From 2719f73b6813d11d13a9650cdd2ab8ec6e69385d Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 9 Jul 2022 15:43:36 +0100 Subject: gentoo resync : 09.07.2022 --- sci-biology/exonerate/Manifest | 6 +-- sci-biology/exonerate/exonerate-2.2.0-r2.ebuild | 48 ---------------------- sci-biology/exonerate/exonerate-2.2.0-r3.ebuild | 45 ++++++++++++++++++++ .../exonerate/files/exonerate-2.2.0-asneeded.patch | 15 ------- .../files/exonerate-2.2.0-autotools.patch | 43 +++++++++++++++++++ sci-biology/exonerate/metadata.xml | 2 +- 6 files changed, 92 insertions(+), 67 deletions(-) delete mode 100644 sci-biology/exonerate/exonerate-2.2.0-r2.ebuild create mode 100644 sci-biology/exonerate/exonerate-2.2.0-r3.ebuild delete mode 100644 sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch create mode 100644 sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch (limited to 'sci-biology/exonerate') diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest index a265c7bd94a4..5474f7a87784 100644 --- a/sci-biology/exonerate/Manifest +++ b/sci-biology/exonerate/Manifest @@ -1,4 +1,4 @@ -AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0 +AUX exonerate-2.2.0-autotools.patch 1407 BLAKE2B b34e8c4d8301d4f416b44f4516154917943e17d30b548c7710e097706ce2c9123770d97d3ae962a268c6253a83ab60159f9285fadab1328be4ad5dc48249ee3f SHA512 f34c35228d23a8fd9402c514312c58bd877a7844487ade7f9f8d545d66c5d350f3f82f1aab1862a7b647b7f7aaaa0dbd8100d34bc0ef7d79969063c30a8558d0 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c -EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1 -MISC metadata.xml 327 BLAKE2B 6aaa3e563d3d8f980c3f42b7e5aa1f8cd5e67e5dcea0f467e6698731480ae7cb587b75516931c351f0e562ddebc4811f359f9ec9fb9c16cb93bc0842bd24d2d7 SHA512 82cd2f3b95540ef6132985b835bf482498f60495c7e4718aaae3bfb500a017bc367cd844992b6b3a3f68be276183f62c91ee517f6a72a19d058775f40a95eb0f +EBUILD exonerate-2.2.0-r3.ebuild 945 BLAKE2B 5df41a4c19730cb7b342dcae7875fba40b7c7404ceb85f4568f55f0eaf9d8446195e922c709ae09a62f4a5c0a35b581ef86f03c3a58ead41b0d70313ec7da76f SHA512 f928328f1cb14719343df4c4d7df4fc834b59a3909c6f47ca9d1358d4d2d1d6d31c404074e45e747b3e5736040897861c00bb9e0974582f3472639638cc4c80d +MISC metadata.xml 654 BLAKE2B c84cf7eb3eed086e51e990906b2ea2645160683ba9314d2d15790e03d077714c1592bd4f305a8f3ed9109e376292118b44a1d10ea9ad1118139874a4e451bf6b SHA512 820b824d3d2a05feee023573580135fa2895832dd1b602c35253c1b8ee46aafdd0e010b5e8a77ce1805058264e3110821d27533a1dfe9d30799a5e63ea1551f1 diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild deleted file mode 100644 index 53ae5a97c6ae..000000000000 --- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Generic tool for pairwise sequence comparison" -HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" -SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" -IUSE="test threads utils" -RESTRICT="!test? ( test )" -REQUIRED_USE="test? ( utils )" - -DEPEND="dev-libs/glib:2" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) - -src_prepare() { - default - sed \ - -e 's: -O3 -finline-functions::g' \ - -i configure.in || die - mv configure.{in,ac} || die - - eautoreconf -} - -src_configure() { - tc-export CC - - econf \ - --enable-glib2 \ - --enable-largefile \ - $(use_enable utils utilities) \ - $(use_enable threads pthreads) -} - -src_install() { - default - - doman doc/man/man1/*.1 -} diff --git a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild new file mode 100644 index 000000000000..73fa9eca83e5 --- /dev/null +++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools toolchain-funcs + +DESCRIPTION="Generic tool for pairwise sequence comparison" +HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" +SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" +IUSE="test utils" +REQUIRED_USE="test? ( utils )" +RESTRICT="!test? ( test )" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-autotools.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # the bootstrapping code loads AR and CC from the environment + tc-export CC RANLIB + export C4_AR="$(tc-getAR)" + + econf \ + --enable-glib2 \ + --enable-largefile \ + --enable-pthreads \ + $(use_enable utils utilities) +} + +src_install() { + default + + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch deleted file mode 100644 index 5c428979a1af..000000000000 --- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix build with --as-needed - -https://bugs.gentoo.org/268094 - ---- a/configure.in -+++ b/configure.in -@@ -289,7 +289,7 @@ - if test "$enable_pthreads" = yes; then - echo "Using PTHREADS" - CFLAGS="$CFLAGS -DUSE_PTHREADS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LIBS="$LIBS -lpthread" - elif test "$enable_pthreads" = no; then - echo "Not using pthreads" - else diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch new file mode 100644 index 000000000000..af95b5c8f77a --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch @@ -0,0 +1,43 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- a/configure.in ++++ b/configure.in +@@ -144,11 +145,6 @@ + elif test "$enable_assert" = no; then + CFLAGS="$CFLAGS -DG_DISABLE_ASSERT" + echo "Turning assertions off" +- if test "$GCC" = "yes"; then +- # Not currently using -fomit-frame-pointer as clashes with -pg +- # CFLAGS="$CFLAGS -O3 -fomit-frame-pointer -finline-functions" +- CFLAGS="$CFLAGS -O3 -finline-functions" +- fi + else + echo "error: must be yes or no: --enable-assert:[$enable_assert]" + exit 1 +@@ -289,7 +285,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else +--- a/src/model/bootstrapper.c ++++ b/src/model/bootstrapper.c +@@ -146,8 +146,12 @@ + + static void Bootstrapper_index_archive(Bootstrapper *bs){ + register gchar *command; ++ register gchar *ranlib = "ranlib"; ++ register gchar *tmp = (gchar*)g_getenv("RANLIB"); ++ if(tmp) ++ ranlib = tmp; + register gint ret_val; +- command = g_strdup_printf("ranlib %s", bs->archive_path); ++ command = g_strdup_printf("%s %s", ranlib, bs->archive_path); + g_message("Indexing archive [%s]", bs->archive_path); + g_print("%s\n", command); + ret_val = system(command); diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index 110611751dc3..421b8ef55beb 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -6,6 +6,6 @@ Gentoo Biology Project - Install all utilities + Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds -- cgit v1.2.3