[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/files/, sci-biology/trnascan-se/
commit: ec69f56bc3a7550b3c5018017b762e109ff19e5a
Author: Ionen Wolkens gentoo org>
AuthorDate: Wed Oct 19 08:57:37 2022 +
Commit: Ionen Wolkens gentoo org>
CommitDate: Wed Oct 19 09:21:44 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ec69f56b
sci-biology/trnascan-se: fix build w/ clang16, pass -std=gnu89
Closes: https://bugs.gentoo.org/874477
Signed-off-by: Ionen Wolkens gentoo.org>
.../files/trnascan-se-1.31-clang16.patch | 62 ++
...e-1.31-r2.ebuild => trnascan-se-1.31-r3.ebuild} | 4 +-
2 files changed, 65 insertions(+), 1 deletion(-)
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch
b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch
new file mode 100644
index ..33889c90cf69
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-clang16.patch
@@ -0,0 +1,62 @@
+https://bugs.gentoo.org/874477
+--- a/eufind_main.c
b/eufind_main.c
+@@ -23,4 +23,5 @@
+ #include
+ #include
++#include
+ #include "squid.h"
+ #include "sqfuncs.h"
+@@ -47,4 +48,14 @@
+ -i: start nucleotide numbering at (def=1)\n\n";
+
++int GetBbox(float*, int*, char*, int, int, int);
++int GetBestABox(TRNA_TYPE*, char*, char*, int, int, int, int, int);
++int GetBestTrxTerm(TRNA_TYPE*, char*, int, float);
++int GetSecABox(TRNA_TYPE*, char*);
++void Get_tRNA_stats(TRNA_TYPE*, char*, int, int);
++int Init_tRNA(TRNA_TYPE*);
++int IntEncodeSeq(char*, char*, int);
++void Save_tRNA(TRNA_TYPE*, SQINFO*, char*, int, int, long int);
++int tRNAOverlap(TRNA_TYPE*, TRNA_TYPE*, int);
++
+ int
+ main (int argc, char **argv)
+--- a/scan_main.c
b/scan_main.c
+@@ -8,4 +8,5 @@
+ #include
+ #include
++#include
+ #include
+ #include
+--- a/score_main.c
b/score_main.c
+@@ -10,4 +10,5 @@
+ #include
+ #include
++#include
+ #include
+ #include
+--- a/trnascan.c
b/trnascan.c
+@@ -69,4 +69,5 @@
+ #include
+ #include
++#include
+ #include
+
+@@ -333,5 +334,5 @@
+ );
+
+-main(int argc, char **argv)
++int main(int argc, char **argv)
+ {
+ /* pointers to the different files fpi=input file, fpo=output file,
+@@ -1419,5 +1420,5 @@
+ /* Calls to this function eliminated for efficiency T. Lowe 11/95 */
+
+-myindex (char *s, char *t)
++int myindex (char *s, char *t)
+ {
+ int i, j, k;
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild
b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild
similarity index 84%
rename from sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild
rename to sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild
index f35c31b22798..f43243921f2f 100644
--- a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild
+++ b/sci-biology/trnascan-se/trnascan-se-1.31-r3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit perl-functions toolchain-funcs
+inherit flag-o-matic perl-functions toolchain-funcs
DESCRIPTION="tRNA detection in large-scale genome sequences"
HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/";
@@ -20,10 +20,12 @@ BDEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
"${FILESDIR}"/${P}-portable-perl-shebangs.patch
+ "${FILESDIR}"/${P}-clang16.patch
)
src_configure() {
tc-export CC
+ append-cflags -std=gnu89 # mid-migration from K&R C, incompatible with
c2x
}
src_test() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/, sci-biology/trnascan-se/files/
commit: 01ccd8f6eb167dedd81a5ba3a3282f9e36893c4b
Author: David Seifert gentoo org>
AuthorDate: Sat Jul 9 09:53:58 2022 +
Commit: David Seifert gentoo org>
CommitDate: Sat Jul 9 09:53:58 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01ccd8f6
sci-biology/trnascan-se: drop 1.31
Signed-off-by: David Seifert gentoo.org>
.../files/trnascan-se-1.31-ldflags.patch | 26 ---
sci-biology/trnascan-se/trnascan-se-1.31.ebuild| 54 --
2 files changed, 80 deletions(-)
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
deleted file mode 100644
index f28b1e8f6bb0..
--- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 53e5c5b..a2d3feb 100644
a/Makefile
-+++ b/Makefile
-@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
- all: $(PROGS) tRNAscan-SE setpaths
-
- covels-SE: $(OBJ) scan_main.o
-- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
-+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ)
$(LIBS)
-
- coves-SE: $(OBJ) score_main.o
-- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
-+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ)
$(LIBS)
-
- eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
-- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \
- pavesi.o $(SQUIDOBJ) $(LIBS)
-
- trnascan-1.4: trnascan.o
-- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
-+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4
trnascan.c
-
- tRNAscan-SE:
- $(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
deleted file mode 100644
index cd8dc152d6d2..
--- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-functions toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/";
-SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S="${WORKDIR}"/tRNAscan-SE-1.3.1/
-
-PATCHES=(
- "${FILESDIR}"/${P}-ldflags.patch
-)
-
-src_prepare() {
- default
- sed \
- -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
- -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR =
${EPRFIX}/usr/share/${PN}:" \
- -e "s:MANDIR = \$(HOME)/man:MANDIR =
${EPREFIX}/usr/share/man:" \
- -e "s:CC = gcc:CC = $(tc-getCC):" \
- -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
- -i Makefile || die
-
- perl_set_version
-}
-
-src_test() {
- emake PATH="${S}:${PATH}" testrun
-}
-
-src_install() {
- dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
-
- newman tRNAscan-SE.man tRNAscan-SE.man.1
-
- dodoc MANUAL README Release.history
-
- insinto /usr/share/${PN}/
- doins *.cm gcode.* Dsignal TPCsignal
-
- dodoc Manual.ps
-
- insinto ${VENDOR_LIB}
- doins -r tRNAscanSE
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/, sci-biology/trnascan-se/files/
commit: 911c75e69d537dd9384a29f76a57fe9af143f13e Author: David Seifert gentoo org> AuthorDate: Sat Jul 9 09:53:57 2022 + Commit: David Seifert gentoo org> CommitDate: Sat Jul 9 09:53:57 2022 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=911c75e6 sci-biology/trnascan-se: improve makefile Signed-off-by: David Seifert gentoo.org> .../files/trnascan-se-1.31-makefile.patch | 140 + .../trnascan-se-1.31-portable-perl-shebangs.patch | 32 + ...e-1.31-r1.ebuild => trnascan-se-1.31-r2.ebuild} | 30 ++--- 3 files changed, 182 insertions(+), 20 deletions(-) diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch new file mode 100644 index ..acf3c2a6d862 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch @@ -0,0 +1,140 @@ +--- a/Makefile b/Makefile +@@ -20,9 +20,9 @@ + PERLBIN = perl + + ## where you want things installed +-BINDIR = $(HOME)/bin +-LIBDIR = $(HOME)/lib/tRNAscan-SE +-MANDIR = $(HOME)/man ++BINDIR = $(EPREFIX)/usr/bin ++LIBDIR = $(EPREFIX)/usr/share/trnascan-se ++MANDIR = $(EPREFIX)/usr/share/man + + ## NOTE !! If you later manually move the location of + ## binaries or data files in the BINDIR or LIBDIR directories, +@@ -33,10 +33,8 @@ + TEMPDIR = /tmp + + ## your compiler +-CC = gcc# GNU cc (if available) otherwise use vendor's cc + + ## any special compiler flags you want +-CFLAGS = -O# ok for most machines (remove -O for DEC OSF/1 cc compiler) + + ## machine specific definitions + # You shouldn't need any. The specific #define's in squid are historical. +@@ -58,7 +56,7 @@ + ### + + SHELL = /bin/sh +-LIBS = -lm ++LIBS += -lm + .SUFFIXES : .c .o + + DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history +@@ -109,20 +107,20 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + +-trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++trnascan-1.4: trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c + + tRNAscan-SE: +- $(PERLDIR)/$(PERLBIN) checkversion.pl ++ $(PERLBIN) checkversion.pl + sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \ + sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \ + sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \ +@@ -200,11 +198,11 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c +- $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ + pavesi-NA.o $(SQUIDOBJ) $(LIBS) + + +@@ -220,7 +218,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -233,16 +231,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) + + ## other programs in Cove package (below) not needed for + ## tR
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/
commit: 24345bb7834073b0027c28b890a36ed5ffd35a12
Author: Sam James gentoo org>
AuthorDate: Sat Jul 2 23:38:32 2022 +
Commit: Sam James gentoo org>
CommitDate: Sat Jul 2 23:38:32 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=24345bb7
sci-biology/trnascan-se: update EAPI 6 -> 8
Closes: https://bugs.gentoo.org/710970
Signed-off-by: Sam James gentoo.org>
sci-biology/trnascan-se/trnascan-se-1.31-r1.ebuild | 53 ++
1 file changed, 53 insertions(+)
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r1.ebuild
b/sci-biology/trnascan-se/trnascan-se-1.31-r1.ebuild
new file mode 100644
index ..cbbcb5f0e11e
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31-r1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-functions toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/";
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-ldflags.patch
+)
+
+src_prepare() {
+ default
+
+ sed \
+ -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
+ -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR =
${EPRFIX}/usr/share/${PN}:" \
+ -e "s:MANDIR = \$(HOME)/man:MANDIR =
${EPREFIX}/usr/share/man:" \
+ -e "s:CC = gcc:CC = $(tc-getCC):" \
+ -e "s;CFLAGS = -O;CFLAGS = ${CFLAGS};" \
+ -i Makefile || die
+
+ perl_set_version
+}
+
+src_test() {
+ emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+ dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+ newman tRNAscan-SE.man tRNAscan-SE.man.1
+
+ dodoc MANUAL README Release.history
+
+ insinto /usr/share/${PN}/
+ doins *.cm gcode.* Dsignal TPCsignal
+
+ dodoc Manual.ps
+
+ insinto ${VENDOR_LIB}
+ doins -r tRNAscanSE
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/files/
commit: dbe543ddfbdf83402b14e5ddea2969cbd486a0fa
Author: Michael Mair-Keimberger gmail com>
AuthorDate: Mon Sep 18 13:16:24 2017 +
Commit: Patrice Clement gentoo org>
CommitDate: Fri Oct 27 21:50:46 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dbe543dd
sci-biology/trnascan-se: remove unused patches.
.../files/trnascan-se-1.23-glibc-2.10.patch| 292 -
.../files/trnascan-se-1.23-ldflags.patch | 26 --
2 files changed, 318 deletions(-)
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
deleted file mode 100644
index e21da6e58db..000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
+++ /dev/null
@@ -1,292 +0,0 @@
-diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c
trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.0 +0300
-+++ trnascan-se-1.23/sqio.c2009-08-05 21:45:53.0 +0300
-@@ -235,7 +235,7 @@
- }
-
- static void
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
- readline(V->f, V->sbuffer);
- }
-@@ -306,7 +306,7 @@
- V->seqlen = 0;
- if (addfirst) addseq(V->sbuffer, V);
- do {
--getline(V);
-+get_line(V);
- done = feof(V->f);
- done |= (*endTest)(V->sbuffer, &addend);
- if (addend || !done)
-@@ -332,7 +332,7 @@
- char *sptr;
- /* load first line of entry */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--getline(V);
-+get_line(V);
- if (feof(V->f)) return;
-
- if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -341,7 +341,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
- }
- do {
--getline(V);
-+get_line(V);
- if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
- SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
- else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -350,7 +350,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
- }
- } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
-- getline(V); /* skip next line, coords */
-+ get_line(V);/* skip next line, coords */
-
- readLoop(0, endPIR, V);
-
-@@ -364,7 +364,7 @@
- /* get next line
-*/
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--getline(V);
-+get_line(V);
- }
-
-
-@@ -382,7 +382,7 @@
- char *nm;
- /* position past ';' comments */
- do {
--getline(V);
-+get_line(V);
- } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
-
- if (!feof(V->f))
-@@ -394,7 +394,7 @@
- }
-
- while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'
--getline(V);
-+get_line(V);
- }
-
- static int
-@@ -416,7 +416,7 @@
- if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- }
-- getline(V);
-+ get_line(V);
- }
-
- if (! feof(V->f))
-@@ -425,7 +425,7 @@
- /* load next line
-*/
- while ((!feof(V->f)) && (*V->sbuffer != ';'))
--getline(V);
-+get_line(V);
- }
-
-
-@@ -443,7 +443,7 @@
- int in_definition;
-
- while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--getline(V);
-+get_line(V);
-
- if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
- {
-@@ -454,7 +454,7 @@
- in_definition = FALSE;
- while (! feof(V->f))
- {
-- getline(V);
-+ get_line(V);
- if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- {
- if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -487,11 +487,11 @@
-
-
- while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") ==
V->sbuffer
--getline(V);
-+get_line(V);
- /* SRE: V->s now holds "//", so sequential
- reads are wedged: fixed Tue Jul 13 1993 */
- while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
--getline(V);
-+get_line(V);
- }
-
- static int
-@@ -521,12 +521,12 @@
- if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-
-- getline(V); /*skip title-junk line*/
-+ get_line(V); /*skip title-junk line*/
-
- readLoop(0, endNBRF, V);
-
- while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
--getline(V);
-+get_line(V);
- }
-
-
-@@ -559,7 +559,7 @@
- } else Die("bogus GCGdata format? %s", V->sbuffer);
-
- /* second line contains free text description */
-- getline(V);
-+ get_line(V);
- SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
-
- if (binary) {
-@@ -579,7 +579,7 @@
- else readLoop(0, endGCGdata, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffe
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/
commit: 529e06ea7c5927e07c85bd485067b32842ad14ad
Author: Justin Lecher gentoo org>
AuthorDate: Sat Apr 29 18:35:40 2017 +
Commit: Justin Lecher gentoo org>
CommitDate: Sat Apr 29 18:49:15 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=529e06ea
sci-biology/trnascan-se: Drop old
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/trnascan-se/Manifest | 1 -
sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild | 44 --
2 files changed, 45 deletions(-)
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
index b82cf548c77..56b13cc497e 100644
--- a/sci-biology/trnascan-se/Manifest
+++ b/sci-biology/trnascan-se/Manifest
@@ -1,2 +1 @@
-DIST trnascan-se-1.23.tar.bz2 482202 SHA256
a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a SHA512
4977febcecf8344fb77aad2eeb278637aebdb1d995fd26823e459b3767d4f40b20f57d343092cc2cb8024b0ccc385879f4b6406c69022f848aa1df0acf1a68d8
WHIRLPOOL
978328857eaef5666fcf38c22afabfb796984b5fa52a02a7167b653164ba0bc32fcb52d35159eef83732046245c598426739cd4ed63bf259ea85130dda17dd70
DIST trnascan-se-1.31.tar.gz 740960 SHA256
862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512
ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d
WHIRLPOOL
aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665
diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
deleted file mode 100644
index c16a96cc551..000
--- a/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="3"
-
-inherit eutils multilib toolchain-funcs
-
-DESCRIPTION="tRNA detection in large-scale genome sequences"
-HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/";
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-RDEPEND="dev-lang/perl"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-glibc-2.10.patch
- epatch "${FILESDIR}"/${P}-ldflags.patch
- sed -e "s%BINDIR = \$(HOME)/bin%BINDIR = ${EPREFIX}/usr/bin%" \
- -e "s%LIBDIR = \$(HOME)/lib/tRNAscan-SE%LIBDIR =
${EPRFIX}/usr/$(get_libdir)/${PN}%" \
- -e "s%MANDIR = \$(HOME)/man%MANDIR =
${EPREFIX}/usr/share/man%" \
- -e "s%CC = gcc%CC = $(tc-getCC)%" \
- -e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \
- -i Makefile || die
-}
-
-src_install() {
- mv tRNAscan-SE.man tRNAscan-SE.man.1 || die
- dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die
- doman tRNAscan-SE.man.1 || die
- dodoc MANUAL README Release.history || die
- insinto /usr/$(get_libdir)/${PN}/
- doins *.cm gcode.* Dsignal TPCsignal || die
- insinto /usr/share/doc/${PF}
- doins Manual.ps || die
-}
-
-src_test() {
- make PATH="${S}:${PATH}" testrun || die
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/
commit: 196ce403dba6344ab0a3924ffad33799657e8103
Author: Justin Lecher gentoo org>
AuthorDate: Fri Apr 14 18:07:20 2017 +
Commit: Justin Lecher gentoo org>
CommitDate: Fri Apr 14 18:59:56 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=196ce403
sci-biology/trnascan-se: Bump EAPI to 6
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/trnascan-se/trnascan-se-1.31.ebuild | 15 ---
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
index ca55fdd5e0f..04ff8bd610e 100644
--- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
+++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-PERL_EXPORT_PHASE_FUNCTIONS=no
-
-inherit eutils perl-module toolchain-funcs
+inherit perl-functions toolchain-funcs
DESCRIPTION="tRNA detection in large-scale genome sequences"
HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/";
@@ -18,9 +16,12 @@ IUSE=""
S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+PATCHES=(
+ "${FILESDIR}"/${P}-ldflags.patch
+)
+
src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-ldflags.patch
+ default
sed \
-e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
-e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR =
${EPRFIX}/usr/share/${PN}:" \
