commit: 7a172acb8e93cf85a11ddd1fdc4170ce9b5ba785 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Wed Mar 8 21:35:39 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Wed Mar 8 22:16:09 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7a172acb
sci-biology/elph: Remove old Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165 sci-biology/elph/Manifest | 1 - sci-biology/elph/elph-0.1.5.ebuild | 36 ------- sci-biology/elph/elph-1.0.1.ebuild | 27 ------ sci-biology/elph/files/elph-0.1.5-usage.patch | 133 -------------------------- 4 files changed, 197 deletions(-) diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest index d5427f694db..a97d2ec7392 100644 --- a/sci-biology/elph/Manifest +++ b/sci-biology/elph/Manifest @@ -1,2 +1 @@ -DIST ELPH-0.1.5.tar.gz 153150 SHA256 6ffa160f85cb2569bdf869cb0514dc624afcef4f2d8a36efbd1228d1a16cf361 SHA512 6a413d1141d8bbe88de8db64657beaf557331c11aa91add7316d301bfd71d8febf8a27aca6e56ed16e94c3d02f4932d7bc367819fceca387925d6ef6591b7a3f WHIRLPOOL d87835f180d33377dad7a23dc3fe5b78777baea1baeda588c897c6250b3eec9f68f66ee9951164764f6826b606f3081e060a10db2667b13e5580c5df355c1ad0 DIST ELPH-1.0.1.tar.gz 113476 SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 WHIRLPOOL 598dc3f95c93e5e36bcd20de3c985c22d650462ab27df31af54ca5b5b50c0a60fcc47637a41c449bdf7e572cee097289916aca4f0de79b804854d233ff3e20ff diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild deleted file mode 100644 index d2d085d4c03..00000000000 --- a/sci-biology/elph/elph-0.1.5.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit eutils toolchain-funcs - -DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" -LICENSE="Artistic" -HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"; -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"; - -SLOT="0" -IUSE="" -KEYWORDS="x86" - -S="${WORKDIR}/ELPH/sources" - -src_unpack() { - unpack ${A} - cd "${S}" - epatch "${FILESDIR}"/${P}-usage.patch - sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" \ - -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" \ - -e "s/LINKER := g++/LINKER := $(tc-getCXX)/" \ - Makefile || die "Failed to patch Makefile." -} - -src_compile() { - make || die "Compilation failed." -} - -src_install() { - dobin elph || die "Failed to install program." - cd "${WORKDIR}"/ELPH - dodoc VERSION || die "Documentation installation failed." - newdoc Readme.ELPH README || die "Readme installation failed." -} diff --git a/sci-biology/elph/elph-1.0.1.ebuild b/sci-biology/elph/elph-1.0.1.ebuild deleted file mode 100644 index e575c68d5d0..00000000000 --- a/sci-biology/elph/elph-1.0.1.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -inherit eutils toolchain-funcs - -DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" -LICENSE="Artistic" -HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"; -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"; - -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -S=${WORKDIR}/ELPH/sources - -src_compile() { - emake CC="$(tc-getCXX)" LINKER="$(tc-getCXX)" \ - CFLAGS="${CXXFLAGS} -D_REENTRANT" LDFLAGS="${LDFLAGS}" || die -} - -src_install() { - dobin elph || die "Failed to install program." - cd "${WORKDIR}"/ELPH - dodoc VERSION || die "Documentation installation failed." - newdoc Readme.ELPH README || die "Readme installation failed." -} diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch deleted file mode 100644 index 139b83c1c1c..00000000000 --- a/sci-biology/elph/files/elph-0.1.5-usage.patch +++ /dev/null @@ -1,133 +0,0 @@ ---- elph.cc.old 2005-01-11 14:17:47.000000000 -0500 -+++ elph.cc 2005-01-27 19:42:30.218350552 -0500 -@@ -26,11 +26,11 @@ - period variable\n\ - -x : print maximum positions within sequences\n\ - -g : find significance of motif\n\ -- -t <matrix> : test if there is significant difference between the two -- input files for a given motif matrix; <matrix> is the file -+ -t <matrix> : test if there is significant difference between the two\n\ -+ input files for a given motif matrix; <matrix> is the file\n\ - containing the motif matrix\n\ -- -l : compute Least Likely Consensus (LLC) for given motif -- -c : in conjunction with -m option: motif is not necessarily in -+ -l : compute Least Likely Consensus (LLC) for given motif\n\ -+ -c : in conjunction with -m option: motif is not necessarily in\n\ - the closest edit distance from input motif\n\ - LEN=n : n = length of motif\n\ - ITERNO=n : n = no of iterations to compute the global maximum;\n\ -@@ -41,7 +41,7 @@ - default = 1000\n\ - " - --// global variables: -+// global variables: - int ITER_NO=10; - int MAX_LOOP=500; - int printmax=0; -@@ -66,7 +66,7 @@ - seqType t; - - GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); -- -+ - // == Process arguments. - - int e; -@@ -83,7 +83,7 @@ - - if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files - -- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); -+ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); - M->twofilesignif(gdet,testfile,SignifNo,print,pattern); - - } -@@ -93,11 +93,11 @@ - // given motif - - M = new Motif(infile,outf,t,pattern); -- if(defLLC) { -+ if(defLLC) { - double llc=M->computeLLC(pattern,print); - fprintf(outf,"LLC = %f\n",llc); - } -- -+ - } - else { - -@@ -108,7 +108,7 @@ - } - - double globAlignProb; -- -+ - globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); - - -@@ -116,13 +116,13 @@ - /*info=M->InfoPar(globAlignProb); - fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); - M->printMotif();*/ -- -+ - // optimizing - fprintf(stderr,"Optimizing...\n"); - globAlignProb=M->optimize(globAlignProb,info,closest); - fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); - fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); -- -+ - if(runsignif) { - M->runforsignif(SignifNo,print,gdet,pattern); - } -@@ -134,17 +134,17 @@ - - seqType Process_Options(GArgs* args) - { -- -- if (args->startNonOpt()) { //parse the non-options arguments -+ -+ if (args->startNonOpt()) { //parse the non-options arguments - //(usually filenames) - infile=args->nextNonOpt(); - } - -- if (infile.is_empty() || args->getOpt('h')!=NULL) -+ if (infile.is_empty() || args->getOpt('h')!=NULL) - GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input - - testfile=args->nextNonOpt(); -- -+ - GString outfile=args->getOpt('o'); - if (!outfile.is_empty()) { - outf=fopen(outfile, "w"); -@@ -156,7 +156,7 @@ - matrixfile=args->getOpt('t'); - - GString param; -- -+ - pattern=args->getOpt('m'); - if(pattern.is_empty()) { - param=args->getOpt("LEN"); -@@ -200,7 +200,7 @@ - - seqType t; - if(args->getOpt('a')!=NULL) t=aac; else t=nucl; -- -+ - return(t); - - } -@@ -210,7 +210,7 @@ - Motif *M; - - double llcmax=-HUGE_VAL; -- GString seed; -+ GString seed; - for(int i1=0;i1<4;i1++) - for(int i2=0;i2<4;i2++) - for(int i3=0;i3<4;i3++)
