reinit the tree, so we can have metadata

4 files changed, 145 insertions, 0 deletions

diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
new file mode 100644
index 000000000000..49cbaae159f1
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -0,0 +1,6 @@
+AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3255 SHA256 26aad2bc72f89444dffdd301cfd4f50ba582b10082f21153e601c6812075ba86 SHA512 a0d4dcb3e7d4ce9b5cbd68168ebe7c8d248aa1166a6a52a0a77031291af8d2d32af0243571b669b9318426f753251d983ebb9b96eb1da81b594f4f4d20d7c249 WHIRLPOOL de7d91731115bca913a65a8f4a44d863433338ea4e5acb7f6a9fefca9a185325b18888d8339d180a49ecb7dfeb91f120a7c7188fe23f340dd21aeb8b3940458e
+DIST embassy-phylipnew-3.69.660.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58
+EBUILD embassy-phylipnew-3.69.660.ebuild 360 SHA256 f709676a2f9165b6fc0463fa866887b346306b71b99659ab8888922a29395e16 SHA512 cadc029f641b4303325f4d4110a130bc46b1e74b2c6246bb31cc07ff2bd8801adc6438cf2253897d3d6c28bf4fd6f9bad098b73d0e664b79bec5899157551e12 WHIRLPOOL ad40e021462a8ee0ada38eae9d4be237ea154889b20d584f498a5b8fe96575f434f62fa298f4b985422bfa7c152b929c8781ac1db9acdb26e1b91d5bb116270f
+MISC ChangeLog 3713 SHA256 16e0941c89aebf00fe14bd00989a743873ac62b951e97cb76f0351d92b87899a SHA512 5184a0b1a6f8e989c0eece6b2b1dcfcfd7c4ef0bcddf9cb25eab69d7eef104c0807b72390d29e5f7ab909a3c9fb224af24f649b3d28f711b1aa4e20f2ece08a7 WHIRLPOOL 0958d0036cbf66b26b46fc41287c62f56c3499b2d66d7fd174ee30ac7a9088c9afec662803c41626fd4ab87101d58b7a57da78e27f3e771234ccb5b9a7ceceee
+MISC ChangeLog-2015 2806 SHA256 142f97be3bcc2cfe360418a11835c21109505aa7085b705e93832b586ce957f9 SHA512 5d9859ac63566d082fb58bb3eb6ca81fce1bcdab06624e7795dcec6f28564c33c87f7b62a642e153c1a1f161cb995ad52b04cf2fed8029d3e5afdd28948135f6 WHIRLPOOL ad62b40aca5b1d875cb26944dcbcbc7f288024e298c3c0d1868e1a72074995bfa3b0ab40c8e7e6686bab57c11e85c013e4826d474a178803e65d6fe0172d0dd4
+MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
new file mode 100644
index 000000000000..69834a313b8f
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+EBO_DESCRIPTION="The Phylogeny Inference Package"
+
+EBO_EAUTORECONF=1
+
+inherit emboss-r2
+
+LICENSE+=" freedist"
+
+KEYWORDS="~amd64 ~x86 ~x86-linux"
+
+S="${WORKDIR}/PHYLIPNEW-3.69.650"
+PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch )
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
new file mode 100644
index 000000000000..1cba944094a2
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
@@ -0,0 +1,111 @@
+ configure.ac           | 49 +++++++------------------------------------------
+ emboss_acd/Makefile.am |  2 +-
+ src/Makefile.am        |  7 ++-----
+ 3 files changed, 10 insertions(+), 48 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index e5bfaf1..09ed517 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -635,33 +635,6 @@ AS_CASE([${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${with_x}" != "xno"],
+@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs],
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${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/emboss_acd/Makefile.am b/emboss_acd/Makefile.am
+index e1c1878..e253c95 100644
+--- 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
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 1883ce9..fb1787f 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${embprefix}/include \
+-	-I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \
+ 	../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
new file mode 100644
index 000000000000..d1b9a7602ec2
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/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>