[gentoo-commits] repo/gentoo:master commit in: sci-biology/elph/, sci-biology/elph/files/

[David Seifert]

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++)