.ebuild
app-text/doxygen/doxygen-9999.ebuild
app-text/doxygen/files/doxygen-1.9.1-do_not_force_libcxx.patch
app-text/doxygen/files/doxygen-1.9.1-ignore-bad-encoding.patch
app-text/doxygen/files/doxygen-1.9.4-link_with_pthread.patch
app-text/doxygen/files/doxygen-1.9.7-musl-1.2.4.patch
app-text/doxygen/files/doxygen-1.9.8-spdlog-link.patch
app-text/doxygen/files/doxygen-1.9.8-suppress-unused-option-libcxx.patch
app-text/doxygen/files/doxygen-1.9.8-unbundle-sqlite.patch
app-text/doxygen/metadata.xml
app-admin/clsync/clsync-0.4.5.ebuild
app-admin/clsync/clsync-9999.ebuild
app-antivirus/clamav/clamav-1.0.3.ebuild
app-antivirus/clamav/clamav-1.1.0.ebuild
app-antivirus/clamav/clamav-1.1.3.ebuild
app-antivirus/clamav/clamav-1.2.1.ebuild
app-arch/rpm/rpm-4.18.0.ebuild
app-arch/rpm/rpm-4.18.1.ebuild
app-arch/rpm/rpm-4.19.1.ebuild
app-backup/dar/dar-2.7.13.ebuild
app-crypt/gpgme/gpgme-1.22.0.ebuild
app-crypt/gpgme/gpgme-1.23.1-r1.ebuild
app-crypt/gpgme/gpgme-1.23.1.ebuild
app-crypt/gpgme/gpgme-1.23.2.ebuild
app-crypt/qca/qca-2.3.7.ebuild
app-crypt/qca/qca-2.3.8.ebuild
app-crypt/tpm2-tss/tpm2-tss-4.0.1.ebuild
app-emulation/open-vm-tools/open-vm-tools-12.2.0.ebuild
app-emulation/open-vm-tools/open-vm-tools-12.2.5.ebuild
app-forensics/sleuthkit/sleuthkit-4.11.1-r1.ebuild
app-doc/doxygen/Manifest
app-doc/doxygen/doxygen-1.10.0.ebuild
app-doc/doxygen/doxygen-1.9.6.ebuild
app-doc/doxygen/doxygen-1.9.7-r1.ebuild
app-doc/doxygen/doxygen-1.9.8.ebuild
app-doc/doxygen/doxygen-9999.ebuild
app-doc/doxygen/files/doxygen-1.9.1-do_not_force_libcxx.patch
app-doc/doxygen/files/doxygen-1.9.1-ignore-bad-encoding.patch
app-doc/doxygen/files/doxygen-1.9.4-link_with_pthread.patch
app-doc/doxygen/files/doxygen-1.9.7-musl-1.2.4.patch
app-doc/doxygen/files/doxygen-1.9.8-spdlog-link.patch
app-doc/doxygen/files/doxygen-1.9.8-suppress-unused-option-libcxx.patch
app-doc/doxygen/files/doxygen-1.9.8-unbundle-sqlite.patch
app-doc/doxygen/metadata.xml
...
Commits on 2024-01-10
sci-visualization/circos: version bump (0.69.9)
33cb541
Michael Mair-Keimberger
authored
and
Andrew Ammerlaan
committed on 2024-01-10 13:27:23 UTC
sci-visualization/circos/circos-0.69.9.ebuild
sci-visualization/circos/Manifest
Commits on 2024-01-08
sci-biology/biopython: sys-devel/flex -> app-alternatives/lex
4f9f556
Sam James
committed on 2024-01-08 12:02:22 UTC
sci-biology/biopython/biopython-1.81-r1.ebuild
Commits on 2023-12-16
sci-biology/pilercr: Stabilize 1.0-r3 amd64, #920144
e081c31
Arthur Zamarin
committed on 2023-12-16 16:17:08 UTC
sci-biology/pilercr/pilercr-1.0-r3.ebuild
dev-libs/igraph: Stabilize 0.10.4-r1 amd64, #920125
e2322f6
Arthur Zamarin
committed on 2023-12-16 16:17:00 UTC
dev-libs/igraph/igraph-0.10.4-r1.ebuild
dev-libs/igraph: Stabilize 0.10.4-r1 x86, #920125
ebd08c2
Arthur Zamarin
committed on 2023-12-16 16:16:59 UTC
dev-libs/igraph/igraph-0.10.4-r1.ebuild