diff options
Diffstat (limited to 'sci-biology')
27 files changed, 104 insertions, 488 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 90ea37bf4b0d..13cd984b5e49 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 9d0ed7aa0212..5ae9c11fe860 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,5 +1,5 @@ -DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68 DIST bcftools-1.19.tar.bz2 7906216 BLAKE2B 43e7ac0fc6ffcf837607fb2fbbd58a72106a89b018d1fd4b24db0eb854a9bf0efd0c7762fae84bf7f51226346777be646d134159ea48e3eb3df71799e9353a3f SHA512 a203c65fa58fca8fb5276e73ed8fc23dfd841e9dc05881304a8b91327d60ac3b5fcf5a55a1f1bab5647037f037ff30f2881791052f6e29cf38c646cbc947a746 -EBUILD bcftools-1.17.ebuild 900 BLAKE2B 98f04325ca039867010c25c5ebff64725de637960c1980cce0faee7b8514d187ca3a309a3db79bb809ebcb9938869884c89b54f232fcf826aa34b38c5dde9c6e SHA512 82bb9a379019f0d9f9c601fad06d4041e5b890cb21618cc37f37f5f6ce0c3d5d9cd1d6223a19b8a53303e8ab3ce4046a21fbd3b7b18fd45243d57226d040ffc4 +DIST bcftools-1.20.tar.bz2 7883049 BLAKE2B 36bfd82c9500f384b75ef93242a5879123f7fd63c893c95a1ce5efbfa9396f2c1fd75025ea2dd48d37e7dc93426ffaffbb2f3c6bdf64128fbdd3af2a2f760b17 SHA512 c77294923a6bb5cb97a2c4947e79aa215612a62f71ba0e4dde627cd3d97ee9a28a3682e8ab2f3bedd0e75e2bb9800915d9430f9504f09ead4492d3583553db2a EBUILD bcftools-1.19.ebuild 901 BLAKE2B 401502d51a1b537d791355000f38403239ca57b41473cb58e1dcd3ab4057582fb19bec5d493df318386fe7c45337046e813a148d44ea0dda49468662d0567570 SHA512 b97efeaccdf86b37e714ff3f0e260f12927fa32eda3376b981d10ce7527b4da8f479e6b049386582e843329fa8e3d5a15236724e5a137d44219d1ebceca38097 +EBUILD bcftools-1.20.ebuild 901 BLAKE2B 401502d51a1b537d791355000f38403239ca57b41473cb58e1dcd3ab4057582fb19bec5d493df318386fe7c45337046e813a148d44ea0dda49468662d0567570 SHA512 b97efeaccdf86b37e714ff3f0e260f12927fa32eda3376b981d10ce7527b4da8f479e6b049386582e843329fa8e3d5a15236724e5a137d44219d1ebceca38097 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1 diff --git a/sci-biology/bcftools/bcftools-1.17.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild index 6adee705bb46..27d474fe35f9 100644 --- a/sci-biology/bcftools/bcftools-1.17.ebuild +++ b/sci-biology/bcftools/bcftools-1.20.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 8eb4fcbc9b00..a6a0a147630b 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,5 +1,5 @@ AUX biopython-1.81-python3.12.patch 472 BLAKE2B 1c4b1c777e6bd7b80503b6a820caa9aad5601337a91c3275c3c7e97060a4f38deac9db77edb3d6ce76f3c20b883cc8c8301fe8cccba311c4280a99fc3264b8a4 SHA512 5e563b40e4278913a4f559b25e60b4b8909240fd367a66c1e43e1c525684482a928748838519a627bcc67c5c9bbd44537192bccf6813f8ee80bcc456af6d9bc9 AUX biopython-1.81-reportlab4.patch 1068 BLAKE2B 1d2c2bf7929f5741f1bcae083d9842b16badba53f3be8fd3352b2b437a670b5032d146dc18610b7b360d503ad6613e9f0632457b8134392e8507900eff191526 SHA512 a576b12b8673471c27c8582f5ecb00ddf4b729a749af21a9ba67c6972dd5e9a535d7116b0ad7d06a5b89ff5b26d042914d23b1909b1081e1226df334e62d57f9 DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed -EBUILD biopython-1.81-r1.ebuild 1627 BLAKE2B ba598f6952dc9eea1ecfa4781e2aba9e6729a5488f003eec8f2fb8947489130da02baef37f540cd5064a3cbf9e2e70309e105d35f21796b3cf127fcd6b91dd93 SHA512 01e938abe556ab05e035f5988987e72259636bbd63c3d04e09c117c069dd9546713ca4823233900a60a340b64224847640e59c1a11f75209436574b9ae535c20 +EBUILD biopython-1.81-r1.ebuild 1628 BLAKE2B c7d242753c209922b83fe1f5ba38e33008fa2669c66a0b101591262ee34ff4b0ba38fd5e350bb45c234ef80a42c954ab9750e5ab7c5845f6c8daf48f7a55a181 SHA512 0a8cca5a42fe265ad3ee97a15cb42bf8c8a47cf10eb862a2094dd601595e017653927a7df18fb86b03a057b17c4e60282b8b88941241291d030524f751ef38f5 MISC metadata.xml 334 BLAKE2B 4d97c23444fdddcca57631fa2ddf4a11cfcef0accf91db65071d520f6601c0626e290e67cbf162abdefe7a74f4b410f8366a23186fc417e1fab7e9ce157d7610 SHA512 a870bd044d0e0d4e2a0c48b50f710845c6269e038790243f1d1de65b1252fd653f0f403fc55b98946df8eb27f24dfae5c84f52fcc38c969afcbdb548ccbb7a59 diff --git a/sci-biology/biopython/biopython-1.81-r1.ebuild b/sci-biology/biopython/biopython-1.81-r1.ebuild index f4fd86ba3ffb..96d83b74b492 100644 --- a/sci-biology/biopython/biopython-1.81-r1.ebuild +++ b/sci-biology/biopython/biopython-1.81-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) DISTUTILS_USE_PEP517="setuptools" DISTUTILS_EXT=1 diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 4a490595f41b..5c166b78848f 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,5 +1,4 @@ -AUX pysam-0.21.0-cython-3.patch 946 BLAKE2B 6b74b084d4f0308a77266c748209a91aa23fc0f51635b45bb2e47efc7d1e2f4a67993305d0f12c74964add24ec49ebb8b56bff720aec065a76257bda5a677cdb SHA512 763bee599547059dfff39f7ae087402dfca67acabc048012663d6cd792c605d6dc07210f777d22e9373c086cd9cd468e7ae3060a501962157ba5f6971c8033a1 -DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 -EBUILD pysam-0.21.0.ebuild 1744 BLAKE2B d6211a396810673da6392e4377a412bc6886c5eb9d5ad45ae85b278ae9d2202c4a706186b64ae3b1ae88fc0b32c532dad494bf69757b3c66dbf96e7001b48d2a SHA512 41be02962a1af5463dcc4ca98ec2af0e6986ec8d8a8101b813954754865c95d75f5f8a0ae20d3c76465475aa94e30fade45734931221eea01ab05cb7746acfce +DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350 +EBUILD pysam-0.22.1.ebuild 1648 BLAKE2B 9d0c666e39b48dea088445a0959d364892f9b2a3e90664788f214ac66df709c70eaaf8c90240488a4c948409f0548641f4d511af983037b3afc481444621f7fb SHA512 e35adedadd3c3726eb817c85f225fc2715eccdcd0c2bed5c11f749d07a7e99b2f28fee0244bd64f1383329d20edb7a2364112483af8a814b447b29fc3d1b762b EBUILD pysam-9999.ebuild 1709 BLAKE2B b7297d21abf0e581c5c2d8a72a7e6805cb5f96f6e878cc979fc0f5a34e57bdd25a2f50abaa9ee10040559e66ee42d3a24696a7093103658175b27858acaac95c SHA512 7e7a782243897a89a3539b3eb79ccd0790c6b0afcf79453526c30371f867faaf8eca6454e64d3bea250ff13753ff400fe5ff3352c080c85285cafa2346e3564a MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7 diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch deleted file mode 100644 index 303a4fb0dcdc..000000000000 --- a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch +++ /dev/null @@ -1,24 +0,0 @@ -From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 -From: John Marshall <jmarshall@hey.com> -Date: Sat, 8 Apr 2023 11:00:46 +1200 -Subject: [PATCH] Remove incorrect type annotation - -The annotation already in pysam/libcbcf.pyi is correct. -Fixes #1179 as reopened on April 6th. ---- - pysam/libcbcf.pyx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx -index 8c088af2..8ecfe5f3 100644 ---- a/pysam/libcbcf.pyx -+++ b/pysam/libcbcf.pyx -@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object): - return bcf_format_get_alleles(self) - - @alleles.setter -- def alleles(self, value: tuple): -+ def alleles(self, value): - # Sets the genotype, supply a tuple of alleles to set. - # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord - # The genotype is reset when an empty tuple, None or (None,) is supplied diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild index 77292ed29613..9070476873e1 100644 --- a/sci-biology/pysam/pysam-0.21.0.ebuild +++ b/sci-biology/pysam/pysam-0.22.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{9..11} ) +PYTHON_COMPAT=( python3_{10..12} ) inherit distutils-r1 @@ -17,30 +17,26 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="=sci-libs/htslib-1.17*:=" +RDEPEND="=sci-libs/htslib-1.20*:=" DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] test? ( - =sci-biology/bcftools-1.17* - =sci-biology/samtools-1.17* + =sci-biology/bcftools-1.20* + =sci-biology/samtools-1.20* )" distutils_enable_tests pytest DISTUTILS_IN_SOURCE_BUILD=1 -PATCHES=( - # backport - # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 - "${FILESDIR}"/${P}-cython-3.patch -) - EPYTEST_DESELECT=( # only work with bundled htslib 'tests/tabix_test.py::TestRemoteFileHTTP' 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' + + 'tests/AlignedSegment_test.py::TestBaseModifications' ) python_prepare_all() { diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest index 820b570e7e04..cc69c7639d9b 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1,4 +1,4 @@ -AUX raxml-7.2.6-makefile.patch 786 BLAKE2B d6fc28b20fc3b00b33cefd93fa90f0db255eec642a3fd760baa5489ab90dbb31d9896fe7a595e9f2e4e47b53ab24e1ef2a80486dbe77062f835fce17687a50ae SHA512 955c1403dbae7d5308f10808c3689d04cd4bc6166647fd5d7c6a5eafca45b42f409a22642a57dc19a8f3ce4e00e2e554988ed5a02954ee85ab805759e60beeea -DIST RAxML-7.2.6.tar.bz2 202803 BLAKE2B 579676ff9fad1563eabb9507015acff010977a89ae087df9b828b80bc9352ed44c98faeaf4c8d884ffa14176bfa28772dc9872ad8b5d401aff8b834c728e5f65 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 -EBUILD raxml-7.2.6.ebuild 902 BLAKE2B 23d2b1a93bf50587d5bcacbaf261ad98eecd4e6d6d86bce62bad4459286bdb678c60ad5699cd22c5d6e03df4fb49ccd95c40bbb30f6ec7990e8f81518709aa66 SHA512 5583a0fcb21f80f1cc1d7fe282f56235b6b0add1699330652f8c6c669cbbb1975eb8e088f566252b897a94e5bb80f2738de538d570951bd7508b5a607324c34f -MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de +AUX raxml-8.2.13-makefile.patch 1996 BLAKE2B 4c11992d1d8575ed54f5b374d7344a7de21dbec2eabb78a74ad894662c3008e2692724a3f7ac9659928bdb0e75a3fd4b6ad3d8c729ebb0ad0dd91c52cfe65d81 SHA512 044adeb9d66f1b8ba628c39914442c57b933957bca73ff856d00963878e8f1055baaf51e4feffb78e3090c7b445f819be3418440fd793340b6e8f65eb80b0e18 +DIST raxml-8.2.13.tar.gz 10201721 BLAKE2B ee48dc599947619d12a54cafef1eee554abc0df30a31ba2fdb501b228dadec9f137acff8f472047f4686304f74d27893696c95ff808baa128c2c3d83539366a1 SHA512 c99dc3f8c8798cda38c644501f474c0261e72c1f3b64d594d5006fa03e8d8c4da3bdf20b8e3c6c9f669c9509d5af27a0c286a2570a54c8ff7df7cd63c1f78885 +EBUILD raxml-8.2.13.ebuild 921 BLAKE2B 2facbdad60a72dc69341aafb8389e28196ba4ef7a9e3bbd71bcb7d0c3f3daedf7bd844798a4456a05344ad80a900936e73a914cee4cfa40d08a47a559aac8036 SHA512 6f2a3e357187c8ec081cd2be94c487263f062cc502e39a77e3c15fad1dad1b3a97ecfa84c2660d2a4a43a12a06bd8547a4710b0ce187dcf11dfab0269cf62e44 +MISC metadata.xml 350 BLAKE2B 7cf3cb5ea8626cadeb2a4709f466742bb1d909c58717aa0988bb4157203db26a7e571d1aec74e1bb73703bcba3f00c6d828d32ea342709a4244f4235bf2313c0 SHA512 6738c142066459babe699d53089935c7c2c1864951cf6a3148beb9015a67ce0dc60e70caa169348126b5b44f7f693b95810b871debacccd91a2643e03820f2ea diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch deleted file mode 100644 index 6b82ed65b770..000000000000 --- a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch +++ /dev/null @@ -1,29 +0,0 @@ - Makefile.gcc | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Makefile.gcc b/Makefile.gcc -index 716b6c6..f0c1de2 100644 ---- a/Makefile.gcc -+++ b/Makefile.gcc -@@ -1,10 +1,10 @@ - # Makefile August 2006 by Alexandros Stamatakis - # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> - --CC = gcc -+CC ?= gcc - - --CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -+CPPFLAGS += -D_GNU_SOURCE - - - -@@ -19,7 +19,7 @@ all : raxmlHPC - GLOBAL_DEPS = axml.h globalVariables.h - - raxmlHPC : $(objs) -- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) -+ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) $(LIBS) - - classify.o : classify.c $(GLOBAL_DEPS) - evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/files/raxml-8.2.13-makefile.patch b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch new file mode 100644 index 000000000000..d774b1fb824d --- /dev/null +++ b/sci-biology/raxml/files/raxml-8.2.13-makefile.patch @@ -0,0 +1,37 @@ +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,7 +1,6 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc + + ARCH := $(shell uname -m) + ifeq ($(ARCH), x86_64) +@@ -10,7 +9,7 @@ + ARCH_CFLAGS= + endif + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast ++CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + + LIBRARIES = -lm + +@@ -23,7 +22,7 @@ + GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + rmqs.o : rmqs.c $(GLOBAL_DEPS) + classify.o : classify.c $(GLOBAL_DEPS) +@@ -51,8 +50,6 @@ + + + +-eigen.o : eigen.c $(GLOBAL_DEPS) +- $(CC) -c -o eigen.o eigen.c + clean : + $(RM) *.o raxmlHPC + diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index ccdff086e20b..dd68d972db31 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">stamatak/standard-RAxML</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild index adb044426381..859016195389 100644 --- a/sci-biology/raxml/raxml-7.2.6.ebuild +++ b/sci-biology/raxml/raxml-8.2.13.ebuild @@ -1,29 +1,30 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit flag-o-matic toolchain-funcs DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" -HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" -SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" -S="${WORKDIR}/RAxML-${PV}" +HOMEPAGE="https://github.com/stamatak/standard-RAxML" +SRC_URI="https://github.com/stamatak/standard-RAxML/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/standard-RAxML-${PV}" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cpu_flags_x86_sse3 +threads" -REQUIRED_USE="cpu_flags_x86_sse3" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) src_configure() { - use cpu_flags_x86_sse3 && append-cppflags -D__SIM_SSE3 - use threads && \ - append-cppflags -D_USE_PTHREADS && \ - append-libs -pthread + use cpu_flags_x86_sse3 && + append-cppflags -D__SIM_SSE3 && + append-cflags -msse3 + use threads && + append-cppflags -D_USE_PTHREADS && + append-cflags -pthread tc-export CC } diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index add06bedafa2..67b2c2142193 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,5 +1,5 @@ -DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 DIST samtools-1.19.2.tar.bz2 9150483 BLAKE2B fb845b2ccd61f1731ef4cdc180f4b9a4ac75e8c73c1ceaa9409b99e8052ca66b88c73fc71fd1067942aa24964f6df8dcb2d93631e5757e0cc200d7a3b9fad461 SHA512 c08d729fed21112855e0acc9cf7f29c7670d38a02ad6b0f2e9b9ef15a18f07e3e194cc4f6913481c98cd3e85dd4dc975dac96155b892da58bbe8ea3679a5270f -EBUILD samtools-1.17.ebuild 926 BLAKE2B c2baac0d68599fadfc1825e2c0046c0596d50cedd15e6859bbfffbd3d735ae6dca2e873d835120da7be8a9c91ce17dd449010dfa956899de69c807da0cc60c7c SHA512 d43c9a9da338c0820f0237925895684077a2df428be3892f3433f050c3082d605a1edefdb265ded6f123eed491dc05578d4e46177eb79d7fdad3eebc710e3764 +DIST samtools-1.20.tar.bz2 9179938 BLAKE2B b534e659899a822e191c779a6ce9247854036da3435a0b63748783edc96d610ff0f02f73bbb5c1eab3ff86dbcca331113f3312a7c3376141ef89b6a8684446e4 SHA512 8526286243d057758cb846311d0a8c728026d31438e87fcc03e0df576f33bcc6da0e18bce141dbdc438a116341c94aa92701cdf10ba6b1301eadedbb34120822 EBUILD samtools-1.19.2.ebuild 926 BLAKE2B a9acf64c51c87cf5d913982d22dba55901111ed1802f5795b0a1bd66979b600d815ee37c29aae83bc2d58c73a61330a4ada70fac4192022d23add1bdc89cf26c SHA512 ab73ecba708535299d9cbfc3c02a6efb292b9c85658247a7eba37b915776493027a2ca98de2e8bfe373a667119a06629a3a86f97eded244b7722887c685710c2 +EBUILD samtools-1.20.ebuild 926 BLAKE2B a9acf64c51c87cf5d913982d22dba55901111ed1802f5795b0a1bd66979b600d815ee37c29aae83bc2d58c73a61330a4ada70fac4192022d23add1bdc89cf26c SHA512 ab73ecba708535299d9cbfc3c02a6efb292b9c85658247a7eba37b915776493027a2ca98de2e8bfe373a667119a06629a3a86f97eded244b7722887c685710c2 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24 diff --git a/sci-biology/samtools/samtools-1.17.ebuild b/sci-biology/samtools/samtools-1.20.ebuild index e105621c7865..42879b0f8698 100644 --- a/sci-biology/samtools/samtools-1.17.ebuild +++ b/sci-biology/samtools/samtools-1.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest index 0eea86b7ad45..c331c63113b8 100644 --- a/sci-biology/treeviewx/Manifest +++ b/sci-biology/treeviewx/Manifest @@ -1,16 +1,6 @@ -AUX treeviewx-0.5.1-70_choose_tree.patch 347 BLAKE2B deb36ebad2fce531b353376d3e115bafad9a21ee7ac62ea7cc9571733e2565903f85e733fc27cef306bb82b038e2bd16c7a69a7666af2aa9c7a04ea04319f244 SHA512 8e83180f7619e61ab6a6cdce7a576820a8e12fc2c0caf73b68c3943a98c7e618fcf0d477276b976039b594d60388a80a24f0502ebbc45ec1be371946f5c0cf1e AUX treeviewx-0.5.1-AM_PROG_AR.patch 239 BLAKE2B efd6bd8e5c2b7e609e5e5184e3f31ecbd639a6c1ee4bdfa10a6c4f7d7f0c1b1cfb29efe95ef8ec886a6290858a009222b41739b0e8473ff5daa23b8930cddd31 SHA512 198c1158006ac01c1c3a1e0f35eb19c39fdf1e05ddf22908a640c1b74eb6779958fa086b7987e86582cee16ea086f64ae1083f2aeaf5b3abb6251e21870c1447 -AUX treeviewx-0.5.1-fix_loading_crash.patch 951 BLAKE2B 7fb391335a57114a9f8ee707ffe908839a064bbe6aeab05fe0b1af8928ccb0504d91ce9e25cc55a7762422f71978e28f1479adae11293249a8a67ce8536f8d05 SHA512 9c205520dce7851520b24532f88348906c4d5a7f0fe392348099ee9f7377b778792170620856d533a275251a024756482bbd4b83d1da8281b84c39cdf2b3a711 -AUX treeviewx-0.5.1-gcc4.3.patch 2601 BLAKE2B 740a3efb736389fa0de40b0f2344e2767450809547189ef6cf659b05b6d80954550b5d5688e03a904ce6f8ec45866dff174cda0dbdbee5b0baff8cef86992240 SHA512 4629ad00ca712163fccbdb029dbb42970d432b2bcaf6b6345a7bf3dca2331ab988742a6dfbc8874e2624988c699b4ba1fff8032dda53afcffbd8264df62b480b -AUX treeviewx-0.5.1-svg.patch 1181 BLAKE2B b647b33738af0a933d0a946aa15d02f67b87175c4845813e9f01578dad6a3052902cc946b2f13dfe19451595364094094e388d8838c6c67b1448f8a32a832a65 SHA512 d71ee136f4f47792ce98826d8f7bca18320f404937abd90cdacd2685f62ed28f48601a105dd1cfb9717891a8930be339b6a663b11784f305d03af0cba24b4c4f -AUX treeviewx-0.5.1-treeview-xpm-not-xbm.patch 519 BLAKE2B 33a73602f4da18a723e292b0903a695add936697fbfd29ef978267f5e2ae1e1aa6dd49754c21900fabaf6259f732d7531f4d571f85ee544bc3d18f99961a31d4 SHA512 324b77dc43a99b55be45e1b561e528c8bb2f56ec4b1c7162987c848d0e6ea034efe262d910ee67fddcf0137b6eaeedfb50f26b8b2106b0459582942f5eccfbd4 -AUX treeviewx-0.5.1-wx30.patch 1722 BLAKE2B bc7d24b8b3953316ea4f8cb9eb26ab78fb7aee2adfce63f1ad6a758eb7d061badbcaf305d913c23fbf84773ead36242ec6995b476a1b795eb4110bc67ed4d135 SHA512 3efeea31429d623c65c958fc0ec859918e8e8b52d83973f7c7a131e47894093a2cbaafbb69c9a962ba12c0cf1ad733f2bf6d605888800d42a784d7bf3535c071 -AUX treeviewx-0.5.1-wxstring-maxlen.patch 1438 BLAKE2B a2dc6fe39c0312559628b61d86975a21db846e4c7cc3a0bb5739dd971417abd3ab9187ea56ef44d37c0394b28d4017981073eb4d890622d0d929f7a4d428950f SHA512 6e02ac59e8a28da8e94d5d6fdea71b3db9bc4501d9becf2d7aa6472d3f9f9b571fe68730390fd4cf6e1e422d618c21c40d86442d6b710e8395db107fc3445392 -AUX treeviewx-wxt.patch 1716 BLAKE2B f869d1d90dd23a7f0e242d9c1d0b0b97e0e053b5b2f00b283073f6e7f2d714cd2bf23656e65af1f3496bef0bf681ebb0618024f259b7f4d6dea777b048a438e4 SHA512 97d074e9501000099d0c5b3e3f56a796b1526499d4ccb44ef6f0b851bde1c27fc78bbc64f439ba5ecd3afa531b752c69148d7cd3b1e5a08a01566ad6155ce25c DIST treeviewx-0.5.1.20100823_p4.tar.gz 358644 BLAKE2B 3b7291415ab536230ac95decdc028dfdf60edcd986c91f76f7dacf5ec65fc31234c4d7023a9ec0fa420b68c9fe85278f8ae25106daa050872750dc5127362c46 SHA512 aec1351cfe58e1d11053c8bd3edbdf2ca74fb4bb5453bde72aa2a1b14623c69540fe7cef20f506291dad0b9358f6c37ea59feb493376b20dbdf3f7fb7df9844e DIST treeviewx_0.5.1+git20100823.7e4d0e9-4.debian.tar.xz 13880 BLAKE2B 6ab73fa79fe9a07dde17ae771edcee8d4f4e1aa25aef5fff66de4a86ee8e24c0edf9c8a4b721c12e1675083b493c65fadfff8bc79d50f28cb54a5b2cd47104a4 SHA512 4e3dbf0fd0383a0a07f924d2e59e9ed74b20c03fe57edc8e728f99dfff0a28f1c366f8a38f52f637d104b1abf98f8023abcdaff7394045642e53f5d7bb6723fd DIST treeviewx_128.png 16298 BLAKE2B 4a5f08352cd21f30e69f77403ecb79d95e8610e672979bbc46b72059bfe02edb711206260bb0b11eb733c544d584df7c9e778fe20ab2f768f18c49362cb72f11 SHA512 4986f86b7a0d4f57bd16aecb504a743ae060c2c5d3015ab2a6057e9df52ab132e6d071b5f992fc2de88529b5166f119654cbfb6c952e16d7e02d18f6d6143ee8 -DIST tv-0.5.1.tar.gz 426745 BLAKE2B 080c4e09f441fd83da3406990bbe97f9e29fa531f47a65533ca887580f8a3ec561bb4766e66e2ef4764f68eee86fdabf48481cece56ddda90f9ffdc3c80b3a1a SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143 -EBUILD treeviewx-0.5.1-r3.ebuild 957 BLAKE2B 6ce825eb0c8fe77bcf255d9a8f17f368f099263dd7c394703045f649246d3e44e2a18ef35c2f30bde461a1d05f0e6c197141a6ec3ff8a54d68084f0eb8868037 SHA512 d2e3f159cfa0e3c32bdfbbf464ca426c6f8db4aac39a53447b1d49015cb29d732429f3deeaadfd7de059cb3a779dca21818d54890aa136258997b672c3810033 EBUILD treeviewx-0.5.1.20100823_p4.ebuild 1170 BLAKE2B 7dcdea82488298e13d4df1853c2fcd8dcafbb0f90a46abbf61459b62229219d38b32d47db565ae72b849bcfd1709986e31cd1cef08a686e256eed85a53face72 SHA512 bcd92d43afef546a1c4da54e24e16367601cfbd2c460ffaa262bd0c8f002a015948f368508fb2354c065233f6ec1a7084cb6dc1283216f35cdebc00db55d88d5 MISC metadata.xml 613 BLAKE2B c3d6181a503990ef30c7dfb8166c2aaefa6709e78f482a45ff182825b7af7ebab6af100efba4dd51159d2e165979085559c4315f1ecc05e1947571843c7a8a73 SHA512 54eb1882193d526a2452804822140028bcad6157edc1f8fc7ca5a7757fca26e4afae7f50434a34dc401a0f1a68f54b0cdfb7727f79c7d2af0fa625accd284157 diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch deleted file mode 100644 index 7a614edff72e..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/tview.cpp -+++ b/tview.cpp -@@ -208,7 +208,7 @@ - pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), - wxSAVE|wxOVERWRITE_PROMPT); - -- if (dialog.ShowModal() == wxID_OK) -+ if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) - { - wxSVGFileDC pictureDC (dialog.GetPath(), 600, 650) ; - OnDraw (&pictureDC); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch deleted file mode 100644 index c136539726a3..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch +++ /dev/null @@ -1,40 +0,0 @@ -Bug: http://code.google.com/p/treeviewx/issues/detail?id=1 -Description: fix crash on loading tree file. -Author: Tim Booth ---- tv-0.5.orig/tview.cpp -+++ tv-0.5/tview.cpp -@@ -278,7 +278,7 @@ - char buf[256]; - strcpy (buf, p->GetLabel().c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - s << wbuf; - #else - s << p->GetLabel().c_str(); -@@ -563,7 +563,7 @@ - char buf[256]; - strcpy (buf, t.GetName().c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - txt << wbuf; - #else - txt << t.GetName().c_str(); -@@ -712,7 +712,7 @@ - char buf[256]; - strcpy (buf, p.GetIthTreeName(i).c_str()); - wchar_t wbuf[256]; -- mbstowcs (wbuf, buf, size_t(wbuf)); -+ mbstowcs (wbuf, buf, 256); - - std::wstring tname = wbuf; - -@@ -1046,6 +1046,7 @@ - void MyCanvas::OnSize(wxSizeEvent& event) - { - Resize (); -+ Refresh(); - event.Skip(); - } - diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch deleted file mode 100644 index 33bd3b1741f6..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp ---- tv-0.5.1/TreeLib/Parse.cpp 2002-02-23 07:22:32.000000000 -0500 -+++ tv-0.5.1.new/TreeLib/Parse.cpp 2008-06-17 06:08:24.000000000 -0400 -@@ -24,6 +24,11 @@ - #include <ctype.h> - #include "Parse.h" - -+ -+ -+ -+#include <cstring> -+ - // Return the next token in the string - tokentype Parser::NextToken () - { -diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp ---- tv-0.5.1/TreeLib/TreeLib.cpp 2004-05-13 08:22:11.000000000 -0400 -+++ tv-0.5.1.new/TreeLib/TreeLib.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -24,6 +24,8 @@ - #include "TreeLib.h" - #include "Parse.h" - -+ -+#include <cstdlib> - #include <vector> - - -diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp ---- tv-0.5.1/TreeLib/treereader.cpp 2003-09-10 08:58:16.000000000 -0400 -+++ tv-0.5.1.new/TreeLib/treereader.cpp 2008-06-17 06:07:15.000000000 -0400 -@@ -28,6 +28,9 @@ - #include <stdlib.h> - #endif - -+#include <cstring> -+#include <cstdlib> -+ - //------------------------------------------------------------------------------ - TreeReader::TreeReader (Tokeniser &p) : parser (p) - { -diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp ---- tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2002-12-10 06:35:49.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp ---- tv-0.5.1/ncl-2.0/src/nexus.cpp 2002-12-10 06:35:50.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp ---- tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2005-04-29 10:28:17.000000000 -0400 -+++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,5 @@ -+ -+#include <cstring> - #include "nexusdefs.h" - #include "xnexus.h" - #include "nexustoken.h" -diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp ---- tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2001-02-02 07:55:40.000000000 -0500 -+++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp 2008-06-17 05:58:17.000000000 -0400 -@@ -1,3 +1,6 @@ -+ -+#include <cstring> -+ - #ifdef __BORLANDC__ - // Undefine __MINMAX_DEFINED so that min and max are correctly defined - #ifdef __MINMAX_DEFINED diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch deleted file mode 100644 index 67a62179bb87..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Olly Betts <olly@survex.com> -Description: Update configure.in to match what it must have said when configure was generated. - One thing I should probably explain about the patch as my change may - seem odd otherwise - upstream's configure.in says "USE_SVG=0" but the - generated configure says "USE_SVG=1", so I've simply updated - configure.in to match what it must have said when configure was - generated. -Forwarded: no ---- tv-0.5.orig/configure.in -+++ tv-0.5/configure.in -@@ -66,7 +66,9 @@ - case "$wx_version" in - 2.4.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_dcsvg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] - ;; -- *) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] -+ 2.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`] -+ ;; -+ *) WX_SVG_LIB= - ;; - esac - -@@ -76,7 +78,7 @@ - - if test "$USE_SVG" = 1 ; then - CXXFLAGS="$CXXFLAGS -DUSE_SVG" -- LIBS="$LIBS -l$WX_SVG_LIB" -+ test -n "$WX_SVG_LIB" && LIBS="$LIBS -l$WX_SVG_LIB" - fi - - AC_OUTPUT(Makefile ncl-2.0/Makefile ncl-2.0/src/Makefile TreeLib/Makefile tv.spec) diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch deleted file mode 100644 index a57ae19aaf26..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: Fix the extension of the icon -Author: Olly Betts <olly@survex.com> -Last-Update: 2014-06-21 -Forwarded: http://code.google.com/p/treeviewx/issues/detail?id=4 - ---- tv-0.5.orig/tv.cpp -+++ tv-0.5/tv.cpp -@@ -215,7 +215,7 @@ - frame->SetIcon(wxIcon("app")); // use the name of the icon in the resource file - #endif - #if defined(__WXGTK__) || defined(__WXMOTIF__) -- frame->SetIcon(wxIcon(wxT("bitmaps/treeview.xbm"))); -+ frame->SetIcon(wxIcon(wxT("/usr/share/pixmaps/treeviewx.xpm"))); - #endif - - #ifdef __WXMAC__ diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch deleted file mode 100644 index a1cfd906f176..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch +++ /dev/null @@ -1,66 +0,0 @@ ---- a/tv.cpp -+++ b/tv.cpp -@@ -163,9 +163,9 @@ - { - // Optional command line argument is name of file to open - #if wxUSE_UNICODE -- wchar_t *InputFile = NULL; -+ const wchar_t *InputFile = NULL; - #else -- char *InputFile = NULL; -+ const char *InputFile = NULL; - #endif - // Read input/output files - if (argc > 1) ---- a/tview.cpp -+++ b/tview.cpp -@@ -62,9 +62,13 @@ - #ifdef __WXMSW__ - #else - #ifdef USE_SVG -+#if wxMAJOR_VERSION >= 3 -+ #include <wx/dcsvg.h> -+#else - #include <wx/svg/dcsvg.h> - #endif - #endif -+#endif - - // GUI interface - #include "tv.h" -@@ -186,7 +190,7 @@ - wxFrame *f = GetMainFrame(); - wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), - pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - - if (dialog.ShowModal() == wxID_OK) - { -@@ -206,7 +210,7 @@ - #endif - wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), - pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFD_SAVE|wxFD_OVERWRITE_PROMPT); - - if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) - { -@@ -361,7 +365,7 @@ - - // Clear the canvas in case we're in single-window mode, - // and the canvas stays. --#if (wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated -+#if (wxMAJOR_VERSION >= 3 || wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated - canvas->ClearBackground(); - #else - canvas->Clear(); -@@ -686,7 +690,7 @@ - wxFontData data; - data.SetInitialFont (LeafFont); - --#ifdef __WXMAC__ -+#if wxMAJOR_VERSION >= 3 || defined __WXMAC__ - wxFontDialog dialog((wxWindow *)GetFrame(), data); - #else - wxFontDialog dialog((wxWindow *)GetMainFrame(), &data); diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch deleted file mode 100644 index 2c5179f778ca..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch +++ /dev/null @@ -1,34 +0,0 @@ -Description: Remove wxSTRING_MAXLEN (removed in wx3.0) and incomp. definition. - The definition wxSTRING_MAXLEN was removed from the public API of wxWidgets. - Its meaning was basically "take all the string", whenever a string length was - expected. The missing definition didn't raise a compilation error because - TreeLib's treedrawer.h contained a fall-back definition, which is however - incompatible with the original definition of wxWidgets and therefore is - interpreted by wxWidgets as a number representing the real string length. - This patch gets rid of the dangerous fall-back definition and of all of its - uses by using alternative wxString constructors that achieve the same - behavior. -Author: Martin Steghöfer <martin@steghoefer.eu> -Last-Update: Sun, 10 Aug 2014 14:06:42 +0200 -Bug-Debian: http://bugs.debian.org/751255 - ---- tv-0.5.orig/TreeLib/treedrawer.cpp -+++ tv-0.5/TreeLib/treedrawer.cpp -@@ -245,7 +245,7 @@ - // error in gcc, which is probably a gcc bug - { - wxCoord w, h, descent; -- wxString s (formatedString.c_str(), wxSTRING_MAXLEN); -+ wxString s (formatedString.c_str()); - pt.x += dc->GetCharWidth(); - pt.y -= dc->GetCharHeight()/2; - dc->DrawText (s, (int)pt.x, (int)pt.y); -@@ -566,7 +566,7 @@ - - #if USE_WXWINDOWS - wxCoord w, h; -- wxString s (buf, wxSTRING_MAXLEN); -+ wxString s (buf); - dc->GetTextExtent (s, &w, &h); - int x = (int)pt2.x; - int y = (int)pt2.y; diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch deleted file mode 100644 index a971e1a85074..000000000000 --- a/sci-biology/treeviewx/files/treeviewx-wxt.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- a/tv.cpp -+++ b/tv.cpp -@@ -312,11 +312,15 @@ - { - #ifdef __WXMSW__ - file_menu->AppendSeparator(); -- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile"); -+ file_menu->Append(SAVEAS_PICTURE_CMD, -+ wxT("Save As Picture...")), -+ wxT("Save picture of tree to metafile"); - #else - #ifdef USE_SVG - file_menu->AppendSeparator(); -- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file"); -+ file_menu->Append(SAVEAS_PICTURE_CMD, -+ wxT("Save As Picture...")), -+ wxT("Save picture of tree to SVG file"); - #endif - #endif - file_menu->AppendSeparator(); ---- a/tview.cpp -+++ b/tview.cpp -@@ -184,10 +184,10 @@ - wxString pictureFileName = GetFrame()->GetTitle(); - pictureFileName += wxT(".emf"); - wxFrame *f = GetMainFrame(); -- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, -- "Enhanced metafile (*.emf)|*.emf", -- wxSAVE|wxOVERWRITE_PROMPT); -- -+ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), -+ pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), -+ wxSAVE|wxOVERWRITE_PROMPT); -+ - if (dialog.ShowModal() == wxID_OK) - { - wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ; -@@ -204,9 +204,9 @@ - #else - wxFrame *f = GetMainFrame(); - #endif -- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, -- "SVG vector picture files (*.svg)|*.svg", -- wxSAVE|wxOVERWRITE_PROMPT); -+ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), -+ pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), -+ wxSAVE|wxOVERWRITE_PROMPT); - - if (dialog.ShowModal() == wxID_OK) - { diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild deleted file mode 100644 index ada60056715e..000000000000 --- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -WX_GTK_VER="3.0" -inherit autotools wxwidgets - -DESCRIPTION="A phylogenetic tree viewer" -HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" -SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/$(ver_cut 1-2)/tv-${PV}.tar.gz" -S="${WORKDIR}/tv-${PV}" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ~x86" - -RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-wxt.patch - "${FILESDIR}"/${P}-gcc4.3.patch - "${FILESDIR}"/${P}-70_choose_tree.patch - "${FILESDIR}"/${P}-fix_loading_crash.patch - "${FILESDIR}"/${P}-wx30.patch - "${FILESDIR}"/${P}-svg.patch - "${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch - "${FILESDIR}"/${P}-wxstring-maxlen.patch - "${FILESDIR}"/${P}-AM_PROG_AR.patch -) - -src_prepare() { - default - mv configure.{in,ac} || die - eautoreconf -} - -src_configure() { - setup-wxwidgets - default -} diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest index 13c0c81fd95e..352d6f97739a 100644 --- a/sci-biology/ucsc-genome-browser/Manifest +++ b/sci-biology/ucsc-genome-browser/Manifest @@ -1,3 +1,3 @@ DIST jksrc.v260.zip 59090224 BLAKE2B 755bb97f50cde97e7634f38aa81f0843de52710cac78f5b0a2ee6129cffc99f730b8e1ab41d24e2faebb3c0a3e1d1309c84307e2dc4af1efe9a30fb0b9ae1670 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 -EBUILD ucsc-genome-browser-260-r1.ebuild 3134 BLAKE2B f9b628c78939377f66c9aca6b68ca3cbebf7c41dde18a8d03dbc4533593069dff0381d0fe206b0287569739a96010661d275c2d43a8ffc9e1ad8f73b4d73be5e SHA512 6f33bd29ac24661d8a495913b6746d60ca4eb95e91e5ca7325420a9b430f9ca8fe990d9167ab2ffd500f151f8cce045601e1dde24efde05b185511c1b06593a7 +EBUILD ucsc-genome-browser-260-r2.ebuild 3247 BLAKE2B 7f8ece657ec2fa39c623712293009645f247f427149e617287d458a97364bf6070a3bc1c94ef2b447c6751e58b0b98f7996c7a941342ed937d9455a84a1233fb SHA512 99716737f5cb5e03ecc162a97a79e8f3369dea1452819c9dce4ae2ec593953b0c031929c0785b8677506483d6537c59d113888b89b804d9796b767f364bfc5cf MISC metadata.xml 436 BLAKE2B f0bf2e08eaadf20a1810abf0e3cd42494197b8fe2593c5f3ee243f58af5676a795009fefbc7f11d2d8e4d42ff9e34790dd7be9999a37839fe6ce780b12714116 SHA512 43d2b6e4519270b495122711c747c906ba64993811a6f4d63af5fc17a6752232dde3717f193432d673e2c183e35fb88421a39077d3d0dad18b712d26c6e64caa diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild index f0bb0676ae85..ef96f491fb51 100644 --- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild @@ -1,32 +1,40 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2024 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 +WEBAPP_MANUAL_SLOT="yes" +# TODO: use WEBAPP_OPTIONAL? inherit toolchain-funcs flag-o-matic webapp DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" HOMEPAGE="http://genome.ucsc.edu/" SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip" +S="${WORKDIR}/kent" LICENSE="blat" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="+mysql +server static-libs" - REQUIRED_USE="server? ( mysql )" -WEBAPP_MANUAL_SLOT="yes" - +# TODO: test with other webservers RDEPEND=" - dev-libs/openssl:0= - media-libs/libpng:0= + dev-libs/openssl:= + media-libs/libpng:= !<sci-biology/ucsc-genome-browser-223 - mysql? ( dev-db/mysql-connector-c:0= ) - server? ( virtual/httpd-cgi )" # TODO: test with other webservers -DEPEND="${RDEPEND} app-arch/unzip" - -S="${WORKDIR}/kent" + mysql? ( dev-db/mysql-connector-c:= ) + server? ( virtual/httpd-cgi ) +" +DEPEND="${RDEPEND}" +BDEPEND=" + app-alternatives/cpio + app-arch/unzip +" + +pkg_setup() { + use server && webapp_pkg_setup +} src_prepare() { default @@ -35,6 +43,8 @@ src_prepare() { # bug #708064 append-flags -fcommon + # bug #831491, bug #919200, bug #921261 + append-flags -std=gnu89 sed \ -e 's/-Werror//' \ @@ -64,10 +74,9 @@ src_compile() { export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" - # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7 - # (and ideally use pkg-config here) - use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ - MYSQLINC="${EPREFIX%/}/usr/include/mysql" + # TODO: use pkg-config here + use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${ESYSROOT}/usr/include/mysql" use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" |