diff options
Diffstat (limited to 'sci-biology')
63 files changed, 517 insertions, 302 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 75d14acf6d14..38ad9f401679 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index bc1d45a744ea..51ab00b29cc3 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,4 +1,4 @@ AUX abyss-2.0.3-prog-AR.patch 350 BLAKE2B 20e1a428ea02c3c67c5df9b92f623ddea58f2054912d0ca788f0a9890057277cd98babe48d089852541db262ab0a69e95ead2a4b31456a62597ae1d4856e8c5e SHA512 747e9d258767c698a95615ae83db18662ec1851c0a6dfcdcec6aea68dc76415e89b3f85f1f8ff6c04fff22052c787a43948f8f3588220e2dc66cc7262788c52a DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 EBUILD abyss-2.0.3-r2.ebuild 1556 BLAKE2B a25f93323564ce83b2a15ed31881a873ddafe688f9277439aef25dbb3a76c6d796984105498c2f547bf00229ce4c465d9e5c22c949c543b29fd61c22a8d52568 SHA512 9c5649115d97c8b6aee3909d092f8429c59c31b9200b71023bb05e3bc2501c3f55a1d4b07c9bacbfd94fc6a10a4a5124a6135b743e29d126856796bab5ea1f3f -MISC metadata.xml 572 BLAKE2B 987284bc0e435174f2592854cf67e44d155b64975a65d69fc988352f9bf0c06bfa412bcbba0e3a5a4819a846d5fd1c5695627b8b75ab7c955abff1b0bb4ad76e SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198 +MISC metadata.xml 572 BLAKE2B 02843f7935e2e1d022754d71f73211099c953b7e44ae1bffdea971bf2ecbf46c4679243706b1f2f3b372c48b2dc963f2a99d9e8026c1e6ff33c824a455b6eb32 SHA512 d6f1b5a798fff4a3e5bebebcb660d470223e97911e06438fa7a8d2aa28a5a3f16891fd4ddce75cec45626b641dba4fa319dd8359dd8520132a993da4463794c3 diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml index 47116e507d89..2a6a2c73d6a0 100644 --- a/sci-biology/abyss/metadata.xml +++ b/sci-biology/abyss/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest index d9ec14eacea8..9c749a7da2e0 100644 --- a/sci-biology/bfast/Manifest +++ b/sci-biology/bfast/Manifest @@ -1,3 +1,6 @@ +AUX bfast-0.7.0a-C99-inline.patch 2316 BLAKE2B 744908af002c5d5af57358baffbaff75a6299b7d0467573e5416c78ab2d4c9fc35dddbdcf308ada17583ca0e732412d1293152240748e84ac5eea243a944e8a1 SHA512 13144864d6a758d6dc0cba59e2a4458242ce33ab77108aafc33967a5343d1f0e2d59f872822e13df8a2f77f1eba2f58c5cc14060a48900509726e48fe6061177 +AUX bfast-0.7.0a-autotools.patch 1268 BLAKE2B b5da950d0230322f0a95b7c1417aec5fc4774a7d40ce4576b10bbc66d21f8d4907e17f3020679f3074cfdbe10f7e69bc3d8b62371ad381a2fb7b17854f146e46 SHA512 d1b00230ef35e82fb633a063c32e48a50866d8c40889cb0e13fddb0866a5b5447ed0f41cc948811f7e50918544ed3d0758ace3e1060a97a33ff5a0c3ee12b29c +AUX bfast-0.7.0a-test-sourcing.patch 1399 BLAKE2B 2cc246d437da36a28d6fd86fe8c4acb78ba06120672158c16305c108298f46f4cabf37193f793e9b32ecb8fddc022f076bc845d06564f23ed9f412f5d7c22378 SHA512 3257038564997ae1b2bdd814e893825951c9cc72934cc204d6a3cd1dd31c796d26b76b6801dca4722be3e10ac309e0d177ddf725a6b6a2c5fe01106bd35d5a5f DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 -EBUILD bfast-0.7.0a.ebuild 902 BLAKE2B c5e520867849c07323fd6002cc881160272259f4b002320453b1e529daeb9b89125da9b51f640bd708cad2f9fbc092dc5e5cb957803e5926a0eee2de18f87e7b SHA512 0807ad435ef822c9697b812b8bfec37fe2aaf701a6e60fac1dd15de821686d94101240cc70b829d46627dfbb0fe3e158ea0daeb873c54ff1f8b594a61be3ffbc +EBUILD bfast-0.7.0a.ebuild 595 BLAKE2B 257ddca11ba647f033b22f98afa4d718f1260687a17cf8386dec115f9e0dfc764a30f94af2cdb4f3f63057e1286e104bb9e3a666dfd44a4f004aa9c84b8f5e92 SHA512 5ce28ea79f9dc037eb432a23f742e7c9efb18be1317324c2200fa0a66f7e938526daa386c146922ae45a1b0f8c96460bdd2700db77c172b18935cd06dc1353eb MISC metadata.xml 346 BLAKE2B cf096d053302cd40548e541557cbe72f41e81328a93b41a6e19ae88122e9939d5e6414eb6f60ee6e96411f43a073151f7d98ab780858afa16c50c1a5e37f2c48 SHA512 b402eeeb37be04022693af8692b128bb257a69b8eeb75170506352fe05fa6e7154c908267bbab7af7d38d1eee26ad6d98e6be5f9c8647181aa491b3fb1680b62 diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild index 97282d2244a4..6a48785022f4 100644 --- a/sci-biology/bfast/bfast-0.7.0a.ebuild +++ b/sci-biology/bfast/bfast-0.7.0a.ebuild @@ -1,11 +1,9 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils flag-o-matic +inherit autotools DESCRIPTION="Blat-like Fast Accurate Search Tool" HOMEPAGE="https://sourceforge.net/projects/bfast/" @@ -13,30 +11,19 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="test" # tests broken, upstream unresponsive -DEPEND="" RDEPEND="dev-perl/XML-Simple" -src_prepare() { - sed \ - -e 's/-m64//' \ - -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \ - -e 's:-g -O2::g' \ - -i configure.ac || die - sed \ - -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \ - -i tests/*sh || die - - sed \ - -e '/docdir/d' \ - -i Makefile.am || die - - use test && AUTOTOOLS_IN_SOURCE_BUILD=1 +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-test-sourcing.patch + "${FILESDIR}"/${P}-C99-inline.patch +) - append-flags -fgnu89-inline - - autotools-utils_src_prepare +src_prepare() { + default + eautoreconf } diff --git a/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch new file mode 100644 index 000000000000..86450c96048a --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch @@ -0,0 +1,74 @@ +--- a/bfast/AlignNTSpace.c ++++ b/bfast/AlignNTSpace.c +@@ -478,7 +478,7 @@ + } + } + +-inline void AlignNTSpaceFillInCell(char *read, ++void AlignNTSpaceFillInCell(char *read, + int32_t readLength, + char *reference, + int32_t referenceLength, +--- a/bfast/AlignNTSpace.h ++++ b/bfast/AlignNTSpace.h +@@ -10,5 +10,5 @@ + void AlignNTSpaceRecoverAlignmentFromMatrix(AlignedEntry*, AlignMatrix*, char*, int, char*, int, int32_t, int32_t, int, int32_t, char, int); + void AlignNTSpaceInitializeAtStart(AlignMatrix*, ScoringMatrix*, int32_t, int32_t); + void AlignNTSpaceInitializeToExtend(AlignMatrix*, ScoringMatrix*, int32_t, int32_t, int32_t, int32_t); +-inline void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t); ++void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t); + #endif +--- a/bfast/BLib.c ++++ b/bfast/BLib.c +@@ -90,7 +90,7 @@ + } + + /* TODO */ +-inline char ToUpper(char a) ++char ToUpper(char a) + { + if(97 <= a && a < 122) return (char)(a - 32); + return a; +--- a/bfast/BLib.h ++++ b/bfast/BLib.h +@@ -16,7 +16,7 @@ + int ParseFastaHeaderLine(char*); + char ToLower(char); + void ToLowerRead(char*, int); +-inline char ToUpper(char); ++char ToUpper(char); + void ToUpperRead(char*, int); + void ReverseRead(char*, char*, int); + void ReverseReadFourBit(int8_t*, int8_t*, int); +--- a/bfast/ScoringMatrix.c ++++ b/bfast/ScoringMatrix.c +@@ -98,14 +98,14 @@ + return 1; + } + +-inline int32_t ScoringMatrixGetNTScore(char a, ++int32_t ScoringMatrixGetNTScore(char a, + char b, + ScoringMatrix *sm) + { + return (ToUpper(a) == ToUpper(b)) ? sm->ntMatch : sm->ntMismatch; + } + +-inline int32_t ScoringMatrixGetColorScore(char a, ++int32_t ScoringMatrixGetColorScore(char a, + char b, + ScoringMatrix *sm) + { +--- a/bfast/ScoringMatrix.h ++++ b/bfast/ScoringMatrix.h +@@ -3,8 +3,8 @@ + + #include "BLibDefinitions.h" + +-inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); +-inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*); ++int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*); + + int ScoringMatrixRead(char*, ScoringMatrix*, int); + void ScoringMatrixInitialize(ScoringMatrix*); diff --git a/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch new file mode 100644 index 000000000000..993f6a554662 --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch @@ -0,0 +1,41 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -8,7 +8,7 @@ + AC_INIT([bfast],[0.7.0a],[bfast-help@lists.sourceforge.net],[bfast]) + AC_COPYRIGHT([See LICENSE for copyright information.]) + AC_CONFIG_AUX_DIR(config) +-AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects]) ++AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects serial-tests]) + AC_CONFIG_SRCDIR([config.h.in]) + AC_CONFIG_HEADERS([config.h]) + +@@ -21,10 +21,10 @@ + + AC_PROG_INSTALL + AC_GNU_SOURCE ++AC_SYS_LARGEFILE + + # set CFLAGS and CXXFLAGS +-default_CFLAGS="-Wall -g -O2 -pthread"; +-extended_CFLAGS="";# "-m64 -D_FILE_OFFSET_BITS=64"; ++default_CFLAGS="-Wall -pthread" + + # Define some variables + GITREV="Revision: undefined$"; +@@ -42,7 +42,7 @@ + AC_DEFINE(HAVE_LIBBZ2, 1, [Define to 1 if you have the <bzlib.h> header file.])], + AC_MSG_ERROR("could not find the bzlib library. Please use --disable-bzlib if you wish to disable bzlib support."))]) + +-CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"; ++CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"; + + # Enable large file support; disable with --disable-largefile + AC_SYS_LARGEFILE +--- a/Makefile.am ++++ b/Makefile.am +@@ -16,5 +16,4 @@ + + SUBDIRS = bfast butil scripts tests + +-docdir = ${datadir}/doc/${PACKAGE} + dist_doc_DATA = LICENSE manual/bfast-book.pdf diff --git a/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch new file mode 100644 index 000000000000..f4dd64e75cac --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch @@ -0,0 +1,79 @@ +--- a/tests/test.cleanup.sh ++++ b/tests/test.cleanup.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Cleaning up files."; + +--- a/tests/test.diff.sh ++++ b/tests/test.diff.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + #error() + #{ +--- a/tests/test.fasta2brg.sh ++++ b/tests/test.fasta2brg.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + TMP_DIR="tmp/"; + + echo " Building a reference genome."; +--- a/tests/test.index.sh ++++ b/tests/test.index.sh +@@ -1,5 +1,5 @@ + #!/bin/sh +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Building an index."; + +--- a/tests/test.initialize.sh ++++ b/tests/test.initialize.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Initializing data for tests."; + +--- a/tests/test.localalign.sh ++++ b/tests/test.localalign.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Running local alignment."; + +--- a/tests/test.match.sh ++++ b/tests/test.match.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Finding matches."; + +--- a/tests/test.postprocess.sh ++++ b/tests/test.postprocess.sh +@@ -1,6 +1,6 @@ + #!/bin/sh + +-. test.definitions.sh ++. ./test.definitions.sh + + echo " Running postprocessing."; + diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest index 5e5e0cabec3e..d244031790d6 100644 --- a/sci-biology/cd-hit/Manifest +++ b/sci-biology/cd-hit/Manifest @@ -2,4 +2,4 @@ AUX cd-hit-4.6.6-fix-build-system.patch 4006 BLAKE2B 28e19d8dbcf2072c1e348c0f4d1 AUX cd-hit-4.6.6-fix-perl-shebangs.patch 4909 BLAKE2B 2bf82ee2713206d4782143fc04f2a924b742cb50ee9b1c99aab3a3f6d1265dee78009106970329146f068544caa4edf5878bd9ee3aaaf69ea8e418702ef1e069 SHA512 3ded78d991ee922761a3a7395b4d422ff29c6fe1c0657b61ad74bc6f9253c7dc82414f8d71cfffae37cac192e96ab03f711257d3091cdd0c9444202bdf5967f5 DIST cd-hit-4.6.6.tar.gz 1152570 BLAKE2B 6a7cf99be947376af19172739626b571e06936b7b0bc8c5cb52069c63e98f0949a44edf7560fa50810d2d96e310df87dcf2e3ebf5a3856ada46dcdcd3595b6c0 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 EBUILD cd-hit-4.6.6.ebuild 997 BLAKE2B 1305388e83140df2e024bc64546b96e849a9f70095dabc29c79ab0a078dff9fd33a091d05df3f07323391e627f28877ad77f52fdf890d20cef5832df0e3053a9 SHA512 fe17e01fc04944df9b86b98dc73a4be2f14300938e3e926f56c952eddad62caf846f0051a7c3a66dbca3132f3a79a8bc21d7a43206bd6d9d784b24c94c3204b8 -MISC metadata.xml 1351 BLAKE2B 255adcb4a5ead5f03add4537d26ccab28869e3d9c883d25be9737f145b417dce343e3ded6732eab937022b949406eded039694b6b67e13c1939e05ccbce96148 SHA512 691c92d76f2bdb3ed31a802fb1003905942abfb7cef3c1d08848e69cc819082e82540217f7fc79ad39d11a2d43c45b845617bd8ad1282a7bde505ed8616b5364 +MISC metadata.xml 1351 BLAKE2B e06e3ea1665bc79924542dd596c3bcbdbd4cfba8be622a8b1f9f4689fc615ca5ded5b40305f296137743ff92f44db5b0ad5aa51218ed2d93902bf12909b5e0c7 SHA512 e43009446e7dc81bd0362ceac2a7c709e24be974344ae009bead94ea8533099ebfacb10a5b3f3d5b93c241c03bbf835b0fb11d1af172eb5a18ca30436adc3cfb diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml index 1f3b075216dd..e4906ff94e3e 100644 --- a/sci-biology/cd-hit/metadata.xml +++ b/sci-biology/cd-hit/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest index 667d2a881591..a15852d6da70 100644 --- a/sci-biology/embassy-cbstools/Manifest +++ b/sci-biology/embassy-cbstools/Manifest @@ -1,4 +1,4 @@ -AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 3167 BLAKE2B f34ccb14802128cf315cb767d519a8440b9fc9bb8fe3bbcb02a310f25304cdf5109dc4625ad62aed2323c1b3d438a99549e625b8440b42bce0477689d6d3fc24 SHA512 0ec7317d719da5466f02813105184d44c18f5ec668e0cdc1e120324216070009da4e38ce34dffb320b438665926f4506437e60757c3103fb03a526c46ca042d8 +AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 2944 BLAKE2B f33ea2bc9579a7a233064e562ae76ede11fa81d9c6c972338e944028192390e797deb13514b1d02a32b1b6b55925a8eeef15f8ed11598ab487e9deb3e7a6a14d SHA512 913542383cf0dcacdf7c18ee258b6bf37fcde77b41a548089e239c9e20e2087cbec0e5244eb946b511bb76ec5930a6a44142ea172d894061bfca5e1228e29047 DIST embassy-cbstools-1.0.0.660.tar.gz 452594 BLAKE2B 68d13e14b4805af7ba1742537e6ebd621553ba6c895cd4bb13a5c1e93e72e03916ba62833f31ec35e69fa9a4ab15d9348dbfe19eb55a82f3ecd86141726e6c01 SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 -EBUILD embassy-cbstools-1.0.0.660.ebuild 352 BLAKE2B e384b07b74042cefb1d5e2e3c646a4006850b6846997daa136a652b569efa8db98092cbf8a2b965a1add167306fcf4b10fe50b1772b75d50d893a95ba900056e SHA512 f85c1ecdd7c16e13c8e1a08441b73a76f66ff770a3ca75eeb745f31b46aa5e2b74172f20de4b520e64e0ed167cf50b55d01ab78b760c9fbfde8ecee689f2703a +EBUILD embassy-cbstools-1.0.0.660.ebuild 349 BLAKE2B 3930b547938c8e72d8e058684c8808385c7dff42b3d6796e854da4f2401be95d652eba027c7c17e715e3a670eb4d8b31837a65d0d0dd285374ef169a8b87852f SHA512 c3354cf9907079e2870e1acf7c8ccfed1225da5c1eff6f97f144373b80ebdfdbb6d4b0fd95632e341e51edd42b15bce88bf7a10ed78a328a4907f86ba24a843d MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild index 6104a470f3f7..873b9cb64520 100644 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Applications from the CBS group" diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch index d29310efcb47..bdaaaf98f23c 100644 --- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index a70d4d2..b8f5e79 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index a70d4d2..b8f5e79 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index a70d4d2..b8f5e79 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index a70d4d2..b8f5e79 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 824a03c..9db171d 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -19,9 +19,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 824a03c..9db171d 100644 endif if ISSHARED -@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -36,7 +34,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -64,6 +62,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest index 8e2a97e9203f..1ef5f7347551 100644 --- a/sci-biology/embassy-clustalomega/Manifest +++ b/sci-biology/embassy-clustalomega/Manifest @@ -1,4 +1,4 @@ -AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2860 BLAKE2B 0a88c8315e40df48d18ef2ca6b5d8e0c266720c852cbe8dac681ceb8802b4b7e6ba18cb1064be5a979b82c37f1a7b83ef445e84ac3dda143e7e2bd2b5f627d10 SHA512 6b1c8a2915c9c48ec203bc131461b9acecc3948da79f36941e2fd97a22bf044a35ee717e0be0b13f46d8a6f81148c29faa1e048ed4066cf768dbc705141a772d +AUX embassy-clustalomega-1.1.0_fix-build-system.patch 2775 BLAKE2B 03c93a180b5bd19d74196a17e093df54a82ad70378222c04041274477f16a94bff901ff4d31b36df3597d6bb6a2e96750688a5e279d2f83b2e745cb82cd18549 SHA512 bbdf887e87e00c5f82f964ffda547ce0437795d13ecb73255901028c1e45def1a5a02decf5cd7be045985cf125669cafb00617def6cc2b5ec543aadae1dfb547 DIST embassy-clustalomega-1.1.0.660.tar.gz 618177 BLAKE2B 5d3f300a0dd825c92c3f953219b2ae8be271a7d89a1237980571b3f9a9027d6a0191ad9e61be87d1ad3334ddd56f9ff11c05d3e277683dc8cdfe511ef3739877 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 -EBUILD embassy-clustalomega-1.1.0.660.ebuild 384 BLAKE2B 5896e2a2c95a3c3c126437af70f13cd16ab286dbf600784600859a32fb8ae26c3f791712d114945dbdc8f6984f47c734b560c62df150e4a1a0b0da30f1820eab SHA512 8504bb9294da8a76c23114476fc16a011c45380b5f0f243bcf5a3bc68db6fd71fb7156f450ee14f78ec7825f8ecd46f4b0a7d0764c3dfd7ba1a2939026b123a4 +EBUILD embassy-clustalomega-1.1.0.660.ebuild 381 BLAKE2B 35ffd764e71b73b85110065818095193d822955fa9890e5e9076e09cade350980d1bcf41ee38b56b363c6dea6ca081dbf0f55ae75c474e08c7ef5555d5a330a0 SHA512 58e8112f9d645a058bc40523b6690673dfc0c0870b8b5495dd8121acd5209896a5ee3ac8c89799188635366df4a50631baeffc2d29ab5278c2e52c46e5736bfa MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild index 2d2a2c62632c..93092e9f884e 100644 --- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Clustal Omega - Multiple Sequence Alignment" diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch index 5525d79b525f..7f92130fb501 100644 --- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f12ed19..b143922 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index f12ed19..b143922 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index f12ed19..b143922 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index f12ed19..b143922 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 9135679..c201149 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 9135679..c201149 100644 endif if ISSHARED -@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -61,6 +59,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest index 22ea27894d13..ebe05ee85f34 100644 --- a/sci-biology/embassy-domainatrix/Manifest +++ b/sci-biology/embassy-domainatrix/Manifest @@ -1,4 +1,4 @@ -AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2860 BLAKE2B 6115c049eb2864641e73968e5b094cddf999f0c74fc44ccd64515ea945039903f0c556e1c3d990cbbc14f502078b61f04966a57a728d3aa38f9b9e4acaa363ec SHA512 9c8dfdd2e6c7f8542a989118dad6c70159c55a7f56593800b9d1896fb717b0c28ea100f5884f3284823ad1e92da6e5fe307e798028475e29d353edfe52b62865 +AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2775 BLAKE2B cfe8ec8c3bd62ebaa789d1f3ee63b961f0ab7c41ef44c78faa7b4913945d84da1fa082dc31ebeb92b105762a25992e2d68b56988177aed9ff444743942687d43 SHA512 505a92947e8f50a2a22ea8888a326723fe47584cab4f2414d703753201daecd0e8030cfe41ff53274a0ca08a6cf9c110557e902d7a038ef7f2baffe046093e2a DIST embassy-domainatrix-0.1.660.tar.gz 474066 BLAKE2B ac5e081ac1a18d8abfbcdf687a43d4a09436c83fd54bed8c75487f8ed74852979adc96fa592df9f86c161fc8b398f1225ec44e565b470c59a5c2268898943270 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b -EBUILD embassy-domainatrix-0.1.660.ebuild 345 BLAKE2B b56c17ed3121410664d7f7bbd55b9ff09229962c300922dd6c3b72bc21017b23c2477d8dce4fe87e63ed393a43a16fd35cdb42adc708504c8db7a2ce9607e7f9 SHA512 0438a817780278fb85fbd6ba9135725e5b6a850318f8b8e95a504b388e649f7a19fc8472145ced331193d64addbaa1603c3c89e0272872f8795a13cf44d0288f +EBUILD embassy-domainatrix-0.1.660.ebuild 342 BLAKE2B f4c97aaa3fa9fb33a060b7973d64308bd90caa10e57497d31d3401e5d87d737a353ee5665ae0ee563f994d972e402090ef2bdbf333b4696886aadaa69136cf88 SHA512 178adf2159cc20c5e23a13b4420bf7ecd77a7b82b1047f4f499abbc9e93b1c6cce1acc6e6e27719bf767077c407de314f0d0c9e8ea93ad985944e7c3eedb452e MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild index 4607d87fdc17..03e728926cb6 100644 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Protein domain analysis add-on package" diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch index a932e1ebe21e..1cd2a1b29b09 100644 --- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index d16cc02..d327a0d 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index d16cc02..d327a0d 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index d16cc02..d327a0d 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index d16cc02..d327a0d 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index d405d00..54be7ca 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index d405d00..54be7ca 100644 endif if ISSHARED -@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -63,6 +61,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest index 5afe28fedab4..deb0216a9f19 100644 --- a/sci-biology/embassy-domalign/Manifest +++ b/sci-biology/embassy-domalign/Manifest @@ -1,4 +1,4 @@ -AUX embassy-domalign-0.1.650_fix-build-system.patch 2908 BLAKE2B eb0b7288b25a96d6b60ee75e8d022efbd5a3a72ac69c93e32a823316799215d8ea2db923620a0e32924e6961df20cfc939e4fa332d255208175d70977cdc0d14 SHA512 5cd02b39812adc44d9b877cca8902b6a66e79c90975b50233a4f8f84392026ffad25d57665e68e5db533f28935f444b4dc75b7120bafd910e415b75737686ad2 +AUX embassy-domalign-0.1.650_fix-build-system.patch 2809 BLAKE2B 01ae7488b764f3d3853d8f6e4fc2f2115d381decbac3d20922d26c079d0242622f553359dab2401481be3cdf28f25495c567682c1b9d2140f3686f312cbc20f5 SHA512 09444e7ee2b263b56177275c4fe9452344720e641acb721e1630696941a3f077c9790357f9d8b775bff4f5df595973f59d1e9f4c3f66b54fa31f53db4e32ce58 DIST embassy-domalign-0.1.660.tar.gz 498669 BLAKE2B d21352b28ca046c1bfe8600a7eba641d670e232571f95f9c75b47486a63f2a2b02516191706c0688e81bc33cda90ebf88a9ce800535dce9a955ccc15e25dd20a SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 -EBUILD embassy-domalign-0.1.660.ebuild 343 BLAKE2B eb2e7187c98b12fc74b1efdaf70d14d64c867db49aba11f4f07617bc727dd5223b011ef7b78981b638010e541f8c534d8886b7d7c4fcb9e40ba3b148a0e17441 SHA512 bdc0f0bf6a006d2091f98c3a3258e402b522a743866db74324333c5ec9d14df181561b0beb75baa6aaec130636e1e866184e5c4ed414ceb4e8365e13801df84c +EBUILD embassy-domalign-0.1.660.ebuild 340 BLAKE2B 8e42cd3a864fe7b85628901b37eba3e72b2d7efcf48ac3b7b48c65735b0983a68d47dd525ed7972e2be9c9b15723c6409de10017718e5945cd7c231153be022a SHA512 236b004af2c4a2e84eebc72f8363af05c757e0251417c8f2971ec4902a067669754980cc65f358a3295a05ea0e3c4a43a9e2b2a7e9e6010632c73ac06c281ed6 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild index a897dba4b060..331bd7e05a71 100644 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Protein domain alignment add-on package" diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch index 033ddf7b6535..079850c2bcc3 100644 --- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 7 ++----- - 2 files changed, 9 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 693eb4d..dc0fda9 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 693eb4d..dc0fda9 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 693eb4d..dc0fda9 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 693eb4d..dc0fda9 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 8785446..fe85f11 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,10 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -92,10 +84,21 @@ index 8785446..fe85f11 100644 endif if ISSHARED -@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -35,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -62,6 +59,6 @@ + ../../../ajax/zlib/libezlib.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest index b75a5a676260..a2b6ac07a746 100644 --- a/sci-biology/embassy-domsearch/Manifest +++ b/sci-biology/embassy-domsearch/Manifest @@ -1,4 +1,4 @@ -AUX embassy-domsearch-0.1.650_fix-build-system.patch 2890 BLAKE2B dfc956c10857a15a99ac57ca6d4986f43bd659903b71fb6e07b3a57fc0ed82f8303f33dcdc2584f4b5756a756a71b68d65cd4b24a984af3a76ec47789a95f673 SHA512 3f012a5646751b43ec66d006df04cbe8fa880d0acd62723962dbb0e1817c5f5db2bd4879c25cf932114aa43291bc70816afef6664088532222e11135f0ab5603 +AUX embassy-domsearch-0.1.650_fix-build-system.patch 2806 BLAKE2B 44cfc67f34b7d4112cf0247231eb82db7433a1aecfffaf1723b4fcd5e186c0d7dd683db52bbc006027b305c2551b760c98116e5fab3eb874bd1a843f38ef2e71 SHA512 73bc497c5e7974d50a1ecd1ea537b923e5670ac1abafe9877b8fb98e4e94688fe7c77d233e4df45952da6f39013f0fa87d80791cdc79d3ed005e3f8070484144 DIST embassy-domsearch-0.1.660.tar.gz 504183 BLAKE2B 598ba359558519967d0e8d895bca453aaeffef3d8a62c3d77b6b2f321118e890ec70c3baa3dd3acc03fc9a19cc380909cf3f14e5569c4ae90d3d5e88817d6e6d SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 -EBUILD embassy-domsearch-0.1.660.ebuild 341 BLAKE2B ad203f06d1de9154b8c9603d1ad5e83ebc95f56c07f9a079b0edf38637b8dbae935efaef91aabdf411121cc5956f44a0027d2b8d9fc7784f3f2781bac339a88d SHA512 b7719faa5c0b7fd20379351f41930926cdea99e5c1b26e23aec3f7aceae12e1db885997782b2c4ca89e0bc5d92e17261e990d644ba04da36d9c219c0e5732afa +EBUILD embassy-domsearch-0.1.660.ebuild 338 BLAKE2B 90d616ea192ce84a7cd8806425ecddbb8cb1c475900616c0aeb7f629ceb9294a05620a23df512a694c606af4e90f4968ddf0643a9800c13adde6556d6382a268 SHA512 64cb26ac31b6dee716132a3ec575e8c19d703e8ba023db382e1ade34ecda2227d2663fc18aa7ef5b5de9bedbb6ff103d2f6ac1a33c1c50e60e18523d54132351 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild index a47adcfb8457..e4c37b996653 100644 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Protein domain search add-on package" diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch index d24857c8386d..ecc702edcb66 100644 --- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f0f97fa..d419d7d 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index f0f97fa..d419d7d 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index f0f97fa..d419d7d 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index f0f97fa..d419d7d 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 9829ebd..433a5c5 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 9829ebd..433a5c5 100644 endif if ISSHARED -@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -61,6 +59,6 @@ + ../../../ajax/pcre/libepcre.la \ ../../../plplot/libeplplot.la $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest index abf651b02922..9b2791335e9d 100644 --- a/sci-biology/embassy-emnu/Manifest +++ b/sci-biology/embassy-emnu/Manifest @@ -1,4 +1,4 @@ AUX embassy-emnu-1.05.650_fix-build-system.patch 3844 BLAKE2B b77be3d3917db4cdfcfce201089595a80b970575f77dffbc366c77ae27010b9a78582b035728008b20ae11b0c7c18b7b20a5fdfcd59b840f85f54a1db2fc5496 SHA512 1836ba79762f62f9e27a770a35b89ae5f2821c4d23dc93b1ab3505404105280256f1c43287471385a5be71659fbe614f5f7f97d78a4743b3b1b90b303a25f674 DIST embassy-emnu-1.05.660.tar.gz 425595 BLAKE2B ed6ab4a0572ac4b57cf0f0b75a3894b1f950f7f373a7c6797ea0c34ba1b0d0e044f2c6951aec7c084340c6b207aa4c8b386055e92ceb9fc83c920fc70e83e665 SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd -EBUILD embassy-emnu-1.05.660.ebuild 470 BLAKE2B 4a5fb352f30c729ded48ba438d978ff7ba85ee419eb1dbe94df07f34dd2b6fa50527615678c166cd627090bb2b15bd88d6d8ffd3d66e16006714d9a175444dec SHA512 ec9df242ed5a421fdbc45b59c1a9a9a3cfe540bde2ea010a29ac56e758d26fa0f1a1c850de644e82486a574850b0702d7d87adebfd851cd40076e17596c88f05 +EBUILD embassy-emnu-1.05.660.ebuild 530 BLAKE2B 063882fbbb297ea4bf5b70dd82cc7d4625f027fd87ecf3ff28e34a5d20834e20db39a8750bd3e6738e829f8c727211c1d3d47c47f2a77ffa436f925dcc8f08c0 SHA512 d4caec2280558dcbdbf7e2a5a2d3d658845781d8f05588fcedb7f7ab33fda937f1aac4e97627ae7a6744258d2384d9859a7dc0ea7af968f60f5f8739f070c296 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild index fd6b02d8d235..dfff5eb5de26 100644 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Simple menu of EMBOSS applications" @@ -10,13 +10,15 @@ EBO_EAUTORECONF=1 inherit emboss-r2 KEYWORDS="~amd64 ~x86 ~x86-linux" -IUSE="ncurses" -RDEPEND="ncurses? ( sys-libs/ncurses:0= )" +RDEPEND="sys-libs/ncurses:0=" +DEPEND="${RDEPEND}" S="${WORKDIR}/EMNU-1.05.650" PATCHES=( "${FILESDIR}"/${PN}-1.05.650_fix-build-system.patch ) src_configure() { - emboss-r2_src_configure $(use_enable ncurses curses) + # --disable-curses is not a thing, + # EMNU hard depends on ncurses really, #752216 + emboss-r2_src_configure --enable-curses } diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest index 861ecba8f320..0fae9cd83198 100644 --- a/sci-biology/embassy-esim4/Manifest +++ b/sci-biology/embassy-esim4/Manifest @@ -1,4 +1,4 @@ -AUX embassy-esim4-1.0.0.650_fix-build-system.patch 3167 BLAKE2B 23dc6aeb76d8396bb03e07abb9e3d6e00d982d050ea02156e43bc4388fdeb3a26a7af77d59c3ec358fe369cf40befae0f79c460c903110a7d71e4bf89512aed3 SHA512 c8f4468998b1e91122e4ee5f355c5db451fa889892c05125edcc2f734051410251de85a9d7aaf5566dc802240d2925c709cfd448c8f96351aaa91c124eb1396f +AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2944 BLAKE2B 19712a0b6fb79a37e990bfbf91471c7a08e1e22c01ae97850ed6c09f7c81272ddf841bd834b88f798598297c4df526f4cb12cb29d6db28f0d0ae1db6d05ce116 SHA512 846197536cf1f308f51ae96bb8186198f1c720ad05fb16c94e36b1aadbc3dbf50b21ddecdb2a52acc0444e0c0db980653f3d90f01b43d334d1cd995868888da8 DIST embassy-esim4-1.0.0.660.tar.gz 473261 BLAKE2B d15029b0723dd739fa9208f9b0ffd7814cbddc630ca2ff15955412f493f7983753acf82bcc8a3fc6ddfd49abe630982ead377e6941dcbff44ddc5d8ab4e7d6e5 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 -EBUILD embassy-esim4-1.0.0.660.ebuild 345 BLAKE2B 9b4041be06278cdc5afee7b710ab21eaa048975f7e2a496547171da92a621e55e0d731c210b60d1a661857fe7de2719a58d1cad42134277adfbf0fdc16f37471 SHA512 baff9c211e98de225f8644a441b99b4693f16068c151b5ee5b59c481e6de564e5cce0f0617bdb52a3d96b642a3b22dd558eab3329098d3ac028527818dc16357 +EBUILD embassy-esim4-1.0.0.660.ebuild 342 BLAKE2B 2e9c56d305a5e31d2376695e89236d7f64751a9bb922dae565e457fc44230e199e767c12208da0bae8f40be23957fcc788139a1d2e25d499e3da1ad0820e7a78 SHA512 082006d670e565b734711759cedc3ea84229c7b13ccf48a1dd823fc8918ea4e2f1d1568b1599ea2587ae0c5a4eb6e6753311df68d8a82b5b55e77dbf5733fa4c MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild index 16b6d29ebdaf..2538510c6bd3 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch index ead54c91b5f3..7a85b4f7bf81 100644 --- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 924220a..2c45f46 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 924220a..2c45f46 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 924220a..2c45f46 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 924220a..2c45f46 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 0620938..0304bb8 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 0620938..0304bb8 100644 endif if ISSHARED -@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -62,6 +60,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest index 9acbe42f919c..5d34609a139f 100644 --- a/sci-biology/embassy-hmmer/Manifest +++ b/sci-biology/embassy-hmmer/Manifest @@ -1,5 +1,5 @@ -AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2860 BLAKE2B cc3075caddedd8c50836b46943caaddecaedc517d93da7d9777f8c6dad97442f185f51e2c755173038c90dcb10097cc4b105ae812e54826552444d5b46374155 SHA512 f215e5c338aa1f0bf791de223f3ee9a13622f70e142c5ad4812dfe171f7d602aab750e1dfe4233324752adc645abf289e63d8981b8497787c785c07de64c7944 +AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2775 BLAKE2B 70ac87074b81a15a4f8641a9c98136b23ef8ad78c2ee17b3762a624366638023e147efaef478b1c79f5a5f1d09a882cb3fecb1eec4131307bc585b08855aae6b SHA512 b0ff185fecd52e5452d3257b2e5bd6f1268d84b491f529d66025534d9353f57ddecefa81a69ae3299ad687b1d3480964c4a1df609c2e77b0db1a511207ac49b6 AUX embassy-hmmer-2.3.2.660-slotted-hmmer2.patch 3392 BLAKE2B 56da7becf8da8195016cb98518a19fc34394d98400dca6bb499d43c57172ed76ec81d5a9216b4a1b5e67b33520431ce87ed1327db99f3f924a36d80ff8c9e0c3 SHA512 18d1595b7cd6091917f9657310b286d2f0d1f6a61c045840b1c551b66162142997b837cc50b47a3a5fa7efec4ffa78e5b9b52804e3c4d41efeed9b4edb6e5507 DIST embassy-hmmer-2.3.2.660.tar.gz 587775 BLAKE2B ae7f7c8722bb06d4e28333837b082045e48179a596026a76c2a42f7905c7ebc42f98dd4f36915e4603322bb6d976ac4fa4e8ce6246cdee025b39ecfcb250bd10 SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a -EBUILD embassy-hmmer-2.3.2.660.ebuild 501 BLAKE2B 3890181b25b9f6ca7793f05765f47723d6c040478af2f197f0ef9ebedd594d293224cf4878fd1e8a0850781252abc54537804116fcf625f38d35439e2cf8020d SHA512 bee21c5e7950f2f11be84c0287010630754681d840fc7393f9fc8e0c05fd14169e03f37a6d99bc4dfb28dae5b9f78a9f509a163cee6722796a3300b0cdab0651 +EBUILD embassy-hmmer-2.3.2.660.ebuild 498 BLAKE2B 7f319b02c38423cd0bcb6fa7f5833ec4c781c04ce52cf18db847406d5934ffb8957cb1a39e712fd3314bb78e08823b8442809c45b4c8b5d5e0c6e638451fadf7 SHA512 cff995afdb31de78ec2feb8e8b0fcc3f4e51f5214b3fd443c5b24a2f4a7dd3ac9e0a712f400734128bce52d7cc80b2fd71882716d7d1ed9007ccaa6a31710ee2 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild index 4fa2defa1f7d..c22ff4141c2f 100644 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="HMMER wrapper - sequence analysis with profile HMMs" diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch index 90c45632eada..303aacda46cd 100644 --- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 037ca00..f539ab6 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 037ca00..f539ab6 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 037ca00..f539ab6 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 037ca00..f539ab6 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index dc789bc..5a8c38e 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index dc789bc..5a8c38e 100644 endif if ISSHARED -@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -66,6 +64,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest index 179b45815bc4..6e6ae833c3fb 100644 --- a/sci-biology/embassy-iprscan/Manifest +++ b/sci-biology/embassy-iprscan/Manifest @@ -1,4 +1,4 @@ -AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 3167 BLAKE2B ef1f3263072850667744e2064929b2cd38620046f1cd2c6ec5c4bed135554cdb7e36d8b58363031051fbb98f294dc9f6c77bc7ac81ff14110baca368e51b8407 SHA512 b2b28377e60790db744f32eb5cd4de5b7e15129b603e21013eeeebaea5c06e6867937b6441f3d8e788effdbb58c57b8841880aa7d4b4eae2b0b83dc72242f4d8 +AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2944 BLAKE2B 0342606ad758dc533186f455062b7019a04a0b7e8d49ca61214de09caf0518bec6b63f0dcc69652eb24bbb8704047cf0f8739cb9c8b8f2883e525176b389aa1a SHA512 98431bf56317a987083fe936f6b5d0d00c5f773bbdab5e3ee4dab6d1d6b6edb5448c4602c11f79aeed05a5642838cae7c3ab692661b18d1d15fdc9793604c856 DIST embassy-iprscan-4.3.1.660.tar.gz 406720 BLAKE2B a7e5a20b8fd1eb1ba562b5db6643542d5062b270d69a2c53aa66f5cb58f48f1d3a480ae062e53341a884eb497fff22d546df42256cdc131afb183067166fa8b6 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 -EBUILD embassy-iprscan-4.3.1.660.ebuild 363 BLAKE2B ca438f24229f607365742c8a1dd9d0fc72ad44a374b7ef6c4446684dfb3a7229bd3b9ca85bbe396fe247a7ea6f9d7b9ea32753f51bdd74919ad718a019e760a3 SHA512 3b140b4b5f4e25d6935b4f159cf636d76dd5437c97fa3c4d0293287db5e1e52cda7db29eb4a0cd4b34aa9596da791725a51a653af27be52cdfbfb76c6ba1c1f6 +EBUILD embassy-iprscan-4.3.1.660.ebuild 360 BLAKE2B c4cc140e02c9eced5cff9976734fcbccde4a61d259cf1787a0a744f0639ea12c27d173e8badfc649f7779dd18978523dc1acf86174e1eccf697351c839fa4c9e SHA512 5e4a54bd7fb3d0522bee736678a7e8e590b07635137089487412c23c2717c6fe9b6aa1075fcf2b8c94656388fe2594c78f5c0f7c9eef91807c355809d82ca527 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild index 3279ed3bc8e8..351ecd1df3f8 100644 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="InterProScan motif detection add-on package" diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch index 8c8a1060e30f..ab627c323253 100644 --- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 9052ca5..c12c268 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 9052ca5..c12c268 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 9052ca5..c12c268 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 9052ca5..c12c268 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 0afc96a..904b41a 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 0afc96a..904b41a 100644 endif if ISSHARED -@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -57,6 +55,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest index 2ed7653d9601..b41ff2714e8c 100644 --- a/sci-biology/embassy-mse/Manifest +++ b/sci-biology/embassy-mse/Manifest @@ -1,4 +1,4 @@ -AUX embassy-mse-3.0.0.650_fix-build-system.patch 4274 BLAKE2B 20674fb79ff55fe7e73f0dc5c62bbe6acec81cb314260a6b879b0881b9f0848204d82301675c5829ef236050af3e4f5d2c31e6cd3a0c2f9554da1408951deb4c SHA512 bfb4663a4b38928f765813cc9b5e773ca712c2333c1650d9c78f457307aa450684f77a20c0a087d3795d5b51f059c6f8113e74da35aa78753c1cc666ba583f4b +AUX embassy-mse-3.0.0.650_fix-build-system.patch 3968 BLAKE2B 97999702bc800bb02c0c77969e17f4ab36e6491d494ff09c3fbb20624f75db7392a5c1dbe91d977e3596855a89ccb70525c01cf7952364fb4bac4a8f403ea5d0 SHA512 8abaabce2566d42209e6863c30c6cbb392afc900d52f819e975662699651b7114257a372a50657419355d0af69f1dea80501fe2b3cf57ce1c8ca731d1b7557e4 DIST embassy-mse-3.0.0.660.tar.gz 491747 BLAKE2B 7d072458577a90fc367c5b6ed72d1d36592e42b83b3a4e31126b925ddc76f1946fba14e22b7410f66eb837f686f848bdb1033f3b62084f1423543d7605c4f6b9 SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 EBUILD embassy-mse-3.0.0.660.ebuild 560 BLAKE2B 9eab17caab14b9c89b455239cbf5006ccb4454be3d54c9233cbda6bf107e44f0b8e88e514d60eae529892d80afd59e53e2d0dadaa113d4de50eecd6a693d7bd7 SHA512 a6b0a375dc3fe6035df488732848ac6dde8209a641c7f201ab2d6b6e463be87b505d486d207c64f2b690fe437772f78196ba223678788b879d2b21b2e3e1cedc MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch index c1095b266d60..23e656dc0a86 100644 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -1,11 +1,3 @@ - ckit/Makefile.am | 2 +- - configure.ac | 67 +++++++++++--------------------------------------- - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++--- - 4 files changed, 18 insertions(+), 59 deletions(-) - -diff --git a/ckit/Makefile.am b/ckit/Makefile.am -index f87b131..a670d2b 100644 --- a/ckit/Makefile.am +++ b/ckit/Makefile.am @@ -2,7 +2,7 @@ @@ -17,11 +9,9 @@ index f87b131..a670d2b 100644 CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ seqspec.c ttyinterface.c nextseqentry.c \ -diff --git a/configure.ac b/configure.ac -index a20d488..eb208bf 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -55,7 +45,7 @@ index a20d488..eb208bf 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -77,7 +67,7 @@ index a20d488..eb208bf 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -91,7 +81,7 @@ index a20d488..eb208bf 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], +@@ -1000,17 +965,13 @@ @@ -116,8 +106,6 @@ index a20d488..eb208bf 100644 -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -125,11 +113,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index b44632a..84e89b5 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ +@@ -18,9 +18,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -140,10 +126,21 @@ index b44632a..84e89b5 100644 endif if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \ +@@ -35,7 +33,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -59,6 +57,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +-LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = ../ckit/libckit.la -lnucleus -lacd -lajaxdb \ + -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) endif diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index cf5e861ca30d..df1af5230960 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -1,5 +1,5 @@ AUX embassy-phylipnew-3.69.650-fno-common.patch 16289 BLAKE2B 346f5d704be918503a80ab224e1892953a2d1d6ef642e6ced95fcb1476954e09d983bd0eef1d6afe71d2c4e043a05a99dd92748151e337ac5d3646d91008c2e9 SHA512 0ea1f10865832a44647f0888eabef1df6e5baadace9fda782f171d52eef70fc7d8ef80317d46eaeb029896b8b0b4ca0d845561ae761daf406f7c26e18ebd1341 AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 39c2d7843ffac8c0a04c70d307d5651f2e53cc386c3a9b1f312d4fd53a9b9ba235a02931c4812a750da8711988e262b1c9a51a7152da20f61cd56c0d21607a89 SHA512 7d46280ffadcbc07e01d09a49a7896539a5c0c271979fcb3e1ffdf385051812adeaabec186c73e2105a710eee2fd340d89bbcbd4ecfa112879fb00cbc58c2dfe DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 -EBUILD embassy-phylipnew-3.69.660.ebuild 409 BLAKE2B 35bac3a33793b140470ef4c627b578317f22efdd7d9c71eeae947f0a6399d94829c5ceeb85d537616811f593b3b54eeda9c1f9bbf0710a20d3eba12891c0f07e SHA512 d088e1121fed9e50066767b58a4d2ea61e5ad5167293cc3780e9bec71f4613d144b985f96d235ab9665a94bff8703a005cdc86916d63cf593941a3e6aeac1165 +EBUILD embassy-phylipnew-3.69.660.ebuild 409 BLAKE2B 52d2e35042acda08f96cab28de1d0dd2c31c6824df7541b195644f67a8325b35b4ce34d8eab9710f0239466feeaa4c0f5f20017891812e702671710797fd0315 SHA512 7511f44570ab985948b8daf6b9267235a930d0c70fc17cff754393e3c2d9028db5360dc60642398a5fd951ae412a70d6d5610a0008137ef646040ccd1904ba27 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild index c5ba6a540bfc..129b42870a79 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="The Phylogeny Inference Package" diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest index faf049a6fa0d..e450e4a537da 100644 --- a/sci-biology/embassy-signature/Manifest +++ b/sci-biology/embassy-signature/Manifest @@ -1,4 +1,4 @@ -AUX embassy-signature-0.1.650_fix-build-system.patch 2860 BLAKE2B 33e2c35f574283d979ceec4fd6c3f007a9e8a0bbf111e8873866de331b6474d5fd6f3dad3af980471ac3155f5e82637e60ea26ce5217a4e9a56fcc120b408e35 SHA512 54a6027b2fb1d17eff98b7c1e9adc61578a2845b30be3b7c40551b4291950ce11900798dbf7d54e1fc9421743a8d313fc42a14cfa39976735ac8cfae5a297954 +AUX embassy-signature-0.1.650_fix-build-system.patch 2775 BLAKE2B ca267498e98a294546429cac0c4276fe7c3dbdfc199d151bb7fc758e805a0f7b6de25094a2f9ec00e21b52a617176a8d45d20424cfbb37276bdc4a0000fb8ed8 SHA512 5e4f72d2960f17a2c758f6bee15f9ddd317e55ae338c46f2b915beba334729d837f573833b54310284db59fa1f1b397d8981ab4b91671cc95bcea7d441820911 DIST embassy-signature-0.1.660.tar.gz 622294 BLAKE2B 8d495b164d7aa18b4bc2db14d12e3f3ef46f2d9c6d9f98e46bebd888781ee71e7ddf88dbdb37c7be52fdd1182337ea7c70cca1247489a14f652b86918e58c46a SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 -EBUILD embassy-signature-0.1.660.ebuild 337 BLAKE2B f444c8dd91ae1f214be4687bced734b1abf883a5f4efbd844ce2ecd30b026e65f22b7aa73695a10a1913b8c8aff569327e88a5555d4635d7409a99c1e75287cd SHA512 ce592d367c64428911a735a5ecc3a24000a5b1e8c3b3fcaf466e5005a962deaf113416cd161039eb445a1a41f7296ca7376531396bed019047c0d97c86296585 +EBUILD embassy-signature-0.1.660.ebuild 334 BLAKE2B 3102c22d5f604cb3241730df137049d99fda38cd1f02a4120c58669c388c2881c6ecc9b9abbe47be05f58a8b6fe0c0fee9fc210eaaf73044aa7987de26cd609c SHA512 d1414951385d7301aa45881866f55433a37f9938e5be14de9d2056a8b87e16767c45421a0e0462c8609806afb379114578b0b3d4908008ca16a780638d8ab9e1 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild index c0ea3e302504..4d873a69a69a 100644 --- a/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild +++ b/sci-biology/embassy-signature/embassy-signature-0.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Protein signature add-on package" diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch index 32e4d684cbb3..10bee217bab1 100644 --- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 2f5ddd0..827543f 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index 2f5ddd0..827543f 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index 2f5ddd0..827543f 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index 2f5ddd0..827543f 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index d77e43c..849f17a 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index d77e43c..849f17a 100644 endif if ISSHARED -@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -67,6 +65,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest index 3b1134f3b481..593fda83a0a3 100644 --- a/sci-biology/embassy-structure/Manifest +++ b/sci-biology/embassy-structure/Manifest @@ -1,4 +1,4 @@ -AUX embassy-structure-0.1.650_fix-build-system.patch 2860 BLAKE2B ab45dd016f21520afcf8bf949f150441b7c7d451e35851ec05edbacd3145f559ccc18550e8c836c0663dffe3fd47bafa0d8501028a7f4bbc51161f02d6b24243 SHA512 8929ee9e2eff5636e4d40ec5d1860d866e90c17cc23f4e75f44fd829409591b869cd5feb13a6c02bb5d80a9a7ed55c06f7be45f61268a768ddfdafe84188237c +AUX embassy-structure-0.1.650_fix-build-system.patch 2775 BLAKE2B 2ef40db164efb8fa5dc3bbe06f5edbd7b2dcc9249e5a58ad3ec21feca8fcabbc78e317a1ea9a7939a4947088abe315c1cc6714fda0c20449a4cd527c1c112cff SHA512 19f51e9f1bc69f0807ee7f3d6bf8d2d21563c0a21eb08bee38cc0d9e68fb0cc1b8035402933cb8e5c12626d5b6a0b7e470518c503eaa5b1d34cc7548bccd6b21 DIST embassy-structure-0.1.660.tar.gz 588118 BLAKE2B 2723eebc309c81cc94fea687819de2c76d30ce87bb7c6dac12e9964c73fd18b497a31db07d12803d87799e42063b73d406520434482bcdb29f23a14756d11750 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 -EBUILD embassy-structure-0.1.660.ebuild 337 BLAKE2B f20f50b58478ea73245f73816d3ea85d5d7bf19224aabed1ac14bc433017e9a37416a7f23b5915f00d80f9d9c82a19555504c9f47febc1a6979c6325ea64562d SHA512 13a68a4590058e36d0ee5e016bfdae8e2115aefdec8d50ff988b0841f6bc1cc210c090da97811c4aaf654e132f32b28bdca559dcf157d7a3a0a66a2dfc946c3d +EBUILD embassy-structure-0.1.660.ebuild 334 BLAKE2B 53e652e9d8c396dc29f76a4142c64488918d01b73d94af8d06356440d1b1e99641941c7d6771b1d53f42448802f56592ad20f0ce8d50be32c1feafdbae1cb31f SHA512 9001c1dd9cc59c5d266b7945153b9cb0092a30654ca42d32e7ba0712231d44fa96c1d74f639f61c360a2576d224fc601ab4714c665d860f4c053b6a2dc36a978 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild index eaf74b5ea841..1c5bb1e9a967 100644 --- a/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild +++ b/sci-biology/embassy-structure/embassy-structure-0.1.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Protein structure add-on package" diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch index bdd9e37714e4..a67bc80f2a23 100644 --- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 6 ++---- - 2 files changed, 9 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index ee482ef..e4af4b1 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -40,7 +34,7 @@ index ee482ef..e4af4b1 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -62,7 +56,7 @@ index ee482ef..e4af4b1 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,9 @@ index ee482ef..e4af4b1 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 81ade5d..2ed0d14 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,10 +83,21 @@ index 81ade5d..2ed0d14 100644 endif if ISSHARED -@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -65,6 +63,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest index 97983069ff2e..e1c6e4c988fd 100644 --- a/sci-biology/embassy-topo/Manifest +++ b/sci-biology/embassy-topo/Manifest @@ -1,4 +1,4 @@ -AUX embassy-topo-2.0.650_fix-build-system.patch 3167 BLAKE2B 84dc4a55e13387263400d03904c14069baf93746ce32878349cbaab3c1d39aad30c448b8bf01fb2cec0a057403a8c8d7befd3869c5c28299e6001f25738a16c6 SHA512 bacff621e9d80d39a4e415736e1524cf69dd86b0253f65fb52ad2dda200cafe8e14af296897c3f695bbe360f2a56862a40dec6b8b0d0e597310f065e191ae770 +AUX embassy-topo-2.0.650_fix-build-system.patch 2944 BLAKE2B c9535f630899346a43a993c3563e202792610c751940a2aed3d41fc633fcffb53c372c702c19104fd709dda6b6093c4897d19336028312757135ccacec3cd8af SHA512 981326c4b27a0db091494da5a2d6215dbdac31544b33601765329c7b4e817ccdcc39e795cdc14719211a8726cb7761d070e83e234e878ac7f82bd226851ad1be DIST embassy-topo-2.0.660.tar.gz 443510 BLAKE2B ba49debdfb9f13051bd32d0d14de3b446a8fde83923e6927df52fd989460c60b5d3023aeaa84d3ab920533c40607f7ba274f64827cefa611a1513f203e08316c SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 -EBUILD embassy-topo-2.0.660.ebuild 342 BLAKE2B 268ee1b91524560d28c58cfacfae4f249fdb9efc3b34aae381e6779005fc7a7022b56c74f61e8cd541dbb9bd112cbb7a9c0a569272e0962252104eba435615be SHA512 c2a0822f7d20ae5c2bb78aa2f3705517fa7371b154a16395d7b13b5835980a11dce9364cb6d0a90f47a39cc729692b4567ceb5085022b3c0ed41535a3a8ab067 +EBUILD embassy-topo-2.0.660.ebuild 339 BLAKE2B 97a0643d61e7dd61025ee0ea1b2b0429bc843737dbed7e53ac955c60c2540a0372b1ad15f8a00d884943e7b791c4e98eb5c04a4fcb1992f031c9a40d1011860c SHA512 50f5b9a761e053206a6a3d1021e5cdbf9f1d557c300185e3d42353f593c2e653263f4a640c536fee938c74ac4924ef54eae9a9df233b32900f544f3512ce46e5 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild index 009adfe73914..3c16f7bf4fa4 100644 --- a/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild +++ b/sci-biology/embassy-topo/embassy-topo-2.0.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Transmembrane protein display" diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch index 3c37879de8c8..600e38928aff 100644 --- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -1,13 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - emboss_acd/Makefile.am | 2 +- - src/Makefile.am | 6 ++---- - 3 files changed, 10 insertions(+), 47 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 8eeb8ca..4fd28ac 100644 --- a/configure.ac +++ b/configure.ac -@@ -635,33 +635,6 @@ AS_CASE([${host_os}], +@@ -635,33 +635,6 @@ @@ -41,7 +34,7 @@ index 8eeb8ca..4fd28ac 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL +@@ -737,21 +710,6 @@ @@ -63,7 +56,7 @@ index 8eeb8ca..4fd28ac 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -874,6 +832,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -77,8 +70,6 @@ index 8eeb8ca..4fd28ac 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am -index e1c1878..e253c95 100644 --- a/emboss_acd/Makefile.am +++ b/emboss_acd/Makefile.am @@ -1,3 +1,3 @@ @@ -86,11 +77,9 @@ index e1c1878..e253c95 100644 -pkgdata_DATA = *.acd +pkgdata_DATA = $(srcdir)/*.acd pkgdatadir=$(prefix)/share/EMBOSS/acd -diff --git a/src/Makefile.am b/src/Makefile.am -index 1cdb0b1..0e86a4b 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ +@@ -17,9 +17,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -101,10 +90,21 @@ index 1cdb0b1..0e86a4b 100644 endif if ISSHARED -@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ +@@ -34,7 +32,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -59,6 +57,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +-LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ - -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ + -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index 6218b012ba4a..dcf9c44204c2 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -1,4 +1,4 @@ -AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3083 BLAKE2B 294e9896615c7d01a804097249673f86d8bf6bf6757763bdbd2cecf9e328a2b324b6918818f8e33917c2000d5a2dad5a66aa6c0e764619d35048d3c5ca032351 SHA512 b09ea9adcc9da002a83e431ff4f3f48075bd885bd35b5690a21ed7d120835a5fa9eaf566fecfd916897e18d539ccc7ea1c8640759996e4979865556eaf8dccb2 +AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3349 BLAKE2B c6d12bee84b5bc5bb987929a1d606c28cab1d5bb318fdf294f01569d90ae4736c818ddf3d5d2fd506fe3d012c35d320c74c0b3185540e19a03b0e7dbcac9e0d6 SHA512 4da6e09711974bf10259558f78208d207f3e07b0156488acfce788d83f05a6872246d6acf3c318195285e1d84b3788aec65d82f989c682b56129c4dfb6df8eae DIST embassy-vienna-1.7.2.660.tar.gz 873165 BLAKE2B 46e976e52ad65490237563af09e483c212a6170c8c79fac8a2f2609040ee6a4cf60c04b00159c4c33d8c2a10f6e457e412287409fc0ea5724c5687dbd65ff06c SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 -EBUILD embassy-vienna-1.7.2.660.ebuild 436 BLAKE2B e61cd8a676a547d75b80035ffaf6e54d8d02e9ae81713f0baf010394231c2e963b2d61926923f7873d7edb726343088b288b9562df4d8957cf18257f20281ae0 SHA512 009ad16069bd0a8134a705a82a2d1ee5a3b5de28d434870e9b7298e64885a8c76f1c604432b2d0808d6f4653906e211b6c848496bbefd0c4324d698fb8285ec3 +EBUILD embassy-vienna-1.7.2.660.ebuild 433 BLAKE2B 2feaec37d75ccd9bb4798f56ed58a06944e06488d4ce8bb2ba924dda2cbce5abf54e6ef1e15cca61620db06b51132143cc001e0ef84f5eeeb4f3e7b95bc23bfc SHA512 0481fac0f109b153119e6e12907cea9083a52b3a85e1c26985b14e45cf9a68e36b188bc16c10f528eb19df73fad511afc13742eaa8cd653e5fdd6559497c7184 MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild index d82532a4f623..6d63add1eea0 100644 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 EBO_DESCRIPTION="Vienna RNA package - RNA folding" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch index 5ce365ed5497..8bd816b0e672 100644 --- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -1,12 +1,6 @@ - configure.ac | 49 +++++++------------------------------------------ - src/Makefile.am | 7 +++---- - 2 files changed, 10 insertions(+), 46 deletions(-) - -diff --git a/configure.ac b/configure.ac -index f5a4ecf..bbe0743 100644 --- a/configure.ac +++ b/configure.ac -@@ -649,33 +649,6 @@ AS_CASE([${host_os}], +@@ -649,33 +649,6 @@ @@ -40,7 +34,7 @@ index f5a4ecf..bbe0743 100644 dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], -@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL +@@ -751,21 +724,6 @@ @@ -62,7 +56,7 @@ index f5a4ecf..bbe0743 100644 dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" -@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs], +@@ -888,6 +846,13 @@ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) @@ -76,11 +70,18 @@ index f5a4ecf..bbe0743 100644 # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -diff --git a/src/Makefile.am b/src/Makefile.am -index 1f5b756..e178914 100644 --- a/src/Makefile.am +++ b/src/Makefile.am -@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \ +@@ -10,7 +10,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leplplot -leexpat \ + -lezlib -lepcre + else +-CYGWIN_LDVIENNA = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl \ ++CYGWIN_LDVIENNA = -lnucleus -lacd -lajaxdb -lensembl \ + -lajaxg -lajax -leplplot -leexpat -lezlib -lepcre + endif + endif +@@ -32,9 +32,7 @@ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else @@ -91,7 +92,16 @@ index 1f5b756..e178914 100644 endif if ISSHARED -@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF) +@@ -49,7 +47,7 @@ + -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre \ + $(NLAIXLIBS) -leplplot + else +-AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ ++AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \ + -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre $(NLAIXLIBS) -leplplot + endif + endif +@@ -87,6 +85,7 @@ endif liboviennarna_la_LDFLAGS = $(LINKFLAGS) @@ -99,10 +109,12 @@ index 1f5b756..e178914 100644 ovrnaalifold_SOURCES = vrnaalifold.c ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c -@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \ +@@ -118,6 +117,6 @@ + ../../../plplot/libeplplot.la \ $(XLIB) else - LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +-LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ - -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++LDADD = liboviennarna.la -lnucleus -lacd -lajaxdb \ + -lensembl -lajaxg -lajax $(NLADD) $(XLIB) endif diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest index 74b2ae8850e5..cf88825b18da 100644 --- a/sci-biology/libgtextutils/Manifest +++ b/sci-biology/libgtextutils/Manifest @@ -2,4 +2,4 @@ AUX libgtextutils-0.6.1-fix-build-system.patch 1719 BLAKE2B 993f1e68f960853a264d AUX libgtextutils-0.6.1-gcc6.patch 724 BLAKE2B 14ebd0ab5ec4685688caa922dacccdaad9101af0814a93b08f0c9ba5e50ac6a02291528b6ad3d61b48a2f29a25b63e421690f19109351f4472cc118886ca0e10 SHA512 74ec8fafc699cadc5d40f5284cd42cfb8c949744b7a16bbf8142c8db71ad6c921551da03f260e82bfe84b69dd5fbd2261031fe22aee6b3396515b1f66576a530 DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6 EBUILD libgtextutils-0.6.1.ebuild 623 BLAKE2B 5bd2ff34a6898b662e6e624a77682a358b9340c6b94b9dfa40bec0637d4074ec648ca6146ee870f9cf5a8141028d23aedc55407aea04fbf2b69d62699d69d547 SHA512 e72eaddb48422afe71140394825964e6778a339ea182d614178061eb294dada1b81e7b5221a1a19d9d2ac720200f6eb4a7eab09f6ef1b7425ce7dda491add449 -MISC metadata.xml 370 BLAKE2B 01c5f6253c80b7fc48e8c7980c62366fd38643da25fdd999cef041558b7d559cb45a22a6125d222569104443c75045e6169f133bc46871ab9f567bdf3f3ae3dc SHA512 b9a044abc657680f9c8fdc80d318b5a9891c5c532eb0831f00bf2f774391c885cf568f6ec3376617da2a5d4d8f9b87283384d595086b3ae57defbc988e96f1c1 +MISC metadata.xml 384 BLAKE2B 5d5964f09ec6c5b7d0e7abba76515794489f29f72f1b0af6783662581a39a8d125f58d4a0138baeeeb503a828ccd4e847ee910b8f455a68ecb6914beb0800e73 SHA512 53a49cfa6f7909adb815de8c83b06caf5cae5b53adc3d7fbcb12b48e02970e00ab34255a5904f35f3f479a9dcc75505bfc7237d1076c3b52540c0802dc65a04a diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml index 38108be67e14..c8c5adb77c88 100644 --- a/sci-biology/libgtextutils/metadata.xml +++ b/sci-biology/libgtextutils/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> + <maintainer type="person" proxied="yes"> <email>mmokrejs@gmail.com</email> <name>Martin Mokrejs</name> </maintainer> diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml index 7a808874b6e6..fb82178e320b 100644 --- a/sci-biology/metadata.xml +++ b/sci-biology/metadata.xml @@ -43,4 +43,3 @@ Kategoria sci-biology zawiera programy naukowe związane z biologią. </longdescription> </catmetadata> - diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest index e70550f4ed6a..105d1d7245df 100644 --- a/sci-biology/mosaik/Manifest +++ b/sci-biology/mosaik/Manifest @@ -4,4 +4,4 @@ AUX mosaik-2.2.30-gcc7.patch 1252 BLAKE2B 896d662807c223cc69eacfa2e1fcb457c696e0 AUX mosaik-2.2.30-remove-platform-code.patch 399 BLAKE2B ec711a9b112efa87b2811e4545bfc58716393576915f71167ff700ccd809be4fad5e07bac7a5cb7df911615f4c996284cd711c1d1cb62c5a18695e719e6574c6 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259 DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10 EBUILD mosaik-2.2.30.ebuild 1105 BLAKE2B 842b161c8fc0cda9cab8101ca6ae0879cedb191983a61a25d21afe0ef5edb4a87e7e62edad27f2642444c2dc58387328c275f7830abd7917146d6febee812ba5 SHA512 55377965262d7942229a269bc1c0c56ff930d544b422305994f0995ca68d06ea3a1745fb759dc70225ff6b76d338b8761236079eb7107edb6225ae7c6d2f372e -MISC metadata.xml 414 BLAKE2B 3c19ab9f4c6a0f4e73d67fe4f280fd252d68120a28e045a39c3ad78a4741921b2141c4433c6babcdc33b16083d4949fc28448f57fcb6c65be8719dd1d0bff8f3 SHA512 2e6887226a0ac7457d1bbce1d76ac0953f0c1d5ff1d4261b7e11e4fa38803f01f8a67a285c2071671d58fcb8912ca8bb66bdfca93e2481be043ec5f2f2353c5b +MISC metadata.xml 414 BLAKE2B dadc852f08ed1944b4433e741d8f3c9f9296ecae8772df46193a89591fba8f3346b5b10d1a7227ba78071cc6e3639544a9f23ee61f79ee595bd10155bf6dfd0d SHA512 b38d4852ceabaa543c162eb26a54a76ba83b9d8f2e1520ec0ef16a07f49ddce9835caa5e16883f9755c99e3dba75e9ab689d254bafef92a859d251a53ff0d42f diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml index a3eca9b62b1c..f513c94ff2f3 100644 --- a/sci-biology/mosaik/metadata.xml +++ b/sci-biology/mosaik/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest index b321e00e6280..18d201537410 100644 --- a/sci-biology/prodigal/Manifest +++ b/sci-biology/prodigal/Manifest @@ -1,4 +1,4 @@ AUX prodigal-2.6.3-fix-build-system.patch 1004 BLAKE2B 5a0323f6f4440e5f45805e8eabc32374f7d47760fa62c426a776a6f5bb573f356241618fbb231522c05ad950b3de71f38787bf848049f4c6fa174726c9134ee8 SHA512 c96e93cbe344bbab43b03b0046b1bca5030f4a731a0b43ea4d4ee87d303502d172fc93975a9d7b907d6ea6beeb865113122e0e2cbca7d660290994bb8214a17b DIST prodigal-2.6.3.tar.gz 610934 BLAKE2B 54a75a694aec216da411717c29c8e896f064b4893d74fa1c736fdea3cd7bff98cb8d597cdbb96dd4cb2f0e82972c99b43eee8f2ddd8678535dc68c831dfd4e08 SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 EBUILD prodigal-2.6.3.ebuild 518 BLAKE2B 80e85e8507eed4b64fecf813c54f2fac707cb8aec21182f40ffebbe83ab867eab3243af5618eeb01fbcf1ac33ff06f3bc060ec78f245da1afa30475b2d4220d8 SHA512 44048cc1a61e2e7decd5b4dda026e4b89ba54decfb1f63ad3d378c3b8ebef707b3e3c2338108186be9a3f9400bca165f3331a1f1dd668345716b15c01189a0e1 -MISC metadata.xml 395 BLAKE2B 1586c9df280da87649ae6b23e4eff71be6db8d61a75a486009dc43ed51f5d3474760563d873f3acbe5fbf349744e6af333caf9575616f7c9af63b3f5b49d7132 SHA512 d824206729a7012b67bc0dff475f08d769484c601165a72c159383cc23247726cc38d9dae85492f39cdae99dc83c2a4adbb44cc8abded5ee8cad8067bec7873a +MISC metadata.xml 395 BLAKE2B 86e625480833e553198146ea3e8a8d6e347c5a307798c5e8cf1918a85f3a6ce1761535287d586ef6d0f0de08f13897af30c7eafa62e5fc395075f43cc0412f48 SHA512 baa75d5c2b96f8bc653af2691f518533ae87bc13179e0d3751cc120e2933eb758ed08f68163d6fa0a312ebc9e017163ed7f95b2ad3135464d87ac58c410a2203 diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml index e086d08df6f7..ce618df82fe3 100644 --- a/sci-biology/prodigal/metadata.xml +++ b/sci-biology/prodigal/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 0c9eb58c3dc7..d244f445e4e2 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -3,4 +3,4 @@ DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e DIST samtools-1.10.tar.bz2 4721173 BLAKE2B 103c71ec5740eac151a4fc40d67286ee00123c7befd5f654cf5c89812bda44f82b38ab662a4a3216ac84434cabab49500b903612137f97f89a7ea38063e8fc08 SHA512 828ec2638592b440e06b81eafc57634416ab54dac6caaecb06f22a90e9bf99da1fd8bb54509cb98591899c4e097ac9038ee5d57ea7bfe1a18967cde4018d840a EBUILD samtools-0.1.20-r4.ebuild 2040 BLAKE2B d90fc78a99b4134ba1a277ceb904c65592f1d29222822f5c97e31a46cbc4138af6adc763c7b05cf26bc0de06ac23ca0b8d8891841ecfd6c1b3fafd270e24216d SHA512 855e19ca8d0dcb9d472398895c666324d00355a7b04c075744e7ac58be1d183f7739f9a254c5bbdaf4171ab6324159860be40171693d0f2f5074884b9eba5e87 EBUILD samtools-1.10.ebuild 991 BLAKE2B 206a77657bc9a82d6a7536d030b726a0450bbba406e4e7ec9cc670ee530b87d871111952c850d4008c436f81d3daeba802eb4a3442b59ff9ab0f5864bc4fcf21 SHA512 efb1f235e3e3996599df79317e9c7c2ca5434b666a93f91c495550ac4846905e99d96dd1a6876d22a489b684bf24a90c6f6afb4cec5677c5c45f28f0c4f35b35 -MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb +MISC metadata.xml 408 BLAKE2B fcff66a327d0396cd0a1b0cb5c00aeb1bc728759d6d39933651f63e22d966af9c33d14f149d2ee008ca48266da1f24ff5919942d143d066898dc635673153df9 SHA512 71a9d6a299db7717ccd851a4519354c1fd7a373dd79af6fa216ebc9b6b0ccbbccc4394ca00c3f842afee492702f079268c5c83815eaaafa446bf0f37750c62ff diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index fe27db1184af..6f516e1d05ac 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index 3b3127ff44d4..14c868e8fd07 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1,4 +1,4 @@ AUX vcftools-0.1.14-buildsystem.patch 1159 BLAKE2B 9eaa626c82b4d23e75f2d31ce31c6161996eb743efbdcb81ad4c3ba306b76a710c4b22670d68178da1b7d2e048d02aea44132f3009d5792dcf248368b53c3482 SHA512 838cade29bbeeee090ea52f546c37b68eee868f3329ceccb710da0dbcf0f14e1b18dcc7b05ceefdbf72d400f450374389649f56fc6981bd86f6e176469b054ea DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B 14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 EBUILD vcftools-0.1.14.ebuild 867 BLAKE2B f25ccc182927cd888c548f4eeb120c526716fc759dc7b8081baf76b9f4cd3a404a2828168577000ff816b02aa8d3e6fec52d883fdc2e6f2ec40f1a9712d024d1 SHA512 260555d8964cf329fe3710547b6ddb5600674525703d0b802d18c2a41d02271ff77c56c4d49bf9fb67966bce76a3d6addc88c5a1e86859425bf0574beecc2c34 -MISC metadata.xml 408 BLAKE2B bc88536408660b74dbe9183850f853f19d123852d6e56845e9d6c5249f5fcff58e205751f70e8b22c9032eaea5d4ea9fac371376ce7725da151aacb8d6c7d5ea SHA512 637b53b7fc140cfde69bd0e39ee1e942a86a3fb77934946e942e12ca65cf01a8c3559d606ab3131ffc762aa3508fb3ab60148b4aaee28b60bc6d97cb8dd00f3e +MISC metadata.xml 408 BLAKE2B 6761b0e43c90b406c9b1253e6f4757f2c1249a5a658eea3be97fbd24d6d1c591ab60abb5b0e3b58f17dbf68e1839b2a0ab12516f903e0d5966788ef6db570666 SHA512 c66cea65d0d2ae25a9861428387f3582dc490dabc6d5de2087f475e6fa0259c2167173c2d916a0293a35db64d46f9faa7f9f70d0a6c19efde2e98f5144e27007 diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml index 6c22d19200ae..95be401e9e2e 100644 --- a/sci-biology/vcftools/metadata.xml +++ b/sci-biology/vcftools/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> |