[gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/, sci-biology/hmmer/files/
commit: 4919e107f95d762348df57ca9a8e75307d9222bc
Author: NHOrus yahoo com>
AuthorDate: Wed May 8 09:30:27 2024 +
Commit: Sam James gentoo org>
CommitDate: Thu May 9 01:09:05 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4919e107
sci-biology/hmmer: Add missing include into configure
There are no autotools source files, so we can't just autoreconf the problem
out of existence
[sam: Revbump.]
Closes: https://bugs.gentoo.org/900551
Signed-off-by: NHOrus yahoo.com>
Closes: https://github.com/gentoo/gentoo/pull/36599
Signed-off-by: Sam James gentoo.org>
.../hmmer-2.3.2-fix-missing-include-in-configure.patch | 18 ++
.../{hmmer-2.3.2-r5.ebuild => hmmer-2.3.2-r6.ebuild} | 3 ++-
2 files changed, 20 insertions(+), 1 deletion(-)
diff --git
a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
new file mode 100644
index ..37683d425edb
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
@@ -0,0 +1,18 @@
+--- a/squid/configure 2024-05-08 09:21:15.751063495 -
b/squid/configure 2024-05-08 09:22:50.491502934 -
+@@ -2493,6 +2493,7 @@
+ cat confdefs.h >>conftest.$ac_ext
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
++#include
+ int
+ main ()
+ {
+@@ -3500,6 +3501,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
+ #include
++#include
+ #if ((' ' & 0x0FF) == 0x020)
+ # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+ # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
similarity index 94%
rename from sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
rename to sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
index b305820faff3..74a8a151b0c4 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -20,6 +20,7 @@ BDEPEND="test? ( dev-lang/perl )"
PATCHES=(
"${FILESDIR}/${P}-fix-perl-shebangs.patch"
"${FILESDIR}/${P}-fix-build-system-destdir.patch"
+ "${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
)
src_configure() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/, sci-biology/hmmer/files/
commit: d31ff028511de2e2cc29e125cae3a6862aa6e2ec
Author: David Seifert gentoo org>
AuthorDate: Thu Jul 7 19:56:56 2022 +
Commit: David Seifert gentoo org>
CommitDate: Thu Jul 7 19:56:56 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d31ff028
sci-biology/hmmer: update EAPI 6 -> 8 (3.1_beta2)
Signed-off-by: David Seifert gentoo.org>
...l-path.patch => hmmer-3.1_beta2-makefile.patch} | 23 +++-
...-3.1_beta2.ebuild => hmmer-3.1_beta2-r1.ebuild} | 32 +-
2 files changed, 41 insertions(+), 14 deletions(-)
diff --git
a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
similarity index 85%
rename from
sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
rename to sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
index b9ff5b92b8f9..1c08d67e7bdd 100644
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
@@ -1,4 +1,5 @@
-Install headers into 'hmmer3' subdir and not into global includedir.
+* Install headers into 'hmmer3' subdir and not into global includedir
+* Respect AR
--- a/easel/Makefile.in
+++ b/easel/Makefile.in
@@ -17,6 +18,26 @@ Install headers into 'hmmer3' subdir and not into global
includedir.
${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install
# "make uninstall" reverses the steps of "make install"
+--- a/libdivsufsort/Makefile.in
b/libdivsufsort/Makefile.in
+@@ -16,7 +16,7 @@
+ CFLAGS= @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
+ CPPFLAGS = @CPPFLAGS@
+ MPILIBS = @MPILIBS@
+-AR= @AR@ rc
++AR= @AR@
+ RANLIB= @RANLIB@
+ INSTALL = @INSTALL@
+
+@@ -43,7 +43,7 @@
+
+
+ libdivsufsort.a: $(OBJS)
+- ${QUIET_AR}${AR} libdivsufsort.a $(OBJS)
++ ${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS)
+ @${RANLIB} libdivsufsort.a
+ @chmod 644 libdivsufsort.a
+
--- a/Makefile.in
+++ b/Makefile.in
@@ -143,6 +143,7 @@
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
similarity index 60%
rename from sci-biology/hmmer/hmmer-3.1_beta2.ebuild
rename to sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
index b65fa0824f9b..666d21cd5532 100644
--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
+++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
@@ -1,49 +1,55 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
+
+inherit toolchain-funcs
MY_PV="${PV/_beta/b}"
DESCRIPTION="Sequence analysis using profile hidden Markov models"
HOMEPAGE="http://hmmer.org/;
SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz;
+S="${WORKDIR}/${PN}-${MY_PV}"
LICENSE="GPL-3"
SLOT="0"
-IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
-RESTRICT="!test? ( test )"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test"
+RESTRICT="!test? ( test )"
RDEPEND="
mpi? ( virtual/mpi )
gsl? ( sci-libs/gsl:= )"
-DEPEND="${RDEPEND}
- test? ( dev-lang/perl )"
+DEPEND="${RDEPEND}"
+BDEPEND="test? ( dev-lang/perl )"
-S="${WORKDIR}/${PN}-${MY_PV}"
PATCHES=(
- "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
- "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
+ "${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch
+ "${FILESDIR}"/${PN}-3.1_beta2-makefile.patch
)
src_configure() {
- # make build verbose, bug 429308
+ # make build verbose, bug #429308
export V=1
econf \
--disable-pic \
- $(use_enable altivec vmx) \
+ --enable-threads \
+ $(use_enable cpu_flags_ppc_altivec vmx) \
$(use_enable cpu_flags_x86_sse sse) \
$(use_enable mpi) \
- $(use_enable threads) \
$(use_with gsl)
}
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
src_install() {
default
dodoc Userguide.pdf
- insinto /usr/share/${PN}
+ insinto /usr/share/hmmer
doins -r tutorial
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/, sci-biology/hmmer/files/
commit: cbfe0e33651a8811229d663a9469cc97957b994e
Author: David Seifert gentoo org>
AuthorDate: Mon Feb 6 20:48:01 2017 +
Commit: David Seifert gentoo org>
CommitDate: Mon Feb 6 21:25:51 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cbfe0e33
sci-biology/hmmer: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3856
sci-biology/hmmer/Manifest | 1 -
sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch | 23
.../hmmer/files/hmmer-3.0-perl-5.16-2.patch| 132 -
sci-biology/hmmer/hmmer-3.0.ebuild | 45 ---
4 files changed, 201 deletions(-)
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index dada007..acffd6e 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -1,3 +1,2 @@
DIST hmmer-2.3.2.tar.gz 1024933 SHA256
d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512
5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
WHIRLPOOL
604cc3f532d6eae3fbca893d991d0714a5a897fbac3059d63fdbebc6221e9321c2b444db2700e7068a11c043c0a7f9f3935617a3aa1878ca06ba18c558d55d40
-DIST hmmer-3.0.tar.gz 3952015 SHA256
6977e6473fcb554b1d5a86dc9eda53918c1bd88d7fd20d7499f1ba719e83 SHA512
752f06b0494a87ccd2cf6aa93e622fd02173eaa0df60df0527b3361dcaa2baf2b45a2daf0123217c0029bc9d95e505a92f1e97039eb8b7218b4c4b65ddad1db5
WHIRLPOOL
a181ce8ddb016bf1209c83fa754163e9ac653acb51fed13dee8598565d2f058a118fca04229aef7e4e5a79aae86712639b8e43bf7e12c50a8bf22e32be9df658
DIST hmmer-3.1b2.tar.gz 5965253 SHA256
dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 SHA512
64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
WHIRLPOOL
0b6d17b5f5efe31873cde93ff33cc5b01c53de8e1daf1ed473ef92d6585f34abcbb31e35e4d02537fbbc2c808131b70a0f51a3832ee332e23246cbc75edc354a
diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
deleted file mode 100644
index 983827b..
--- a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch
+++ /dev/null
@@ -1,23 +0,0 @@
easel/Makefile.in
-+++ easel/Makefile.in
-@@ -26,8 +26,7 @@
- LDFLAGS = @LDFLAGS@
- SIMDFLAGS= @SIMD_CFLAGS@
- CPPFLAGS = @CPPFLAGS@
--LIBGSL = @LIBGSL@
--LIBS = @LIBS@ @PTHREAD_LIBS@
-+LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@
-
- # Other tools
- #
-@@ -252,8 +251,8 @@
- else \
-DFILE=${srcdir}/esl_$${BASENAME}.c ;\
- fi;\
-- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I.
-I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\
-- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir}
-L. -D$${DFLAG} $${DFILE} -leasel -lm
-+ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I.
-I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\
-+ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir}
-L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
-
-
- # install: installs libeasel.a in ${libdir}/
diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch
b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch
deleted file mode 100644
index 19d38c8..
--- a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch
+++ /dev/null
@@ -1,132 +0,0 @@
- easel/devkit/autodoc |4 ++--
- easel/devkit/esl-dependencies |4 ++--
- easel/devkit/sqc |7 +++
- easel/testsuite/coverage_report.pl |4 ++--
- easel/testsuite/driver_report.pl |4 ++--
- easel/testsuite/valgrind_report.pl |4 ++--
- profmark/rocplot.pl|4 ++--
- 7 files changed, 15 insertions(+), 16 deletions(-)
-
-diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc
-index 16bda4d..f5c5efc 100755
a/easel/devkit/autodoc
-+++ b/easel/devkit/autodoc
-@@ -49,8 +49,8 @@
- #
- # SRE, Tue Nov 30 19:43:47 2004
-
--require "getopts.pl";
--('n:t');
-+use Getopt::Std;
-+getopts('n:t');
- $cfile = shift;
-
- if ($opt_t) { $show_api_table = 1; }
-diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies
-index a4dc126..b61fa7a 100755
a/easel/devkit/esl-dependencies
-+++ b/easel/devkit/esl-dependencies
-@@ -13,8 +13,8 @@
- # SRE, Mon Jun 11 11:15:31 2007
- # SVN $Id$
-
--require "getopts.pl"
--('1afr');
-+use Getopt::Std;
-+getopts('1afr');
-
- if ($opt_1) { $show_summary_table = 1; }
- if ($opt_a) { $list_augfiles = 1; }
-diff --git a/easel/devkit/sqc b/easel/devkit/sqc
-index af3adf6..0cdb458 100755
a/easel/devkit/sqc
-+++ b/easel/devkit/sqc
-@@ -205,12 +205,11 @@
- # SRE, Tue Aug 6 11:16:39 2002
- # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $
-
--require "getopts.pl";
--require "importenv.pl";
-+use Getopt::Std;
-
- # Parse our command line
- #
--('v');
[gentoo-commits] repo/gentoo:master commit in: sci-biology/hmmer/, sci-biology/hmmer/files/
commit: 895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7
Author: David Seifert gentoo org>
AuthorDate: Sun Oct 9 14:52:52 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Oct 9 15:14:23 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=895b3abf
sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2
Gentoo-bug: 328911, 586960
* EAPI=6
* Introduce SLOT=2 and rename binaries and
static libraries
Package-Manager: portage-2.3.1
.../hmmer-2.3.2-fix-build-system-destdir.patch | 22 +
.../files/hmmer-2.3.2-fix-perl-shebangs.patch | 108 +
sci-biology/hmmer/hmmer-2.3.2-r4.ebuild| 75 ++
3 files changed, 205 insertions(+)
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
new file mode 100644
index ..110c61f
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
@@ -0,0 +1,22 @@
+Make the build system respect DESTDIR, in order to allow staged builds.
+
+--- a/Makefile.in
b/Makefile.in
+@@ -109,13 +109,13 @@
+ # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
+ # Creates these directories if they don't exist.
+ install:
+- mkdir -p ${BINDIR}
+- -mkdir -p ${MANDIR}/man${MANSUFFIX}
++ mkdir -p ${DESTDIR}${BINDIR}
++ -mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX}
+ for file in $(PROGS) $(PVMPROGS); do\
+- cp src/$$file $(BINDIR)/;\
++ cp src/$$file ${DESTDIR}$(BINDIR)/;\
+ done
+ -for file in hmmer $(PROGS); do\
+- $(INSTMAN) documentation/man/$$file.man
$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++ $(INSTMAN) documentation/man/$$file.man
${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ done
+
+ # uninstall: Reverses the steps of "make install".
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
new file mode 100644
index ..783d053
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
@@ -0,0 +1,108 @@
+* Fix ancient perl 4 modules that are long gone.
+* Fix perl shebangs to be portable and usable on Prefix.
+See also:
https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/squid/Testsuite/bug-1-sfetch-paths
b/squid/Testsuite/bug-1-sfetch-paths
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ # Test for bug #1: sfetch/SSI path bug.
+ # sfetch can't follow paths out of current directory if it's using
+--- a/squid/Testsuite/x-base-afetch
b/squid/Testsuite/x-base-afetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-alistat
b/squid/Testsuite/x-base-alistat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-seqstat
b/squid/Testsuite/x-base-seqstat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-sfetch
b/squid/Testsuite/x-base-sfetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-shuffle
b/squid/Testsuite/x-base-shuffle
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-sindex
b/squid/Testsuite/x-base-sindex
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/squid/Testsuite/x-base-sreformat
b/squid/Testsuite/x-base-sreformat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ use testsuite;
+
+--- a/testsuite/sqc
b/testsuite/sqc
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ # sqc
+ # quality control script for exercising code, regression testing,
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug 6 11:16:39 2002
+ # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $
+
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+
+ # Parse our command line
+ #
+-('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1;}
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs, $opt_r; }
+@@ -506,7 +505,7 @@
+ #
+ sub tempname {
+ my ($dir, $name, $suffix);
+-if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+
+ foreach $suffix ("aa".."zz") {
+ $name = "$dir"."sre".$suffix.$$;
+--- a/testsuite/test1-conversion.pl
b/testsuite/test1-conversion.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+
+ # Test hmmconvert.
+ #
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
new file mode 100644
index ..7cecfe6
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
@@ -0,0 +1,75 @@
+#
