[gentoo-commits] proj/sci:master commit in: sci-biology/staden/

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* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-03-06 21:20 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2011-03-06 21:20 UTC (permalink / raw
  To: gentoo-commits

commit:     0d07adffb5c46caf3d42b8bb9a5bcf433e1a98c7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar  6 21:20:03 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar  6 21:20:03 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d07adff

sci-biology/staden-2.0.0_beta8: provide LDPATH=/usr/lib/staden through /etc/env.d/99staden to /etc/ld.so.conf

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/staden/staden-2.0.0_beta8.ebuild |    7 +++++++
 1 files changed, 7 insertions(+), 0 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
index a79bfd2..a4e1e47 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -65,4 +65,11 @@ src_install() {
 	emake install DESTDIR="${D}" || die "make install failed"
 	#cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
 	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
+
+	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
+	# subsequently, apps linked against /usr/lib/staden can be run because
+	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
+	# somehow for gap2caf, for example
+	echo 'LDPATH=/usr/lib/staden' > 99staden || die
+	doenvd 99staden
 }



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-06-21 11:54 Justin Lecher
  0 siblings, 0 replies; 20+ messages in thread
From: Justin Lecher @ 2011-06-21 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     bb79d45d1a14d26cdd95f9efecdad1b746c5af6a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 21 11:31:44 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 21 11:31:44 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bb79d45d

Added fortran-2.eclass support

(Portage version: 2.2.0_alpha41/git/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

---
 sci-biology/staden/ChangeLog                 |    8 +++++
 sci-biology/staden/staden-2.0.0_beta8.ebuild |   42 ++++++++++++-------------
 sci-biology/staden/staden-9999.ebuild        |   38 ++++++++++-------------
 3 files changed, 44 insertions(+), 44 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
new file mode 100644
index 0000000..6064fae
--- /dev/null
+++ b/sci-biology/staden/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/staden
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
+  staden-9999.ebuild:
+  Added fortran-2.eclass support
+

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
index a4e1e47..a5d9990 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -4,12 +4,13 @@
 
 EAPI=3
 
-inherit eutils flag-o-matic base
+inherit eutils fortran-2 flag-o-matic base multilib
 
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)."
+DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
-		http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
+SRC_URI="
+	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
+	http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
 
 LICENSE="staden"
 SLOT="0"
@@ -22,22 +23,23 @@ IUSE="debug fortran X png curl tcl tk zlib"
 #
 # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
 #
-# 
 #
-DEPEND=">=dev-lang/tk-8.4
-		>=dev-lang/tcl-8.4
-		dev-tcltk/tklib
-		>=sci-libs/io_lib-1.12.2
-		>=sys-libs/zlib-1.2
-		>=media-libs/libpng-1.2
-		sci-biology/samtools
-		>=app-arch/xz-utils-4.999"
+#
+DEPEND="
+	dev-lang/tk
+	dev-tcltk/tklib
+	>=sci-libs/io_lib-1.12.2
+	>=sys-libs/zlib-1.2
+	>=media-libs/libpng-1.2
+	sci-biology/samtools
+	>=app-arch/xz-utils-4.999"
 
 # maybe we should depend on app-arch/lzma or app-arch/xz-utils?
 
-RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
-		tk? ( >=dev-tcltk/itk-3.2 )
-		>=dev-tcltk/iwidgets-4.0"
+RDEPEND="${DEPEND}
+	>=dev-tcltk/iwidgets-4.0
+	tcl? ( >=dev-tcltk/itcl-3.2 )
+	tk? ( >=dev-tcltk/itk-3.2 )"
 
 S="${WORKDIR}"/staden-2.0.0b8-src
 
@@ -54,11 +56,7 @@ src_configure(){
 	myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK
 	use amd64 && myconf="${myconf} --enable-64bit"
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	econf ${myconf} || die "configure failed"
-}
-
-src_compile() {
-	emake || die "emake failed"
+	econf ${myconf}
 }
 
 src_install() {
@@ -70,6 +68,6 @@ src_install() {
 	# subsequently, apps linked against /usr/lib/staden can be run because
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
 	# somehow for gap2caf, for example
-	echo 'LDPATH=/usr/lib/staden' > 99staden || die
+	echo 'LDPATH=/usr/$(get_libdir)/staden' > 99staden || die
 	doenvd 99staden
 }

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index fa67b6f..3f78adb 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=3
 
-inherit eutils flag-o-matic base subversion # autotools
+inherit eutils fortran-2 flag-o-matic base multilib subversion # autotools
 
-DESCRIPTION="A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin)."
+DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden"
 # https://staden.svn.sourceforge.net/svnroot/staden staden
 if [ "$PV" == "9999" ]; then
@@ -28,23 +28,22 @@ IUSE="debug fortran X png curl tcl tk zlib"
 #
 # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
 #
-# 
 #
-DEPEND="dev-vcs/subversion
-		>=dev-lang/tk-8.4
-		>=dev-lang/tcl-8.4
-		dev-tcltk/tklib
-		>=sci-libs/io_lib-1.12.2
-		>=sys-libs/zlib-1.2
-		>=media-libs/libpng-1.2
-		sci-biology/samtools
-		>=app-arch/xz-utils-4.999"
+DEPEND="
+	dev-lang/tk
+	dev-tcltk/tklib
+	>=sci-libs/io_lib-1.12.2
+	>=sys-libs/zlib-1.2
+	>=media-libs/libpng-1.2
+	sci-biology/samtools
+	>=app-arch/xz-utils-4.999"
 
 # maybe we should depend on app-arch/lzma or app-arch/xz-utils?
 
-RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
-		tk? ( >=dev-tcltk/itk-3.2 )
-		>=dev-tcltk/iwidgets-4.0"
+RDEPEND="${DEPEND}
+	>=dev-tcltk/iwidgets-4.0
+	tcl? ( >=dev-tcltk/itcl-3.2 )
+	tk? ( >=dev-tcltk/itk-3.2 )"
 
 src_unpack() {
 	if [ "$PV" == "9999" ]; then
@@ -67,12 +66,7 @@ src_configure() {
 	use amd64 && myconf="${myconf} --enable-64bit"
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
 	use debug && append-cxxflags "-DCACHE_REF_DEBUG"
-	econf ${myconf} || die "configure failed"
-	emake || die "emake failed"
-}
-
-src_compile() {
-	emake || die "emake failed"
+	econf ${myconf}
 }
 
 src_install() {



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-06-23  9:31 Justin Lecher
  0 siblings, 0 replies; 20+ messages in thread
From: Justin Lecher @ 2011-06-23  9:31 UTC (permalink / raw
  To: gentoo-commits

commit:     f2e7b5afbcd05203a63a7ced22f2ff57f251bd32
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 23 09:23:44 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 23 09:23:44 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f2e7b5af

Streamlined fortran-2 eclass usage

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/staden/ChangeLog                 |    4 ++++
 sci-biology/staden/staden-2.0.0_beta8.ebuild |    3 ++-
 sci-biology/staden/staden-9999.ebuild        |    3 ++-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index fa96390..1bf6d72 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -6,6 +6,10 @@
   staden-9999.ebuild:
   Streamlined fortran-2 eclass usage
 
+  23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
+  staden-9999.ebuild:
+  Streamlined fortran-2 eclass usage
+
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
   staden-9999.ebuild:
   Added fortran-2.eclass support

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
index 993be4c..f4f2411 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -31,7 +31,8 @@ DEPEND="
 	>=media-libs/libpng-1.2
 	sci-biology/samtools
 	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2"
+	>=sys-libs/zlib-1.2
+	virtual/fortran"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 3add863..47f7694 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -34,7 +34,8 @@ DEPEND="
 	>=media-libs/libpng-1.2
 	sci-biology/samtools
 	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2"
+	>=sys-libs/zlib-1.2
+	virtual/fortran"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-06-23  9:31 Justin Lecher
  0 siblings, 0 replies; 20+ messages in thread
From: Justin Lecher @ 2011-06-23  9:31 UTC (permalink / raw
  To: gentoo-commits

commit:     0a1e03d17371b6e44f2b7816e6db2ea86ec76ecb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 23 09:22:43 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 23 09:22:43 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a1e03d1

Streamlined fortran-2 eclass usage

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/staden/ChangeLog                 |    4 ++++
 sci-biology/staden/staden-2.0.0_beta8.ebuild |   20 +++++++++-----------
 sci-biology/staden/staden-9999.ebuild        |   23 +++++++++++------------
 3 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 6064fae..fa96390 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
+  staden-9999.ebuild:
+  Streamlined fortran-2 eclass usage
+
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
   staden-9999.ebuild:
   Added fortran-2.eclass support

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
index a5d9990..993be4c 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -4,10 +4,10 @@
 
 EAPI=3
 
-inherit eutils fortran-2 flag-o-matic base multilib
+inherit base eutils flag-o-matic fortran-2 multilib
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden"
+HOMEPAGE="http://sourceforge.net/projects/staden/"
 SRC_URI="
 	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
 	http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
@@ -15,27 +15,23 @@ SRC_URI="
 LICENSE="staden"
 SLOT="0"
 KEYWORDS="~x86 ~amd64"
-IUSE="debug fortran X png curl tcl tk zlib"
+IUSE="curl debug fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
 # edit src/mk/linux.mk accordingly
-
 #
 # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
 #
 #
 #
 DEPEND="
+	app-arch/xz-utils
 	dev-lang/tk
 	dev-tcltk/tklib
-	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2
 	>=media-libs/libpng-1.2
 	sci-biology/samtools
-	>=app-arch/xz-utils-4.999"
-
-# maybe we should depend on app-arch/lzma or app-arch/xz-utils?
-
+	>=sci-libs/io_lib-1.12.2
+	>=sys-libs/zlib-1.2"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
@@ -68,6 +64,8 @@ src_install() {
 	# subsequently, apps linked against /usr/lib/staden can be run because
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
 	# somehow for gap2caf, for example
-	echo 'LDPATH=/usr/$(get_libdir)/staden' > 99staden || die
+	cat >> "${T}"/99staden <<- EOF
+	LDPATH=/usr/$(get_libdir)/staden
+	EOF
 	doenvd 99staden
 }

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 3f78adb..3add863 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -4,23 +4,21 @@
 
 EAPI=3
 
-inherit eutils fortran-2 flag-o-matic base multilib subversion # autotools
+inherit base eutils flag-o-matic fortran-2 multilib subversion
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden"
+HOMEPAGE="http://sourceforge.net/projects/staden/"
 # https://staden.svn.sourceforge.net/svnroot/staden staden
 if [ "$PV" == "9999" ]; then
 	ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk"
-	#KEYWORDS="~amd64 ~x86"
 else
 	SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz"
-	#KEYWORDS="~amd64 ~x86"
 fi
 
 LICENSE="staden"
 SLOT="0"
 KEYWORDS=""
-IUSE="debug fortran X png curl tcl tk zlib"
+IUSE="curl debug fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
 # edit src/mk/linux.mk accordingly
@@ -30,16 +28,13 @@ IUSE="debug fortran X png curl tcl tk zlib"
 #
 #
 DEPEND="
+	app-arch/xz-utils
 	dev-lang/tk
 	dev-tcltk/tklib
-	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2
 	>=media-libs/libpng-1.2
 	sci-biology/samtools
-	>=app-arch/xz-utils-4.999"
-
-# maybe we should depend on app-arch/lzma or app-arch/xz-utils?
-
+	>=sci-libs/io_lib-1.12.2
+	>=sys-libs/zlib-1.2"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
@@ -71,6 +66,10 @@ src_configure() {
 
 src_install() {
 	emake install DESTDIR="${D}" || die "make install failed"
-	echo "STADENROOT="${EPREFIX}"/usr/share/staden" > "${S}"/99staden
+
+	cat >> "${S}"/99staden <<- EOF
+	STADENROOT="${EPREFIX}"/usr/share/staden
+	EOF
+
 	doenvd "${S}"/99staden || die
 }



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-07-08 14:09 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2011-07-08 14:09 UTC (permalink / raw
  To: gentoo-commits

commit:     410e964b0b98cb7d5d4a6e0c74caeb498ea98180
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul  8 14:09:40 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul  8 14:09:40 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=410e964b

sci-biology/staden: Documented that we have to install somehow /usr/share/doc/staden/manual/gap4.index which is looked up when user accesses built-in help menu item

(Portage version: 2.1.10.4/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/staden/ChangeLog                 |    6 ++++++
 sci-biology/staden/staden-2.0.0_beta8.ebuild |    1 +
 sci-biology/staden/staden-9999.ebuild        |    1 +
 3 files changed, 8 insertions(+), 0 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 1bf6d72..243d4e7 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  staden-2.0.0_beta8.ebuild, staden-9999.ebuild:
+  Documented that we have to install somehow
+  /usr/share/doc/staden/manual/gap4.index which is looked up when user accesses
+  built-in help menu item
+
   23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
   staden-9999.ebuild:
   Streamlined fortran-2 eclass usage

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
index f4f2411..88a6147 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -57,6 +57,7 @@ src_configure(){
 }
 
 src_install() {
+	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
 	emake install DESTDIR="${D}" || die "make install failed"
 	#cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
 	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 47f7694..8fc8b94 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -66,6 +66,7 @@ src_configure() {
 }
 
 src_install() {
+	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
 	emake install DESTDIR="${D}" || die "make install failed"
 
 	cat >> "${S}"/99staden <<- EOF



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-12-12 14:01 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2011-12-12 14:01 UTC (permalink / raw
  To: gentoo-commits

commit:     af67cc9273a5089c2c01aba5dc8cf8eed7d5aa3b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 12 14:01:34 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 12 14:01:34 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af67cc92

fix determination of svn-based checkout number required for building

(Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/staden/ChangeLog          |    4 ++++
 sci-biology/staden/staden-9999.ebuild |   11 +++++++++--
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 243d4e7..e98e9ca 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild:
+  fix determination of svn-based checkout number required for building
+  staden-9999.ebuild
+
   08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   staden-2.0.0_beta8.ebuild, staden-9999.ebuild:
   Documented that we have to install somehow

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 8fc8b94..175b343 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -6,6 +6,10 @@ EAPI=3
 
 inherit base eutils flag-o-matic fortran-2 multilib subversion
 
+if [ "$PV" == "9999" ]; then
+	inherit autotools
+fi
+
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden/"
 # https://staden.svn.sourceforge.net/svnroot/staden staden
@@ -17,7 +21,7 @@ fi
 
 LICENSE="staden"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE="curl debug fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
@@ -63,11 +67,14 @@ src_configure() {
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
 	use debug && append-cxxflags "-DCACHE_REF_DEBUG"
 	econf ${myconf}
+	# edit system.mk to place there proper version number of the svn-controlled checkout
+	SVNVERSION=`svnversion ${ESVN_STORE_DIR}/${ESVN_PROJECT}/${ESVN_REPO_URI##*/}`
+	sed -e "s/^SVNVERS.*/SVNVERS = "${SVNVERSION}"/" -i system.mk
 }
 
 src_install() {
 	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
-	emake install DESTDIR="${D}" || die "make install failed"
+	emake install DESTDIR="${D}" SVN_VERSION="${SVNVERSION}" || die "make install failed"
 
 	cat >> "${S}"/99staden <<- EOF
 	STADENROOT="${EPREFIX}"/usr/share/staden



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2011-12-12 14:02 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2011-12-12 14:02 UTC (permalink / raw
  To: gentoo-commits

commit:     2910f64001e37f7b2aa6bae47b4eead792bedd5e
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 12 14:02:45 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 12 14:02:45 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2910f640

removed arches for this -9999 ebuild for sanity

(Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/staden/staden-9999.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 175b343..1759969 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -21,7 +21,7 @@ fi
 
 LICENSE="staden"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE="curl debug fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available



^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2014-01-06 17:41 Justin Lecher
  0 siblings, 0 replies; 20+ messages in thread
From: Justin Lecher @ 2014-01-06 17:41 UTC (permalink / raw
  To: gentoo-commits

commit:     acd93b597aa723d17972af14e053f9b27c42d036
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 17:38:30 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 17:38:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=acd93b59

sci-biology/staden: Punt base.eclass; transfer changes to live ebuild

Package-Manager: portage-2.2.8

---
 sci-biology/staden/ChangeLog                 |  6 ++-
 sci-biology/staden/metadata.xml              | 10 ++--
 sci-biology/staden/staden-2.0.0_beta9.ebuild |  4 +-
 sci-biology/staden/staden-9999.ebuild        | 70 ++++++++++++----------------
 4 files changed, 44 insertions(+), 46 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 0a9092b..84aac83 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/staden
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild,
+  staden-9999.ebuild, metadata.xml:
+  Punt base.eclass; transfer changes to live ebuild
+
 *staden-2.0.0_beta9 (26 Nov 2012)
 
   26 Nov 2012; Justin Lecher <jlec@gentoo.org> -staden-2.0.0_beta8.ebuild,

diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/staden/metadata.xml
+++ b/sci-biology/staden/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>

diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index b1d51c1..90dd7ef 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -78,7 +78,9 @@ src_install() {
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
 	# somehow for gap2caf, for example
 	cat >> "${T}"/99staden <<- EOF
+	STADENROOT="${EPREFIX}"/usr/share/staden
 	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
 	EOF
+
 	doenvd "${T}"/99staden
 }

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 1759969..af6725a 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,23 +1,17 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
-inherit base eutils flag-o-matic fortran-2 multilib subversion
+AUTOTOOLS_AUTORECONF=yes
 
-if [ "$PV" == "9999" ]; then
-	inherit autotools
-fi
+inherit autotools-utils flag-o-matic fortran-2 multilib subversion
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden/"
-# https://staden.svn.sourceforge.net/svnroot/staden staden
-if [ "$PV" == "9999" ]; then
-	ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk"
-else
-	SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz"
-fi
+SRC_URI=""
+ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk"
 
 LICENSE="staden"
 SLOT="0"
@@ -26,59 +20,57 @@ IUSE="curl debug fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
 # edit src/mk/linux.mk accordingly
-
 #
 # this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
 #
 #
+#
 DEPEND="
 	app-arch/xz-utils
 	dev-lang/tk
 	dev-tcltk/tklib
-	>=media-libs/libpng-1.2
+	media-libs/libpng:0
 	sci-biology/samtools
 	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2
-	virtual/fortran"
+	sys-libs/zlib"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
 	tk? ( >=dev-tcltk/itk-3.2 )"
 
-src_unpack() {
-	if [ "$PV" == "9999" ]; then
-		subversion_src_unpack
-		S="${WORKDIR}"/"${P}"/src/ || die
-		cd "${S}" || die
-		./bootstrap || die "bootstrap failed"
-	else
-		unpack ${A} || die
-		S="${WORKDIR}"/staden-2.0.0b7-src || die "Cannot cd ${WORKDIR}/staden-2.0.0b7-src"
-		cd "${S}" || die "Cannot cd ${S}"
-		./bootstrap || die "bootstrap failed"
-	fi
+S="${WORKDIR}"/"${P}"/src/
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	sed \
+		-e 's:svnversion:false:' \
+		-i configure.in || die
+
+	AT_M4DIR=ac_stubs autotools-utils_src_prepare
 }
 
 src_configure() {
-	local myconf
-	use X && myconf=" --with-x"
-	myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK, see http://bugs.gentoo.org/show_bug.cgi?id=311847#c10
-	use amd64 && myconf="${myconf} --enable-64bit"
+	local myeconfargs=()
+	use X && myeconfargs+=( --with-x )
+	myeconfargs+=(
+		--with-tklib=/usr/$(get_libdir)/tklib
+		)
+	use amd64 && myeconfargs+=( --enable-64bit )
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	use debug && append-cxxflags "-DCACHE_REF_DEBUG"
-	econf ${myconf}
+		autotools-utils_src_configure
 	# edit system.mk to place there proper version number of the svn-controlled checkout
-	SVNVERSION=`svnversion ${ESVN_STORE_DIR}/${ESVN_PROJECT}/${ESVN_REPO_URI##*/}`
-	sed -e "s/^SVNVERS.*/SVNVERS = "${SVNVERSION}"/" -i system.mk
+	sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die
 }
 
 src_install() {
 	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
-	emake install DESTDIR="${D}" SVN_VERSION="${SVNVERSION}" || die "make install failed"
+	autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
 
-	cat >> "${S}"/99staden <<- EOF
+	cat >> "${T}"/99staden <<- EOF
 	STADENROOT="${EPREFIX}"/usr/share/staden
+	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
 	EOF
 
-	doenvd "${S}"/99staden || die
+	doenvd "${T}"/99staden
 }


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2014-03-24 13:30 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2014-03-24 13:30 UTC (permalink / raw
  To: gentoo-commits

commit:     26464ebb2bd43d9373d91da92a30eab32959988c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 13:29:06 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 13:29:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=26464ebb

sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we do not have to change ''. Thanks to Justin Lercher for the patch.

Package-Manager: portage-2.2.7

---
 sci-biology/staden/ChangeLog          | 5 ++++-
 sci-biology/staden/staden-9999.ebuild | 4 +---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 84aac83..1b635ed 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild:
+  sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we do
+  not have to change ''. Thanks to Justin Lercher for the patch.
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild,
   staden-9999.ebuild, metadata.xml:
   Punt base.eclass; transfer changes to live ebuild
@@ -35,4 +39,3 @@
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild,
   staden-9999.ebuild:
   Added fortran-2.eclass support
-

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index af6725a..2c1d490 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -11,7 +11,7 @@ inherit autotools-utils flag-o-matic fortran-2 multilib subversion
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden/"
 SRC_URI=""
-ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk"
+ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/src"
 
 LICENSE="staden"
 SLOT="0"
@@ -38,8 +38,6 @@ RDEPEND="${DEPEND}
 	tcl? ( >=dev-tcltk/itcl-3.2 )
 	tk? ( >=dev-tcltk/itk-3.2 )"
 
-S="${WORKDIR}"/"${P}"/src/
-
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
 src_prepare() {


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2015-05-02 16:29 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
  To: gentoo-commits

commit:     f7a47c86b471b35c82be337f6252a1f38ddd5717
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May  2 16:10:32 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May  2 16:10:32 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7a47c86

added PYTHON_USEDEP

Package-Manager: portage-2.2.18

 sci-biology/staden/ChangeLog                 | 6 +++++-
 sci-biology/staden/staden-2.0.0_beta9.ebuild | 2 +-
 sci-biology/staden/staden-9999.ebuild        | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 1b635ed..7612a35 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/staden
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  staden-2.0.0_beta9.ebuild, staden-9999.ebuild:
+  added PYTHON_USEDEP
+
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild:
   sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we do
   not have to change ''. Thanks to Justin Lercher for the patch.

diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index 90dd7ef..68f4a34 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 2c1d490..b9b0767 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2015-05-02 16:29 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
  To: gentoo-commits

commit:     8a4575ff108e373ca08606303eeb36e8f9ae8da0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May  2 16:17:41 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May  2 16:17:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a4575ff

sci-biology/staden: added SLOT operator

Package-Manager: portage-2.2.18

 sci-biology/staden/ChangeLog                 | 4 ++++
 sci-biology/staden/staden-2.0.0_beta9.ebuild | 2 +-
 sci-biology/staden/staden-9999.ebuild        | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 7612a35..e874d29 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -4,6 +4,10 @@
 
   02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   staden-2.0.0_beta9.ebuild, staden-9999.ebuild:
+  sci-biology/staden: added SLOT operator
+
+  02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  staden-2.0.0_beta9.ebuild, staden-9999.ebuild:
   added PYTHON_USEDEP
 
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild:

diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index 68f4a34..152ee6c 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -28,7 +28,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
 #
 DEPEND="
 	app-arch/xz-utils
-	dev-lang/tk
+	dev-lang/tk:*
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index b9b0767..af64ca0 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -27,7 +27,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
 #
 DEPEND="
 	app-arch/xz-utils
-	dev-lang/tk
+	dev-lang/tk:*
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2015-08-07 13:01 Justin Lecher
  0 siblings, 0 replies; 20+ messages in thread
From: Justin Lecher @ 2015-08-07 13:01 UTC (permalink / raw
  To: gentoo-commits

commit:     4f21f572fac94b4541ee55dbf3c6a719144482ad
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug  7 13:01:40 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug  7 13:01:40 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f21f572

sci-biology/staden: Fix SLOT operators, bug #556946

Package-Manager: portage-2.2.20
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/staden/ChangeLog                 | 4 ++++
 sci-biology/staden/staden-2.0.0_beta9.ebuild | 2 +-
 sci-biology/staden/staden-9999.ebuild        | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index e874d29..9dd6b53 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Aug 2015; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild,
+  staden-9999.ebuild:
+  sci-biology/staden: Fix SLOT operators, bug #556946
+
   02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   staden-2.0.0_beta9.ebuild, staden-9999.ebuild:
   sci-biology/staden: added SLOT operator

diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index 152ee6c..fa64a74 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -28,7 +28,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
 #
 DEPEND="
 	app-arch/xz-utils
-	dev-lang/tk:*
+	dev-lang/tk:0=
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index af64ca0..84082e9 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -27,7 +27,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
 #
 DEPEND="
 	app-arch/xz-utils
-	dev-lang/tk:*
+	dev-lang/tk:0=
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2016-03-23 19:04 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2016-03-23 19:04 UTC (permalink / raw
  To: gentoo-commits

commit:     694eb11ff758972f56126f309b9ed3663eef7f0f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 23 19:04:14 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 23 19:04:14 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=694eb11f

sci-biology/staden: version bump; remove unused USE=curl, introduce USE=doc for a separate package

Package-Manager: portage-2.2.26

 ...en-2.0.0_beta9.ebuild => staden-2.0.0_beta10.ebuild} | 17 ++++++-----------
 sci-biology/staden/staden-9999.ebuild                   |  9 ++++-----
 2 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
similarity index 76%
rename from sci-biology/staden/staden-2.0.0_beta9.ebuild
rename to sci-biology/staden/staden-2.0.0_beta10.ebuild
index 7f86914..b9cfef0 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -9,15 +9,13 @@ AUTOTOOLS_AUTORECONF=yes
 inherit autotools-utils eutils flag-o-matic fortran-2 multilib
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden/"
-SRC_URI="
-	http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz
-	http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
+HOMEPAGE="http://sourceforge.net/projects/staden"
+SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"
 
 LICENSE="staden"
 SLOT="0"
 KEYWORDS="~x86 ~amd64"
-IUSE="curl debug fortran png tcl tk X zlib"
+IUSE="debug doc fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
 # edit src/mk/linux.mk accordingly
@@ -37,7 +35,9 @@ DEPEND="
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )"
+	tk? ( >=dev-tcltk/itk-3.2 )
+	net-misc/curl
+	doc? ( sci-biology/staden_doc )"
 
 S="${WORKDIR}"/staden-${PV/_beta/b}-src
 
@@ -69,10 +69,6 @@ src_configure(){
 
 src_install() {
 	autotools-utils_src_install
-	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
-	#cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src || die "failed to cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src"
-	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
-
 	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
 	# subsequently, apps linked against /usr/lib/staden can be run because
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
@@ -81,6 +77,5 @@ src_install() {
 	STADENROOT="${EPREFIX}"/usr/share/staden
 	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
 	EOF
-
 	doenvd "${T}"/99staden
 }

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index ef3a752..58e92e9 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -16,7 +16,7 @@ ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/sr
 LICENSE="staden"
 SLOT="0"
 KEYWORDS=""
-IUSE="curl debug fortran png tcl tk X zlib"
+IUSE="debug doc fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
 # edit src/mk/linux.mk accordingly
@@ -36,7 +36,9 @@ DEPEND="
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )"
+	tk? ( >=dev-tcltk/itk-3.2 )
+	net-misc/curl
+	doc? ( sci-biology/staden_doc )"
 
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
@@ -62,13 +64,10 @@ src_configure() {
 }
 
 src_install() {
-	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
 	autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
-
 	cat >> "${T}"/99staden <<- EOF
 	STADENROOT="${EPREFIX}"/usr/share/staden
 	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
 	EOF
-
 	doenvd "${T}"/99staden
 }


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2016-03-25 16:39 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2016-03-25 16:39 UTC (permalink / raw
  To: gentoo-commits

commit:     2c1c899d5aef1ce1932a9d052a80ef63b4b76938
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 25 16:38:47 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 25 16:38:47 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c1c899d

sci-biology/staden: io_lib/bam.h appeared first in io_lib-1.13.8

Package-Manager: portage-2.2.26

 sci-biology/staden/staden-2.0.0_beta10.ebuild | 3 ++-
 sci-biology/staden/staden-9999.ebuild         | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index d14c042..b2a2b13 100644
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -24,13 +24,14 @@ IUSE="debug doc fortran png tcl tk X zlib"
 #
 #
 #
+
 DEPEND="
 	app-arch/xz-utils
 	dev-lang/tk:0=
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools
-	>=sci-libs/io_lib-1.12.2
+	>=sci-libs/io_lib-1.13.8
 	sys-libs/zlib"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 58e92e9..37a6a93 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -31,7 +31,7 @@ DEPEND="
 	dev-tcltk/tklib
 	media-libs/libpng:0
 	sci-biology/samtools
-	>=sci-libs/io_lib-1.12.2
+	>=sci-libs/io_lib-1.13.8
 	sys-libs/zlib"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2016-03-25 17:28 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2016-03-25 17:28 UTC (permalink / raw
  To: gentoo-commits

commit:     f1f4beff666e399956c2f733a99dbaac9a573427
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 25 17:27:42 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 25 17:27:42 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1f4beff

sci-biology/staden: add a note about some tutorial available

Package-Manager: portage-2.2.26

 sci-biology/staden/staden-2.0.0_beta10.ebuild | 4 ++++
 sci-biology/staden/staden-9999.ebuild         | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index b2a2b13..9ddda96 100644
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -79,3 +79,7 @@ src_install() {
 	EOF
 	doenvd "${T}"/99staden
 }
+
+pkg_postinst(){
+	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
+}

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 37a6a93..8ebdc03 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -71,3 +71,7 @@ src_install() {
 	EOF
 	doenvd "${T}"/99staden
 }
+
+pkg_postinst(){
+	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
+}


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2016-04-01 14:19 Marius Brehler
  0 siblings, 0 replies; 20+ messages in thread
From: Marius Brehler @ 2016-04-01 14:19 UTC (permalink / raw
  To: gentoo-commits

commit:     cf0b1de6b656ee7f00dfd199d98970c562828e1f
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Apr  1 14:17:24 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Apr  1 14:17:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf0b1de6

sci-biology/staden: Fix copyright and dependcies

Package-Manager: portage-2.2.26
RepoMan-Options: --force

 sci-biology/staden/staden-2.0.0_beta10.ebuild | 4 ++--
 sci-biology/staden/staden-9999.ebuild         | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index 9ddda96..942b533 100644
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.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
 # $Id$
 
@@ -30,7 +30,7 @@ DEPEND="
 	dev-lang/tk:0=
 	dev-tcltk/tklib
 	media-libs/libpng:0
-	sci-biology/samtools
+	sci-biology/samtools:0
 	>=sci-libs/io_lib-1.13.8
 	sys-libs/zlib"
 RDEPEND="${DEPEND}

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 8ebdc03..b785ba6 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.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
 # $Id$
 
@@ -30,7 +30,7 @@ DEPEND="
 	dev-lang/tk:0=
 	dev-tcltk/tklib
 	media-libs/libpng:0
-	sci-biology/samtools
+	sci-biology/samtools:0
 	>=sci-libs/io_lib-1.13.8
 	sys-libs/zlib"
 RDEPEND="${DEPEND}


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2016-04-01 14:19 Marius Brehler
  0 siblings, 0 replies; 20+ messages in thread
From: Marius Brehler @ 2016-04-01 14:19 UTC (permalink / raw
  To: gentoo-commits

commit:     8f655583a96557445a62a25d7fecb3c52f791c30
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Apr  1 14:18:24 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Apr  1 14:18:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f655583

sci-biology/staden: Drop keywords since keywords were droped for staden_doc

Package-Manager: portage-2.2.26

 sci-biology/staden/staden-2.0.0_beta10.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index 942b533..bc5dab7 100644
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz
 
 LICENSE="staden"
 SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS=""
 IUSE="debug doc fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2019-10-22 10:52 Martin Mokrejs
  0 siblings, 0 replies; 20+ messages in thread
From: Martin Mokrejs @ 2019-10-22 10:52 UTC (permalink / raw
  To: gentoo-commits

commit:     cad3d25dae697461e1a6d295f2bdf99e9c2f626a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 22 10:51:46 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 22 10:51:46 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cad3d25d

sci-biology/staden: sourceforge moved SVN repo URL

Also, somehow I cannot set "${S}" to src because svn would checkout the
source tree there, so one would need ./src/src to access configure.in.
Overwriting "${S}" inside each function helps.

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/staden/staden-9999.ebuild | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 0253c9eb5..4be43217f 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -9,8 +9,7 @@ inherit autotools-utils flag-o-matic fortran-2 multilib subversion
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden/"
-SRC_URI=""
-ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/src"
+ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk"
 
 LICENSE="staden"
 SLOT="0"
@@ -42,6 +41,7 @@ RDEPEND="${DEPEND}
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
 src_prepare() {
+	cd "${WORKDIR}"/"${P}"/src || die
 	sed \
 		-e 's:svnversion:false:' \
 		-i configure.in || die
@@ -50,6 +50,8 @@ src_prepare() {
 }
 
 src_configure() {
+	cd "${WORKDIR}"/"${P}"/src || die
+	S="${WORKDIR}"/"${P}"/src
 	local myeconfargs=()
 	use X && myeconfargs+=( --with-x )
 	myeconfargs+=(
@@ -62,7 +64,15 @@ src_configure() {
 	sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die
 }
 
+src_compile(){
+	cd "${WORKDIR}"/"${P}"/src || die
+	S="${WORKDIR}"/"${P}"/src
+	default
+}
+
 src_install() {
+	cd "${WORKDIR}"/"${P}"/src || die
+	S="${WORKDIR}"/"${P}"/src
 	autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
 	cat >> "${T}"/99staden <<- EOF
 	STADENROOT="${EPREFIX}"/usr/share/staden


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2021-01-18 15:32 Andrew Ammerlaan
  0 siblings, 0 replies; 20+ messages in thread
From: Andrew Ammerlaan @ 2021-01-18 15:32 UTC (permalink / raw
  To: gentoo-commits

commit:     d02fe7fbe1b779c21cf1fed579d8fc4494f967d5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 18 15:32:24 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Jan 18 15:32:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d02fe7fb

sci-biology/staden: EAPI bump

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/staden/staden-2.0.0_beta10.ebuild | 84 ---------------------------
 sci-biology/staden/staden-2.0.0_beta11.ebuild | 30 ++++------
 sci-biology/staden/staden-9999.ebuild         | 45 +++++---------
 3 files changed, 26 insertions(+), 133 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
deleted file mode 100644
index 53c4d2212..000000000
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils eutils flag-o-matic fortran-2 multilib
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
-	app-arch/xz-utils
-	dev-lang/tk:0=
-	dev-tcltk/tklib
-	media-libs/libpng:0
-	sci-biology/samtools:0
-	>=sci-libs/io_lib-1.13.8
-	sys-libs/zlib"
-RDEPEND="${DEPEND}
-	>=dev-tcltk/iwidgets-4.0
-	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )
-	net-misc/curl
-	doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-src
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
-	"${FILESDIR}"/${P}-zlib.patch )
-
-src_prepare() {
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	autotools-utils_src_configure
-}
-
-src_install() {
-	autotools-utils_src_install
-	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
-	# subsequently, apps linked against /usr/lib/staden can be run because
-	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
-	# somehow for gap2caf, for example
-	cat >> "${T}"/99staden <<- EOF
-	STADENROOT="${EPREFIX}"/usr/share/staden
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
-	EOF
-	doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
-	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}

diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
index b8e5425c7..523f8bf05 100644
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils eutils flag-o-matic fortran-2 multilib
+inherit flag-o-matic fortran-2 multilib
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="https://sourceforge.net/projects/staden"
@@ -41,31 +39,27 @@ RDEPEND="${DEPEND}
 
 S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-PATCHES=("${FILESDIR}"/${P}-ldflags.patch)
+PATCHES=(
+	"${FILESDIR}"/${P}-ldflags.patch
+)
 
 src_prepare() {
+	default
 	sed \
 		-e 's:svnversion:false:' \
 		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
 }
 
 src_configure(){
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	autotools-utils_src_configure
+	econf \
+		$(use_enable X x)
+		$(use_enable amd64 64bit)
+		--with-tklib=/usr/$(get_libdir)/tklib
 }
 
 src_install() {
-	autotools-utils_src_install
+	default
 	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
 	# subsequently, apps linked against /usr/lib/staden can be run because
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index 961155bf6..c18aea8cc 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils flag-o-matic fortran-2 multilib subversion
+inherit flag-o-matic fortran-2 multilib subversion
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
 HOMEPAGE="https://sourceforge.net/projects/staden/"
@@ -38,42 +36,27 @@ RDEPEND="${DEPEND}
 	net-misc/curl
 	doc? ( sci-biology/staden_doc )"
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
 src_prepare() {
-	cd "${WORKDIR}"/"${P}"/src || die
+	default
 	sed \
 		-e 's:svnversion:false:' \
 		-i configure.in || die
-
-	AT_M4DIR=ac_stubs autotools-utils_src_prepare
 }
 
-src_configure() {
-	cd "${WORKDIR}"/"${P}"/src || die
-	S="${WORKDIR}"/"${P}"/src
-	local myeconfargs=()
-	use X && myeconfargs+=( --with-x )
-	myeconfargs+=(
-		--with-tklib=/usr/$(get_libdir)/tklib
-		)
-	use amd64 && myeconfargs+=( --enable-64bit )
+src_configure(){
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
-		autotools-utils_src_configure
-	# edit system.mk to place there proper version number of the svn-controlled checkout
-	sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die
-}
-
-src_compile(){
-	cd "${WORKDIR}"/"${P}"/src || die
-	S="${WORKDIR}"/"${P}"/src
-	default
+	econf \
+		$(use_enable X x)
+		$(use_enable amd64 64bit)
+		--with-tklib=/usr/$(get_libdir)/tklib
 }
 
 src_install() {
-	cd "${WORKDIR}"/"${P}"/src || die
-	S="${WORKDIR}"/"${P}"/src
-	autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
+	default
+	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
+	# subsequently, apps linked against /usr/lib/staden can be run because
+	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
+	# somehow for gap2caf, for example
 	cat >> "${T}"/99staden <<- EOF
 	STADENROOT="${EPREFIX}"/usr/share/staden
 	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"


^ permalink raw reply related	[flat|nested] 20+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/
@ 2021-02-03  8:24 Andrew Ammerlaan
  0 siblings, 0 replies; 20+ messages in thread
From: Andrew Ammerlaan @ 2021-02-03  8:24 UTC (permalink / raw
  To: gentoo-commits

commit:     993814b38eec8da6e9bf112ec45aa380410a08c7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb  3 08:24:44 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb  3 08:24:44 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=993814b3

sci-biology/staden: fix configure phase

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/staden/staden-2.0.0_beta11.ebuild | 10 +++++-----
 sci-biology/staden/staden-9999.ebuild         |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
index 523f8bf05..d6b1b8de1 100644
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.
 
 LICENSE="staden"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE="debug doc fortran png tcl tk X zlib"
 
 # either g77 or gfortran must be available
@@ -40,7 +40,7 @@ RDEPEND="${DEPEND}
 S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
 
 PATCHES=(
-	"${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}/${P}-ldflags.patch"
 )
 
 src_prepare() {
@@ -53,9 +53,9 @@ src_prepare() {
 src_configure(){
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
 	econf \
-		$(use_enable X x)
-		$(use_enable amd64 64bit)
-		--with-tklib=/usr/$(get_libdir)/tklib
+		$(use_enable X x) \
+		$(use_enable amd64 64bit) \
+		--with-tklib="/usr/$(get_libdir)/tklib"
 }
 
 src_install() {

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index c18aea8cc..7b61a0fa0 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -46,9 +46,9 @@ src_prepare() {
 src_configure(){
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
 	econf \
-		$(use_enable X x)
-		$(use_enable amd64 64bit)
-		--with-tklib=/usr/$(get_libdir)/tklib
+		$(use_enable X x) \
+		$(use_enable amd64 64bit) \
+		--with-tklib="/usr/$(get_libdir)/tklib"
 }
 
 src_install() {


^ permalink raw reply related	[flat|nested] 20+ messages in thread

end of thread, other threads:[~2021-02-03  8:24 UTC | newest]

Thread overview: 20+ messages (download: mbox.gz follow: Atom feed
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2011-12-12 14:01 [gentoo-commits] proj/sci:master commit in: sci-biology/staden/ Martin Mokrejs
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2021-02-03  8:24 Andrew Ammerlaan
2021-01-18 15:32 Andrew Ammerlaan
2019-10-22 10:52 Martin Mokrejs
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2016-04-01 14:19 Marius Brehler
2016-03-25 17:28 Martin Mokrejs
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2014-01-06 17:41 Justin Lecher
2011-12-12 14:02 Martin Mokrejs
2011-07-08 14:09 Martin Mokrejs
2011-06-23  9:31 Justin Lecher
2011-06-23  9:31 Justin Lecher
2011-06-21 11:54 Justin Lecher
2011-03-06 21:20 Martin Mokrejs

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