* [gentoo-commits] repo/gentoo:master commit in: sci-biology/elph/, sci-biology/elph/files/
@ 2017-03-08 22:16 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-03-08 22:16 UTC (permalink / raw
To: gentoo-commits
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++)
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/elph/, sci-biology/elph/files/
@ 2023-09-07 9:13 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2023-09-07 9:13 UTC (permalink / raw
To: gentoo-commits
commit: 763cc65174197beee59a0d1fa56011c6d4a23cf5
Author: Brahmajit Das <brahmajit.xyz <AT> gmail <DOT> com>
AuthorDate: Thu Sep 7 09:13:26 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 7 09:13:26 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=763cc651
sci-biology/elph: Fix C++17 does not allow register storage class
Closes: https://github.com/gentoo/gentoo/pull/32664
Closes: https://bugs.gentoo.org/898116
Signed-off-by: Brahmajit Das <brahmajit.xyz <AT> gmail.com>
Signed-off-by: David Seifert <soap <AT> gentoo.org>
.../{elph-1.0.1-r2.ebuild => elph-1.0.1-r3.ebuild} | 7 +-
.../files/elph-1.0.1-drop-register-keyword.patch | 102 +++++++++++++++++++++
2 files changed, 107 insertions(+), 2 deletions(-)
diff --git a/sci-biology/elph/elph-1.0.1-r2.ebuild b/sci-biology/elph/elph-1.0.1-r3.ebuild
similarity index 78%
rename from sci-biology/elph/elph-1.0.1-r2.ebuild
rename to sci-biology/elph/elph-1.0.1-r3.ebuild
index 66309522b312..6cfc05845358 100644
--- a/sci-biology/elph/elph-1.0.1-r2.ebuild
+++ b/sci-biology/elph/elph-1.0.1-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -14,7 +14,10 @@ LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-PATCHES=( "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch )
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch
+ "${FILESDIR}"/${PN}-1.0.1-drop-register-keyword.patch
+)
src_configure() {
tc-export CC CXX
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<length() && chars()[istart]==c;istart++);
+ if (istart==length()) {
+ make_unique(); //edit operation ahead
+@@ -384,8 +384,8 @@ GString& GString::trim(char c) {
+ }
+
+ GString& GString::trim(char* c) {
+- register int istart;
+- register int iend;
++ int istart;
++ int iend;
+ for (istart=0; istart<length() && strchr(c, chars()[istart])!=NULL ;istart++);
+ if (istart==length()) {
+ replace_data(0); //string was entirely trimmed
+@@ -405,7 +405,7 @@ GString& GString::trim(char* c) {
+ GString& GString::trimR(char c) {
+ //only trim the right end
+ //register int istart;
+- register int iend;
++ int iend;
+ for (iend=length()-1; iend>=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<length() && chars()[istart]==c;istart++);
+ if (istart==length()) {
+ replace_data(0); //string was entirely trimmed
+@@ -457,7 +457,7 @@ GString& GString::trimL(char c) {
+ }
+
+ GString& GString::trimL(char* c) {
+- register int istart;
++ int istart;
+ for (istart=0; istart<length() && strchr(c,chars()[istart])!=NULL;istart++);
+ if (istart==length()) {
+ replace_data(0); //string was entirely trimmed
+@@ -598,7 +598,7 @@ bool GString::is_space() const {
+ if (my_data == &null_data)
+ return false;
+
+- for (register const char *p = chars(); *p; p++)
++ for (const char *p = chars(); *p; p++)
+ if (!isspace(*p))
+ return false;
+
+@@ -889,7 +889,7 @@ GString& GString::append(const GString& s) {
+
+ GString& GString::upper() {
+ make_unique(); //edit operation ahead
+- for (register char *p = chrs(); *p; p++)
++ for (char *p = chrs(); *p; p++)
+ *p = (char) toupper(*p);
+
+ return *this;
+@@ -900,7 +900,7 @@ GString& GString::upper() {
+ GString& GString::lower() {
+ make_unique();
+
+- for (register char *p = chrs(); *p; p++)
++ for (char *p = chrs(); *p; p++)
+ *p = (char) tolower(*p);
+
+ return *this;
^ permalink raw reply related [flat|nested] 2+ messages in thread
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2017-03-08 22:16 David Seifert
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