diff options
Diffstat (limited to 'sci-biology/bfast')
| -rw-r--r-- | sci-biology/bfast/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/bfast/bfast-0.7.0a.ebuild | 39 | ||||
| -rw-r--r-- | sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch | 74 | ||||
| -rw-r--r-- | sci-biology/bfast/files/bfast-0.7.0a-autotools.patch | 41 | ||||
| -rw-r--r-- | sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch | 79 |
5 files changed, 211 insertions, 27 deletions
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."; + |