From 95f4ecedd41206e678e2ddec24f8382ba2287dd1 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 31 Mar 2024 02:13:53 +0100 Subject: gentoo auto-resync : 31:03:2024 - 02:13:53 --- sci-biology/Manifest.gz | Bin 19177 -> 19181 bytes sci-biology/emboss/Manifest | 2 +- sci-biology/emboss/emboss-6.6.0-r2.ebuild | 71 ---------------------------- sci-biology/emboss/emboss-6.6.0-r3.ebuild | 74 ++++++++++++++++++++++++++++++ 4 files changed, 75 insertions(+), 72 deletions(-) delete mode 100644 sci-biology/emboss/emboss-6.6.0-r2.ebuild create mode 100644 sci-biology/emboss/emboss-6.6.0-r3.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 7cbee1615b6a..0038f5895b89 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index 0ea050322bf5..091bc88d9ab8 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,5 +1,5 @@ AUX README.gentoo 1522 BLAKE2B 566213e78e6c74fc6c8745391fbdbc477c9d1793f74e68fb0465ba4f842203e1670dd6216c4181326a4ccbf0c051daa99a376a15dd5b0714473f84ed8404e8f7 SHA512 a5441a056ebb11d24b83b8bfb9182f0753b85ec5ba126a123eb97c55fc665dadff2cc5f16c8e4314535f1b6a206c200324c0c5d5db6af109c841ee68ac76bb07 DIST EMBOSS-6.6.0.tar.gz 117962028 BLAKE2B 91bf3c680290bd975d2ddb5251089d7f75f8a44a26e1247e93d2c9cf2f23e6b89c4218022ba1af0c940136ff56782f40d2c4604dc756b400ae23f223da7f3cca SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a DIST emboss-6.6.0-patches-r1.tar.xz 5384 BLAKE2B 7899141862880d000e1624e9df914b1918cd02645c0d14128bcffd41d76e3669404a718f25471795268e4a00d610377186b7cb73a126e30f74df80d04d22faf9 SHA512 95825a3bcaa6340d26fde65f3b77574e42fd424440ee48f2fad94b6e696346fe4f6e4ab48c7dcfe1e9c3311a8a7750defc004c2db40cc36f42e980a19e6bd0bd -EBUILD emboss-6.6.0-r2.ebuild 1856 BLAKE2B 47210e9b1e240a470048887a52a058309385afca0cdefce8142147b467d216450e81a63346ef1e70bdcdbc8169b1811540f6b8cf562b2946c74e9a295a60cf25 SHA512 0e3efcf08ffe7cbddbe9aa0e5375a4396e36022e7e363d522d44d897cba2436f969615d5a5cd06e99acc61e3997f69ae23de79663903c3370cbf50eb96b2954c +EBUILD emboss-6.6.0-r3.ebuild 1966 BLAKE2B f00944b87edd2a37b5637ffc34eeff3358b7a10ad860d4e2fd33ebf8b98a7a52a3f1fd4226955fd763d076a8277ab288290cf02d6adfa2b3147fab38fdafeb30 SHA512 106fe0447e4a535fec618eb94758d0c3dbeb232685943e29a2bdc44f352fd68ea5c11cd59a6e57e47924a404363881d3e057b2a2eb314e3c6cc36dd2ca6420b8 MISC metadata.xml 1097 BLAKE2B 76363bb35212d819328fc6ef0fe303ed3819ebd3c1742039af2863ffc1fd4c7c5cff20b6451aa92b8718487ec1a7d2a2fff8236088b8bd945b1c439a4de09115 SHA512 4b1afa15e346442138361754f9ec176a36194c6b77d002f26cadf16f1ba0f57219274144e41125ef37668f5d9e892ae370cc98e6b6ee0ded83a233ace417a0ee diff --git a/sci-biology/emboss/emboss-6.6.0-r2.ebuild b/sci-biology/emboss/emboss-6.6.0-r2.ebuild deleted file mode 100644 index 79d3034a0985..000000000000 --- a/sci-biology/emboss/emboss-6.6.0-r2.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit autotools emboss-r3 readme.gentoo-r1 - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI=" - ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz - https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz" -S="${WORKDIR}/${P^^}" - -LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="minimal" - -RDEPEND=" - !dev-build/cons - !games-action/xbomber -" -PDEPEND=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/primer3 - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - )" - -PATCHES=( - "${WORKDIR}"/patches/${P}-fix-build-system.patch - "${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch - "${WORKDIR}"/patches/${P}-plplot-declarations.patch - "${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch - "${WORKDIR}"/patches/${P}-C99-bool.patch - "${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch -) - -src_prepare() { - default - eautoreconf -} - -src_install() { - emboss-r3_src_install - - readme.gentoo_create_doc - - # Install env file for setting libplplot and acd files path. - newenvd - 22emboss <<- EOF - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" - EOF - - # Remove useless dummy files - find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \ - || die "Failed to remove dummy files" - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \ - || die "Failed to move CODON directory" -} - -pkg_postinst() { - readme.gentoo_print_elog -} diff --git a/sci-biology/emboss/emboss-6.6.0-r3.ebuild b/sci-biology/emboss/emboss-6.6.0-r3.ebuild new file mode 100644 index 000000000000..5a43c0ff89ef --- /dev/null +++ b/sci-biology/emboss/emboss-6.6.0-r3.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools emboss-r3 readme.gentoo-r1 + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI=" + ftp://emboss.open-bio.org/pub/${PN^^}/${P^^}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${P}-patches-r1.tar.xz" +S="${WORKDIR}/${P^^}" + +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="minimal" + +RDEPEND=" + !dev-build/cons + !games-action/xbomber +" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/primer3 + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + )" + +PATCHES=( + "${WORKDIR}"/patches/${P}-fix-build-system.patch + "${WORKDIR}"/patches/${P}-FORTIFY_SOURCE-fix.patch + "${WORKDIR}"/patches/${P}-plplot-declarations.patch + "${WORKDIR}"/patches/${P}-qa-implicit-declarations.patch + "${WORKDIR}"/patches/${P}-C99-bool.patch + "${WORKDIR}"/patches/${P}-Wimplicit-function-declaration.patch +) + +src_prepare() { + default + eautoreconf +} + +src_install() { + emboss-r3_src_install + + readme.gentoo_create_doc + + # Install env file for setting libplplot and acd files path. + newenvd - 22emboss <<- EOF + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + + # Remove useless dummy files + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete \ + || die "Failed to remove dummy files" + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} \ + || die "Failed to move CODON directory" + + # collision with dev-texlive/texlive-latexextra, bug #927976 + mv "${ED}"/usr/bin/{,emboss-}wordcount || die +} + +pkg_postinst() { + readme.gentoo_print_elog +} -- cgit v1.2.3