* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/
@ 2011-02-15 23:43 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2011-02-15 23:43 UTC (permalink / raw
To: gentoo-commits
commit: 0556e6d156adfe70616199e629fe3bbc20fceff7
Author: Martin Mokrejs <mmokrejs <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 15 23:43:34 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 15 23:43:34 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0556e6d1
sci-biology/staden-2.0.0_beta8: new release
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/staden/files/rpath.patch | 123 ++++++++++++++++++++
...aden-2.0.0.ebuild => staden-2.0.0_beta8.ebuild} | 18 ++-
2 files changed, 134 insertions(+), 7 deletions(-)
diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch
new file mode 100644
index 0000000..7bda217
--- /dev/null
+++ b/sci-biology/staden/files/rpath.patch
@@ -0,0 +1,123 @@
+diff -cr staden-2.0.0b8-src/ac_stubs/tcl.m4 staden-2.0.0b8-src.orig/ac_stubs/tcl.m4
+*** staden-2.0.0b8-src/ac_stubs/tcl.m4 Wed Feb 9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/ac_stubs/tcl.m4 Tue Feb 15 15:12:37 2011
+***************
+*** 2245,2250 ****
+--- 2245,2252 ----
+
+ AC_SUBST(LD_LIBRARY_PATH_VAR)
+
++ AC_SUBST(CC_SEARCH_FLAGS)
++
+ # These must be called after we do the basic CFLAGS checks and
+ # verify any possible 64-bit or similar switches are necessary
+ TEA_TCL_EARLY_FLAGS
+diff -cr staden-2.0.0b8-src/configure staden-2.0.0b8-src.orig/configure
+*** staden-2.0.0b8-src/configure Wed Feb 9 11:39:59 2011
+--- staden-2.0.0b8-src.orig/configure Tue Feb 15 15:12:37 2011
+***************
+*** 745,750 ****
+--- 745,751 ----
+ SHLIB_LD_LIBS
+ SHLIB_CFLAGS
+ LD_LIBRARY_PATH_VAR
++ CC_SEARCH_FLAGS
+ TCL_INCLUDES
+ TCL_TOP_DIR_NATIVE
+ TK_INCLUDES
+***************
+*** 13888,13893 ****
+--- 13889,13896 ----
+
+
+
++
++
+ # These must be called after we do the basic CFLAGS checks and
+ # verify any possible 64-bit or similar switches are necessary
+
+***************
+*** 15886,15891 ****
+--- 15889,15895 ----
+ SHLIB_LD_LIBS!$SHLIB_LD_LIBS$ac_delim
+ SHLIB_CFLAGS!$SHLIB_CFLAGS$ac_delim
+ LD_LIBRARY_PATH_VAR!$LD_LIBRARY_PATH_VAR$ac_delim
++ CC_SEARCH_FLAGS!$CC_SEARCH_FLAGS$ac_delim
+ TCL_INCLUDES!$TCL_INCLUDES$ac_delim
+ TCL_TOP_DIR_NATIVE!$TCL_TOP_DIR_NATIVE$ac_delim
+ TK_INCLUDES!$TK_INCLUDES$ac_delim
+***************
+*** 15905,15911 ****
+ LTLIBOBJS!$LTLIBOBJS$ac_delim
+ _ACEOF
+
+! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 53; then
+ break
+ elif $ac_last_try; then
+ { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+--- 15909,15915 ----
+ LTLIBOBJS!$LTLIBOBJS$ac_delim
+ _ACEOF
+
+! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 54; then
+ break
+ elif $ac_last_try; then
+ { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+diff -cr staden-2.0.0b8-src/staden.profile staden-2.0.0b8-src.orig/staden.profile
+*** staden-2.0.0b8-src/staden.profile Wed Feb 9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/staden.profile Tue Feb 15 15:12:37 2011
+***************
+*** 46,54 ****
+ then
+ [ x"$STADEN_PREPEND" != "x" ] \
+ && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
+! || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB
+ else
+! LD_LIBRARY_PATH=$STADLIB
+ fi
+ export LD_LIBRARY_PATH
+ fi
+--- 46,54 ----
+ then
+ [ x"$STADEN_PREPEND" != "x" ] \
+ && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
+! || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB:$STADENROOT/lib
+ else
+! LD_LIBRARY_PATH=$STADLIB:$STADENROOT/lib
+ fi
+ export LD_LIBRARY_PATH
+ fi
+diff -cr staden-2.0.0b8-src/system.mk.in staden-2.0.0b8-src.orig/system.mk.in
+*** staden-2.0.0b8-src/system.mk.in Wed Feb 9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/system.mk.in Tue Feb 15 15:12:37 2011
+***************
+*** 61,66 ****
+--- 61,67 ----
+ # How else do we get commas in a subst text or pattern?
+ comma = ,
+
++ LIB_RUNTIME_DIR = ${prefix}/lib/staden
+ CC = @CC@
+ #CDEBUG = -Wall -Wno-sign-compare -Wno-pointer-sign -Wno-parentheses -Wno-unused -Wno-char-subscripts -Wno-pointer-to-int-cast -Wno-int-to-pointer-cast
+ CFLAGS = @CFLAGS@ $(DEFINES) $(INCLUDES)
+***************
+*** 68,76 ****
+ CXXFLAGS = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
+ CPP = @CPP@
+ CPPFLAGS = @CPPFLAGS@
+! LDFLAGS = -L$(L) @LDFLAGS@
+ #CLDFLAGS = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
+! CLDFLAGS = -L$(L)
+ CXXLDFLAGS = $(CLDFLAGS)
+ F77 = @F77@
+ FFLAGS = @FFLAGS@
+--- 69,77 ----
+ CXXFLAGS = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
+ CPP = @CPP@
+ CPPFLAGS = @CPPFLAGS@
+! LDFLAGS = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
+ #CLDFLAGS = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
+! CLDFLAGS = -L$(L) @CC_SEARCH_FLAGS@
+ CXXLDFLAGS = $(CLDFLAGS)
+ F77 = @F77@
+ FFLAGS = @FFLAGS@
diff --git a/sci-biology/staden/staden-2.0.0.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
similarity index 64%
rename from sci-biology/staden/staden-2.0.0.ebuild
rename to sci-biology/staden/staden-2.0.0_beta8.ebuild
index 3678c92..a79bfd2 100644
--- a/sci-biology/staden/staden-2.0.0.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -6,9 +6,10 @@ EAPI=3
inherit eutils flag-o-matic base
-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"
-SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-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"
@@ -38,11 +39,12 @@ RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
tk? ( >=dev-tcltk/itk-3.2 )
>=dev-tcltk/iwidgets-4.0"
-S="${WORKDIR}"/staden-2.0.0b7-src
+S="${WORKDIR}"/staden-2.0.0b8-src
-src_unpack() {
- unpack ${A}
- cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b7-src"
+src_prepare() {
+ unpack ${A} || die
+ cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b8-src"
+ epatch "${FILESDIR}"/rpath.patch || die "failed to apply -rpath=/usr/lib/staden patch"
./bootstrap || die "bootstrap failed"
}
@@ -61,4 +63,6 @@ src_compile() {
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"
}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/
@ 2016-03-25 16:22 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-03-25 16:22 UTC (permalink / raw
To: gentoo-commits
commit: 60fc8171be2882a2861b36fab0c7333cc349fb57
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 25 16:22:20 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 25 16:22:20 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=60fc8171
sci-biology/staden: rename patch files; remove unnecessary patch
Package-Manager: portage-2.2.26
...9-ldflags.patch => staden-2.0.0_beta10-ldflags.patch} | 0
...0_beta9-zlib.patch => staden-2.0.0_beta10-zlib.patch} | 0
.../staden/files/staden-2.0.0_beta9-libpng-1.5.patch | 16 ----------------
sci-biology/staden/staden-2.0.0_beta10.ebuild | 1 -
4 files changed, 17 deletions(-)
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
similarity index 100%
rename from sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
rename to sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
similarity index 100%
rename from sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
rename to sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
deleted file mode 100644
index 50694a8..0000000
--- a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- tk_utils/tkTrace.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tk_utils/tkTrace.c b/tk_utils/tkTrace.c
-index beeb478..42a4e11 100644
---- a/tk_utils/tkTrace.c
-+++ b/tk_utils/tkTrace.c
-@@ -2123,7 +2123,7 @@ int drawable_to_png(DNATrace *t, FILE *fp, Display *disp, Drawable d,
- goto error;
-
- /* PNG requires setjmp/longjmp to be used */
-- if (setjmp(png_ptr->jmpbuf))
-+ if (setjmp (png_jmpbuf (png_ptr)))
- goto error;
-
- /* Create the info bits */
diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index b9cfef0..d14c042 100644
--- a/sci-biology/staden/staden-2.0.0_beta10.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -45,7 +45,6 @@ AUTOTOOLS_IN_SOURCE_BUILD=1
PATCHES=(
"${FILESDIR}"/${P}-ldflags.patch
- "${FILESDIR}"/${P}-libpng-1.5.patch
"${FILESDIR}"/${P}-zlib.patch )
src_prepare() {
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/
@ 2016-07-31 20:37 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-07-31 20:37 UTC (permalink / raw
To: gentoo-commits
commit: 87faa2f0b78c074a433f5ff20612b34b7b8c4557
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 20:36:50 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 20:36:50 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87faa2f0
sci-biology/staden: version bump, beta10-zlib.patch patch not needed now
Package-Manager: portage-2.3.0
.../staden/files/staden-2.0.0_beta11-ldflags.patch | 30 ++++++++
sci-biology/staden/staden-2.0.0_beta11.ebuild | 83 ++++++++++++++++++++++
2 files changed, 113 insertions(+)
diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
new file mode 100644
index 0000000..735feb3
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
@@ -0,0 +1,30 @@
+ abi/Makefile | 2 +-
+ alf/Makefile | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/abi/Makefile b/abi/Makefile
+index 3c1f8fb..58b4353 100644
+--- a/abi/Makefile
++++ b/abi/Makefile
+@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
+ $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
+
+ getABIdate: $(OBJSD)
+- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
++ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
+
+ getABIcomment: $(OBJSC)
+ $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
+diff --git a/alf/Makefile b/alf/Makefile
+index 94b7480..ef41a26 100644
+--- a/alf/Makefile
++++ b/alf/Makefile
+@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
+ ALFOBJ = alfsplit.o
+
+ alfsplit: $(ALFOBJ)
+- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
++ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
+
+ RSOBJ = $(ALFBIN)/2rs.o
+
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
new file mode 100644
index 0000000..8094672
--- /dev/null
+++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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="http://sourceforge.net/projects/staden"
+SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
+
+LICENSE="staden"
+SLOT="0"
+KEYWORDS=""
+IUSE="debug doc fortran png tcl tk X zlib"
+
+# either g77 or gfortran must be available
+# edit src/mk/linux.mk accordingly
+#
+# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
+#
+#
+#
+
+DEPEND="
+ app-arch/xz-utils
+ dev-lang/tk:0=
+ dev-tcltk/tklib
+ media-libs/libpng:0
+ sci-biology/samtools:0
+ >=sci-libs/io_lib-1.13.8
+ sys-libs/zlib"
+RDEPEND="${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}-2016-src
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+PATCHES=("${FILESDIR}"/${P}-ldflags.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"
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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