reinit the tree, so we can have metadata

4 files changed, 145 insertions, 0 deletions

diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest
new file mode 100644
index 000000000000..7d8b7b7889e9
--- /dev/null
+++ b/sci-biology/embassy-vienna/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-vienna-1.7.2.650_fix-build-system.patch 3083 SHA256 0831ff5582301bb74750a5c4b7006b5ccfb7dfeeaa4c5772c051ed628715a390 SHA512 b09ea9adcc9da002a83e431ff4f3f48075bd885bd35b5690a21ed7d120835a5fa9eaf566fecfd916897e18d539ccc7ea1c8640759996e4979865556eaf8dccb2 WHIRLPOOL 1ca51a2336916b491eb26b846f0810d8ecd722ed9552c1faa83d360a94e8724cb50be3873788e67c05ef10368c43985fde61a61ecb765261195a4eab90289e8c
+DIST embassy-vienna-1.7.2.660.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2
+EBUILD embassy-vienna-1.7.2.660.ebuild 436 SHA256 df9e13e427b920830067db610d4e1165d0f4adaa0e7970e04a83f7f5320960f0 SHA512 009ad16069bd0a8134a705a82a2d1ee5a3b5de28d434870e9b7298e64885a8c76f1c604432b2d0808d6f4653906e211b6c848496bbefd0c4324d698fb8285ec3 WHIRLPOOL b007cccee75f2b5ad1b2c8dfbe2a64cc510de3accc86c0419699303727cdd881ce190c97967b5e9d08218a13a699318909ffb99c5d892e2b355c506c3a56fe45
+MISC ChangeLog 3854 SHA256 b48b7425e67aa4ff49d83c33f50413c2d783f08d4b2426b6ea2d2c99f5d9509d SHA512 4ded7e01a2a4574c210d7de8baffed5a696489b6a6715fc75cba19c19c987593a5b600c2d24b535310f2f1364952a95eea77c75e540f4634aa09224cf15ceb69 WHIRLPOOL 2b2c4aa1ead8586d396b1b895574107300bbaa1d515ec1287431b74e45830d6998f16fa24ee0b1dcc741885749db8c3dfe00b40ea108e77b5651159c116ba5c2
+MISC ChangeLog-2015 2134 SHA256 4ce8df30009ff6337fa540ba1ad4ae9478c67968b46048a3dcb3ab2a1c2eb0b2 SHA512 55156fd3adf143e66a1f93578657c70ecd3e54134d238e07e094e2344b842bb8df0f5346eb8e7f92257e751f50b06e643c282551b8eed4a3eca661eb11dce810 WHIRLPOOL f24c077f90166fbec7400263a1b4016fb69576bf2c188238d4d60efdcf682a5b7da9c8237eef639ab90ec210a3f146edcc4297ab9065901c3a3646f84fdf2db1
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
new file mode 100644
index 000000000000..d82532a4f623
--- /dev/null
+++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.660.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="Vienna RNA package - RNA folding"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2 flag-o-matic
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+S="${WORKDIR}/VIENNA-1.7.2.650"
+PATCHES=( "${FILESDIR}"/${PN}-1.7.2.650_fix-build-system.patch )
+
+src_configure() {
+	append-cflags -std=gnu89
+	emboss-r2_src_configure
+}
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
new file mode 100644
index 000000000000..5ce365ed5497
--- /dev/null
+++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch
@@ -0,0 +1,108 @@
+ configure.ac    | 49 +++++++------------------------------------------
+ src/Makefile.am |  7 +++----
+ 2 files changed, 10 insertions(+), 46 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index f5a4ecf..bbe0743 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -649,33 +649,6 @@ AS_CASE([${host_os}],
+ 
+ 
+ 
+-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${with_x}" != "xno"],
+@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd],
++  [],[PKG_CHECK_MODULES([PLPLOT], [plplot])]
++  )
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1f5b756..e178914 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF)
+ endif
+ 
+ liboviennarna_la_LDFLAGS = $(LINKFLAGS)
++liboviennarna_la_LIBADD = -lajax
+ 
+ ovrnaalifold_SOURCES = vrnaalifold.c
+ ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c
+@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \
+ 	$(XLIB)
+ else
+ LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \
+-	-lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++	-lensembl -lajaxg -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-vienna/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://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>