Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #335603

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 152 insertions, 27 deletions

diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog
index d50f17925693..90c7fbada465 100644
--- a/sci-biology/embassy-phylipnew/ChangeLog
+++ b/sci-biology/embassy-phylipnew/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-phylipnew
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.15 2011/10/20 08:50:46 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.16 2015/03/28 17:13:13 jlec Exp $
+
+*embassy-phylipnew-3.69.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-phylipnew-3.69.650.ebuild,
+  +files/embassy-phylipnew-3.69.650_fix-build-system.patch, metadata.xml:
+  Import latest changes from science overlay, thanks Ted Tanberry for the work;
+  fixes #335603
 
   20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org>
   embassy-phylipnew-3.68.ebuild, embassy-phylipnew-3.67.ebuild:
@@ -65,4 +73,3 @@
   +embassy-phylipnew-3.6b.ebuild:
   Initial import. This package will probably replace EMBASSY-PHYLIP in new
   EMBASSY releases.
-
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
index 0f54fcd90510..1b69d0ba825a 100644
--- a/sci-biology/embassy-phylipnew/Manifest
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -1,28 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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-DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
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+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
+DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945
+DIST embassy-6.1.0-phylipnew-3.68.tar.gz 1626990 SHA256 b22ec1efdae59160073acdcb57c660b58e0bd04d57fa8a86d8b0f48ec77bce78
+DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58
+EBUILD embassy-phylipnew-3.67.ebuild 542 SHA256 caaf16c790c0df32de03bb4b520cb123e9f544622b4fe8e0a75aff98f7d7f763 SHA512 b04ac52ba9068ae2ab2fe5e910ce6b3bb94e205a5c58bc8cba8a812992290299735bdb5138051287c3d98ee2db77f411e54a43da7259905e030b9dcfc4a8d400 WHIRLPOOL c7e7b02e801dfc48d692d6bd771684d4c66bed6dbdd7daa8761b359e5ea03a635ddd40d94c3b73af00e23bb928e668c123a7b5d148ec9741f17d57d9afa0955e
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+EBUILD embassy-phylipnew-3.69.650.ebuild 471 SHA256 217856328224548bedc41ef0b3671ac2306f7978495c73b788ef9a697fdaaf19 SHA512 6b386311b42e1037336a39505da03a779f623a9c62773f634372b5adc0db1f7742ef2b1cb73022fb5f32a9637454bcc334c47a8d04b7bbd83788599e77d79358 WHIRLPOOL 8b7255fb17062701a71f16c255faf9b1adc24648afceb14cd8cc0766b352e6b9cc8107f7ae793ac26d8abd79f17d47e6da120a54d3f2e50bcf091a8ec1695fb1
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diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
new file mode 100644
index 000000000000..f84223e5232b
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild,v 1.1 2015/03/28 17:13:13 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="the Phylogeny Inference Package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+LICENSE+=" freedist"
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
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..e0efb74bd79e
--- /dev/null
+++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch
@@ -0,0 +1,98 @@
+--- PHYLIPNEW-3.69.650/configure.ac
++++ PHYLIPNEW-3.69.650/configure.ac
+@@ -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${with_x}" != "xno"],
+@@ -781,21 +754,6 @@
+ 
+ 
+ 
+-dnl "Export" these variables for PCRE
+-
+-AC_SUBST([HAVE_MEMMOVE])
+-AC_SUBST([HAVE_STRERROR])
+-AC_SUBST([PCRE_MAJOR])
+-AC_SUBST([PCRE_MINOR])
+-AC_SUBST([PCRE_DATE])
+-AC_SUBST([PCRE_VERSION])
+-AC_SUBST([PCRE_LIB_VERSION])
+-AC_SUBST([PCRE_POSIXLIB_VERSION])
+-AC_SUBST([POSIX_MALLOC_THRESHOLD])
+-
+-
+-
+-
+ dnl Test if --enable-localforce given
+ locallink="no"
+ embprefix="/usr/local"
+@@ -918,6 +876,11 @@
+ AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"])
+ 
+ 
++AS_IF([test "x${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- PHYLIPNEW-3.69.650/src/Makefile.am
++++ PHYLIPNEW-3.69.650/src/Makefile.am
+@@ -16,10 +16,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${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 @@
+ 	../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+--- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am
++++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am
+@@ -1,3 +1,3 @@
+ 
+-pkgdata_DATA = *.acd
++pkgdata_DATA = $(srcdir)/*.acd
+ pkgdatadir=$(prefix)/share/EMBOSS/acd
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-phylipnew/metadata.xml
+++ b/sci-biology/embassy-phylipnew/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
+  <herd>sci-biology</herd>
 </pkgmetadata>