* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2015-03-31 20:26 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-03-31 20:26 UTC (permalink / raw
To: gentoo-commits
commit: 529d9a71cf4c1b3ae1dc6e437923544e2cc84741
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 31 20:26:02 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 31 20:26:02 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=529d9a71
sci-biology/bambus: fix installation process and use current perl-module files from amos package instead
Package-Manager: portage-2.2.18
sci-biology/bambus/ChangeLog | 7 +++++
sci-biology/bambus/bambus-2.33.ebuild | 57 ++++++++++++++++++++---------------
2 files changed, 39 insertions(+), 25 deletions(-)
diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog
new file mode 100644
index 0000000..9140d87
--- /dev/null
+++ b/sci-biology/bambus/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/bambus
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
+ sci-biology/bambus: fix installation process and use current perl-module files
+ from amos package instead
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 2c05ad1..71ecb4b 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,15 +1,17 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
inherit eutils
DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+ http://sourceforge.net/projects/amos/files/bambus
http://www.tigr.org/software/bambus"
-SRC_URI="http://sourceforge.net/projects/amos/files/bambus/2.33/bambus-2.33.tar.gz"
+SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
+ http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
LICENSE="Artistic"
SLOT="0"
@@ -26,28 +28,32 @@ RDEPEND="${DEPEND}
src_prepare() {
# epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
- sed -i 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' Makefile || die
- sed -i 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' src/Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' doc/Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' src/IO/Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' src/DotLib/Makefile || die
- sed -i 's:INSTDIR:DESTDIR:g' src/grommit/Makefile || die
- sed -i 's:^CC:#CC:' Makefile || die
- sed -i 's:^CXX:#CXX:' Makefile || die
- sed -i 's:^LD:#LD:' Makefile || die
- sed -i 's:^AR:#AR:' Makefile || die
- sed -i 's:^export:#export:' Makefile || die
- sed -i 's:-Wl::' src/grommit/Makefile || die
- sed -i 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/ -shared -fPIC:' src/grommit/Makefile || die
- sed -i 's:make all:make all DESTDIR=$(DESTDIR):' Makefile || die
- sed -i 's:make install:make install DESTDIR=$(DESTDIR):' Makefile || die
- sed -i 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)) -shared -fPIC:' src/grommit/Makefile || die
- sed -i 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS):' src/grommit/Makefile || die
- sed -i 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' src/goBambus.pl || die
+ sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
+ sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die
+ sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die
+ sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die
+ sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die
+ sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die
+ sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die
+ sed -e 's:^AR\t=:#AR=:' -i Makefile || die
+ sed -e 's:^export:#export:' -i Makefile || die
+ sed -e 's:-Wl::' -i src/grommit/Makefile || die
+ # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die
+ sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die
+ sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die
+ sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die
+ sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die
+ sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die
+ sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die
+ sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die
+ sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die
einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present"
- einfo "in sci-biology/tigr-foundation-libs. It sees bambus-2.33/src/TIGR_Foundation_CC/ contains"
+ einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains"
einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied"
einfo "over from some old GNU libc and maybe could be completely dropped?"
einfo "Affected would be:"
@@ -59,7 +65,7 @@ src_prepare() {
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die
- sed -i "s:/export/usr/local:${D}/usr:g" Makefile || die
+ sed -e "s:/export/usr/local:${D}/usr:g" -i Makefile || die
}
src_compile() {
@@ -99,6 +105,7 @@ src_install() {
rmdir "${D}"/usr/doc || die
dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
+ dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 67aadfe6bebdb0f0aa3e17f20e9ce3ee06a0c425
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:32:21 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:32:21 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=67aadfe6
sci-biology/bambus: actually do not install the outdated *.pm files but rely on them from sci-biology/amos
Package-Manager: portage-2.2.18
sci-biology/bambus/ChangeLog | 4 ++++
sci-biology/bambus/bambus-2.33.ebuild | 4 ----
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog
index fe020a7..a1f191b 100644
--- a/sci-biology/bambus/ChangeLog
+++ b/sci-biology/bambus/ChangeLog
@@ -3,6 +3,10 @@
# $Header: $
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
+ sci-biology/bambus: actually do not install the outdated *.pm files but rely
+ on them from sci-biology/amos
+
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
sci-biology/bambus: fixed installation of perl-related files
31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index a89101c..7ac757a 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -107,10 +107,6 @@ src_install() {
dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
-
- perl_set_version
- insinto ${VENDOR_LIB}
- doins "${D}"/usr/lib/DotLib.pm
rm -rf "${D}"/usr/lib
}
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: a7b6591d86eac5c9ffc69f5f4f5b9bbb9cb3251a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:12:24 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:12:24 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a7b6591d
sci-biology/bambus: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/bambus/ChangeLog | 3 +++
sci-biology/bambus/bambus-2.33.ebuild | 8 +++++++-
2 files changed, 10 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog
index 9140d87..fe020a7 100644
--- a/sci-biology/bambus/ChangeLog
+++ b/sci-biology/bambus/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
+ sci-biology/bambus: fixed installation of perl-related files
+
31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild:
sci-biology/bambus: fix installation process and use current perl-module files
from amos package instead
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 71ecb4b..a89101c 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -4,7 +4,8 @@
EAPI=5
-inherit eutils
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
@@ -106,6 +107,11 @@ src_install() {
dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
+
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ doins "${D}"/usr/lib/DotLib.pm
+ rm -rf "${D}"/usr/lib
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2015-09-23 10:19 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2015-09-23 10:19 UTC (permalink / raw
To: gentoo-commits
commit: f5615b674dcdbddefac76b816a12458dd895fcb6
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 10:15:57 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 10:15:57 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5615b67
sci-biology/bambus: Drop unnecessary dep on python
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bambus/bambus-2.33.ebuild | 58 ++++++++++++++++++-----------------
1 file changed, 30 insertions(+), 28 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index d5b7c7f..13b7b62 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -8,10 +8,12 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
-HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
- http://sourceforge.net/projects/amos/files/bambus
- http://www.tigr.org/software/bambus"
-SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
+HOMEPAGE="
+ http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+ http://sourceforge.net/projects/amos/files/bambus
+ http://www.tigr.org/software/bambus"
+SRC_URI="
+ http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
LICENSE="Artistic"
@@ -19,25 +21,25 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="sci-biology/tigr-foundation-libs"
-RDEPEND="${DEPEND}
- dev-lang/perl
- dev-lang/python
- dev-perl/XML-Parser
- dev-perl/Config-IniFiles
- dev-perl/GraphViz"
+RDEPEND="
+ sci-biology/tigr-foundation-libs
+ dev-lang/perl
+ dev-perl/XML-Parser
+ dev-perl/Config-IniFiles
+ dev-perl/GraphViz"
+DEPEND="${RDEPEND}"
src_prepare() {
# epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die
+ sed \
+ -e 's:INSTDIR:DESTDIR:g' \
+ -i Makefile src/Makefile doc/Makefile || die
sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die
- sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die
+ sed \
+ -e 's:INSTDIR:DESTDIR:g' \
+ -i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die
sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die
sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die
sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die
@@ -70,7 +72,7 @@ src_prepare() {
}
src_compile() {
- emake DESTDIR="${D}/usr" || die "emake failed"
+ emake DESTDIR="${D}/usr"
# TODO:
#ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
@@ -87,7 +89,7 @@ src_compile() {
}
src_install() {
- emake DESTDIR="${D}/usr" install || die "emake install failed"
+ emake DESTDIR="${D}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${D}"/usr/lib/TIGR/$f; done || die
for f in printScaff untangle; do rm "${D}"/usr/bin/$f; done || die
@@ -96,18 +98,18 @@ src_install() {
# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \
ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \
- LogMsg.hh Options.hh Logger.hh FileSystem.hh; do \
- rm "${D}"/usr/include/$f; \
- done || die
- rm "${D}"/usr/lib/libTigrFoundation.a || die
+ LogMsg.hh Options.hh Logger.hh FileSystem.hh; do
+ rm "${ED}"/usr/include/$f || die
+ done
+ rm "${ED}"/usr/lib/libTigrFoundation.a || die
- mkdir -p "${D}"/usr/share/doc/"${P}" || die
- mv "${D}"/usr/doc/* "${D}"/usr/share/doc/"${P}" || die
- rmdir "${D}"/usr/doc || die
+ dodir /usr/share/doc/${P}
+ mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
+ rmdir "${ED}"/usr/doc || die
- dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
+ dobin "${FILESDIR}"/goBambus.pl
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
- rm -rf "${D}"/usr/lib
+ rm -rf "${ED}"/usr/lib || die
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2016-09-01 15:16 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-09-01 15:16 UTC (permalink / raw
To: gentoo-commits
commit: 654417b952acb054c64e9be152306150f47410ed
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 1 15:16:27 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 1 15:16:27 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=654417b9
sci-biology/bambus: respect EPREFIX
Package-Manager: portage-2.3.0
sci-biology/bambus/bambus-2.33.ebuild | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 13b7b62..456e5c5 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -72,7 +72,7 @@ src_prepare() {
}
src_compile() {
- emake DESTDIR="${D}/usr"
+ emake DESTDIR="${ED}/usr"
# TODO:
#ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
@@ -89,10 +89,10 @@ src_compile() {
}
src_install() {
- emake DESTDIR="${D}/usr" install
+ emake DESTDIR="${ED}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
- for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${D}"/usr/lib/TIGR/$f; done || die
- for f in printScaff untangle; do rm "${D}"/usr/bin/$f; done || die
+ for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
+ for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die
# we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but
# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2016-09-01 15:29 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-09-01 15:29 UTC (permalink / raw
To: gentoo-commits
commit: 2518a22efd0348e75c50e742d98be61210916e81
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 1 15:29:10 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 1 15:29:10 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2518a22e
sci-biology/bambus: respect EPREFIX also in src/TIGR_Foundation_CC/Makefile
Package-Manager: portage-2.3.0
sci-biology/bambus/bambus-2.33.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 456e5c5..504b0ee 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -68,7 +68,7 @@ src_prepare() {
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die
- sed -e "s:/export/usr/local:${D}/usr:g" -i Makefile || die
+ sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
}
src_compile() {
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2017-02-22 2:05 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2017-02-22 2:05 UTC (permalink / raw
To: gentoo-commits
commit: c662d396f4bf1577a5fca3afd3cbd80931a2d517
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 22 02:05:07 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 22 02:05:07 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c662d396
sci-biology/bambus: remove direct dev-lang/perl DEPENDcy
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/bambus/bambus-2.33.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 504b0ee4b..dfaa9493e 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -23,7 +23,6 @@ IUSE=""
RDEPEND="
sci-biology/tigr-foundation-libs
- dev-lang/perl
dev-perl/XML-Parser
dev-perl/Config-IniFiles
dev-perl/GraphViz"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2022-01-25 19:15 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 19:15 UTC (permalink / raw
To: gentoo-commits
commit: 129a8a0e6f647116139aa84ccf4a30cebf315860
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 16:14:38 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 16:14:38 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=129a8a0e
sci-biology/bambus: drop ED from src_compile
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../{bambus-2.33.ebuild => bambus-2.33-r1.ebuild} | 25 ++++------------------
1 file changed, 4 insertions(+), 21 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33-r1.ebuild
similarity index 85%
rename from sci-biology/bambus/bambus-2.33.ebuild
rename to sci-biology/bambus/bambus-2.33-r1.ebuild
index e92c8c8da..1e2078c94 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module toolchain-funcs
@@ -70,23 +70,6 @@ src_prepare() {
sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
}
-src_compile() {
- emake DESTDIR="${ED}/usr"
-
- # TODO:
- #ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
- # ld: warning: creating a DT_TEXTREL in object.
- #
- # * QA Notice: The following files contain runtime text relocations
- # * Text relocations force the dynamic linker to perform extra
- # * work at startup, waste system resources, and may pose a security
- # * risk. On some architectures, the code may not even function
- # * properly, if at all.
- # * For more information, see http://hardened.gentoo.org/pic-fix-guide.xml
- # * Please include the following list of files in your report:
- # * TEXTREL usr/bin/grommit
-}
-
src_install() {
emake DESTDIR="${ED}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
@@ -102,13 +85,13 @@ src_install() {
done
rm "${ED}"/usr/lib/libTigrFoundation.a || die
- dodir /usr/share/doc/${P}
+ dodir /usr/share/doc/${PF}
mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
rmdir "${ED}"/usr/doc || die
dobin "${FILESDIR}"/goBambus.pl
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
- rm -rf "${ED}"/usr/lib || die
+ rm -r "${ED}"/usr/lib || die
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2022-01-26 10:17 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2022-01-26 10:17 UTC (permalink / raw
To: gentoo-commits
commit: d703c5a43cf46b3e7228f8beaeb66b7bba525638
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 26 10:02:49 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Jan 26 10:02:49 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d703c5a4
sci-biology/bambus: fix PMS violation
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/bambus/{bambus-2.33-r1.ebuild => bambus-2.33-r2.ebuild} | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bambus/bambus-2.33-r1.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
similarity index 98%
rename from sci-biology/bambus/bambus-2.33-r1.ebuild
rename to sci-biology/bambus/bambus-2.33-r2.ebuild
index 1e2078c94..475c7f0b1 100644
--- a/sci-biology/bambus/bambus-2.33-r1.ebuild
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -66,11 +66,12 @@ src_prepare() {
einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
- cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
- sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
}
src_install() {
+ pushd src/TIGR_Foundation_CC || die
+ sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
+ popd || die
emake DESTDIR="${ED}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambus/
@ 2023-02-17 20:48 Horea Christian
0 siblings, 0 replies; 10+ messages in thread
From: Horea Christian @ 2023-02-17 20:48 UTC (permalink / raw
To: gentoo-commits
commit: 57333cb1cef7d8598fef4fdae69e6263c925b4ec
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Feb 17 20:48:08 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Feb 17 20:48:18 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57333cb1
sci-biology/bambus: SRC_URI now has HTTPS
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/bambus/bambus-2.33-r2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
index 475c7f0b1..1cb7aad1b 100644
--- a/sci-biology/bambus/bambus-2.33-r2.ebuild
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="
https://sourceforge.net/projects/amos/files/bambus"
SRC_URI="
https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
- http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https
+ https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
LICENSE="Artistic"
SLOT="0"
^ permalink raw reply related [flat|nested] 10+ messages in thread
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2016-09-01 15:29 Martin Mokrejs
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