From 2cd907d16458ba3a99ec82155d7268e2d991a078 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Thu, 7 Sep 2023 16:28:34 +0100 Subject: gentoo auto-resync : 07:09:2023 - 16:28:34 --- sci-biology/Manifest.gz | Bin 19483 -> 19478 bytes sci-biology/elph/Manifest | 3 +- sci-biology/elph/elph-1.0.1-r2.ebuild | 29 ------ sci-biology/elph/elph-1.0.1-r3.ebuild | 32 +++++++ .../files/elph-1.0.1-drop-register-keyword.patch | 102 +++++++++++++++++++++ 5 files changed, 136 insertions(+), 30 deletions(-) delete mode 100644 sci-biology/elph/elph-1.0.1-r2.ebuild create mode 100644 sci-biology/elph/elph-1.0.1-r3.ebuild create mode 100644 sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 57b0615153e5..ec29c72c51eb 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest index 0cd0952651bd..bbcc457d1960 100644 --- a/sci-biology/elph/Manifest +++ b/sci-biology/elph/Manifest @@ -1,4 +1,5 @@ +AUX elph-1.0.1-drop-register-keyword.patch 2987 BLAKE2B e88400d819ec011e521c4a96ba99926c08ba72b23f7491caa4a5e15e0d338931a631664ce228ae7fa431ae707bd944f36e7619b35d6fbd544e44825ca75b87f1 SHA512 dec8efb7a0293db4bc7888e7a849df235a7e3f945445fd81f590448b7094d0a80548bb557c25a27d67bda2cbaaa8176c5d3a70998d1fb3f104ba838ca89dfdcf AUX elph-1.0.1-fix-build-system.patch 1303 BLAKE2B 66103bd295fddd45f90734a49a8b673efcd91234abb4355408bca284d1d498bb98a9392b8467117e4ae034780579573a2cf26c78bef245cea8d0dac01c759322 SHA512 d39611f80cd2e67e94f3d1dd7eb1dfe59ac3b221956ab72f3951b5716825387e7d3ed04608e75abfc43ae2cbc53ace474e602ddbd93441c2da74f04516ba2ba5 DIST ELPH-1.0.1.tar.gz 113476 BLAKE2B 7c34e9f847560bf46d1bc6bbb720a0cd0afd91b29c23dac98056d2b9eea39146dda72468cad96892eb551cdfb03b224ea22b8e4cee40f19774e24fa843f55192 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 -EBUILD elph-1.0.1-r2.ebuild 648 BLAKE2B 9d7f03f660318cb8c774cd6cb40dafc747319f6fbed2816b800e1c26f6d7cfb020e1e10daa57debd12adc6ad9a69c1988ceaee2a718785222a1794fb988a8a31 SHA512 f29f0e8ee451d4c0781c4d745c5d2e930b27a8bf520d169e1c0090ca983745475deaded45af8360cb198d257aae025723cadcc112cf560eac880d486eb528358 +EBUILD elph-1.0.1-r3.ebuild 704 BLAKE2B d7a519618d41ba72db9304a7c67d344920d601216499d8f25655dfbe822433510b51a5f5e3f673c64de6bf1f12d8e6682e5e90d675ef37bd58298592d8f034a9 SHA512 89882f5019e0aeec229d686164db7f9dd75551cbe81b1948ed5334770fe8ee6abc003d7fbd26313fa3e1d2fed44999e2d0f6bb3f507ba2226293796314d895b9 MISC metadata.xml 618 BLAKE2B 4c12f3466489b131857dca3df864faa163d047d038aee453a02a4ab436c742e6df4f93b437643f6b4f449fcbc657dfd0d8a12b3e7ec7f90faa50ffd745dfe7bb SHA512 a19d27931ae95a971d786ff739807ce36f40a05122b1cd454f46a75f3a506b17206bf90516f9eda3aef4c1820026413aef88c3fa9bfc15516ec9c859c8b6bce7 diff --git a/sci-biology/elph/elph-1.0.1-r2.ebuild b/sci-biology/elph/elph-1.0.1-r2.ebuild deleted file mode 100644 index 66309522b312..000000000000 --- a/sci-biology/elph/elph-1.0.1-r2.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" -HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" -S="${WORKDIR}/${PN^^}/sources" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -PATCHES=( "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch ) - -src_configure() { - tc-export CC CXX -} - -src_install() { - dobin elph - - cd "${WORKDIR}"/ELPH || die - dodoc VERSION - newdoc Readme.ELPH README -} diff --git a/sci-biology/elph/elph-1.0.1-r3.ebuild b/sci-biology/elph/elph-1.0.1-r3.ebuild new file mode 100644 index 000000000000..6cfc05845358 --- /dev/null +++ b/sci-biology/elph/elph-1.0.1-r3.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" +S="${WORKDIR}/${PN^^}/sources" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( + "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0.1-drop-register-keyword.patch +) + +src_configure() { + tc-export CC CXX +} + +src_install() { + dobin elph + + cd "${WORKDIR}"/ELPH || die + dodoc VERSION + newdoc Readme.ELPH README +} diff --git a/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch new file mode 100644 index 000000000000..c05a280d4679 --- /dev/null +++ b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch @@ -0,0 +1,102 @@ +Bug: https://bugs.gentoo.org/898116 + +--- a/GBase.cpp ++++ b/GBase.cpp +@@ -208,8 +208,8 @@ char* rstrstr(char* rstart, char *lend, char* substr) { /*like strstr, but star + + //hash function used for strings in GHash + int strhash(const char* str){ +- register int h=0; +- register int g; ++ int h=0; ++ int g; + while (*str) { + h=(h<<4)+*str++; + g=h&0xF0000000; +--- a/GString.cpp ++++ b/GString.cpp +@@ -364,8 +364,8 @@ GString& GString::appendfmt(const char *fmt,...) { + } + + GString& GString::trim(char c) { +- register int istart; +- register int iend; ++ int istart; ++ int iend; + for (istart=0; istart=0 && chars()[iend]==c;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -423,7 +423,7 @@ GString& GString::trimR(char c) { + } + + GString& GString::trimR(char* c) { +- register int iend; ++ int iend; + for (iend=length()-1; iend>=0 && strchr(c,chars()[iend])!=NULL;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -440,7 +440,7 @@ GString& GString::trimR(char* c) { + } + + GString& GString::trimL(char c) { +- register int istart; ++ int istart; + for (istart=0; istart