Adding metadata

4 files changed, 0 insertions, 150 deletions

diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
deleted file mode 100644
index 97873ce451cf..000000000000
--- a/sci-biology/embassy-esim4/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST embassy-esim4-1.0.0.660.tar.gz 473261 BLAKE2B d15029b0723dd739fa9208f9b0ffd7814cbddc630ca2ff15955412f493f7983753acf82bcc8a3fc6ddfd49abe630982ead377e6941dcbff44ddc5d8ab4e7d6e5 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
deleted file mode 100644
index 940abbd9e388..000000000000
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
-
-inherit autotools emboss-r3 flag-o-matic
-
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/ESIM4-1.0.0.650"
-PATCHES=( "${FILESDIR}"/${PN}-1.0.0.650_fix-build-system.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# -Werror=lto-type-mismatch
-	# https://bugs.gentoo.org/862258
-	#
-	# Upstream is dead since 2013.
-	filter-lto
-
-	emboss-r3_src_configure
-}
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
deleted file mode 100644
index 7ffa00c52f75..000000000000
--- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch
+++ /dev/null
@@ -1,110 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -635,33 +635,6 @@
- 
- 
- 
--dnl PCRE library definitions - see the MAJOR and MINOR values
--dnl to see which version's configure.in these lines come from
--
--dnl Provide the current PCRE version information. Do not use numbers
--dnl with leading zeros for the minor version, as they end up in a C
--dnl macro, and may be treated as octal constants. Stick to single
--dnl digits for minor numbers less than 10. There are unlikely to be
--dnl that many releases anyway.
--
--PCRE_MAJOR="7"
--PCRE_MINOR="9"
--PCRE_DATE="11-Apr-2009"
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}"
--
--dnl Default values for miscellaneous macros
--
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10"
--
--dnl Provide versioning information for libtool shared libraries that
--dnl are built by default on Unix systems.
--
--PCRE_LIB_VERSION="0:1:0"
--PCRE_POSIXLIB_VERSION="0:0:0"
--
--
--
--
- dnl FIXME: This does no longer seem required with Autoconf 2.67?
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place
- dnl AS_IF([test "x${with_x}" != "xno"],
-@@ -737,21 +710,6 @@
- 
- 
- 
--dnl "Export" these variables for PCRE
--
--AC_SUBST([HAVE_MEMMOVE])
--AC_SUBST([HAVE_STRERROR])
--AC_SUBST([PCRE_MAJOR])
--AC_SUBST([PCRE_MINOR])
--AC_SUBST([PCRE_DATE])
--AC_SUBST([PCRE_VERSION])
--AC_SUBST([PCRE_LIB_VERSION])
--AC_SUBST([PCRE_POSIXLIB_VERSION])
--AC_SUBST([POSIX_MALLOC_THRESHOLD])
--
--
--
--
- dnl Test if --enable-localforce given
- locallink="no"
- embprefix="/usr/local"
-@@ -874,6 +832,13 @@
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
- 
- 
-+AS_IF([test "x${enable_systemlibs}" = "xyes"],
-+[
-+dnl using system libraries
-+  PKG_CHECK_MODULES([PLPLOT], [plplotd],
-+  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
-+  )
-+])
- 
- 
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
---- a/emboss_acd/Makefile.am
-+++ b/emboss_acd/Makefile.am
-@@ -1,3 +1,3 @@
- 
--pkgdata_DATA = *.acd
-+pkgdata_DATA = $(srcdir)/*.acd
- pkgdatadir=$(prefix)/share/EMBOSS/acd
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -17,9 +17,7 @@
- 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
- 	-I../../../ajax/acd -I../../../plplot
- else
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
--	$(NLINCLUDES) \
--	-I${embprefix}/include/epcre
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
- endif
- 
- if ISSHARED
-@@ -34,7 +32,7 @@
- -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \
-  $(NLAIXLIBS) -leplplot
- else
--AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \
-+AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -lnucleus -lacd \
- -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot
- endif
- endif
-@@ -62,6 +60,6 @@
- 	../../../plplot/libeplplot.la \
- 	$(XLIB)
- else
--LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
--        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
-+LDADD = -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
-+        -lajax $(NLADD) $(XLIB)
- endif
diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
deleted file mode 100644
index 55784cd1ea18..000000000000
--- a/sci-biology/embassy-esim4/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">emboss</remote-id>
-  </upstream>
-</pkgmetadata>