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

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

[Andrew Ammerlaan]

commit:     eb68f5ca4d8266b2137e914bc287988d2fdbf72d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 15:38:07 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 15:38:07 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb68f5ca

sci-biology/staden: drop live

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../staden/files/staden-2.0.0_beta10-ldflags.patch | 30 ----------
 .../staden/files/staden-2.0.0_beta10-zlib.patch    | 16 -----
 sci-biology/staden/staden-9999.ebuild              | 69 ----------------------
 3 files changed, 115 deletions(-)

diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- 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/files/staden-2.0.0_beta10-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
deleted file mode 100644
index 39537604e..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- gap5/zfio.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/gap5/zfio.c b/gap5/zfio.c
-index 35da12a..1b628e4 100644
---- a/gap5/zfio.c
-+++ b/gap5/zfio.c
-@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
- 	if (c != EOF)
- 	    ungetc(c, zf->fp);
-     } else {
--	c = gzgetc(zf->gz);
-+	c = gzgetc((gzFile)zf->gz);
- 	if (c != EOF)
- 	    gzungetc(c, zf->gz);
-     }

diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
deleted file mode 100644
index b2ed35724..000000000
--- a/sci-biology/staden/staden-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2 subversion
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden/"
-ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk"
-
-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 )"
-
-src_prepare() {
-	default
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-}
-
-src_configure(){
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	econf \
-		$(use_enable X x) \
-		$(use_enable amd64 64bit) \
-		--with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-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'
-	# 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"
-}