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, 182 insertions, 26 deletions

diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog
index c2462e926bc1..e4f8e1310b0c 100644
--- a/sci-biology/embassy-emnu/ChangeLog
+++ b/sci-biology/embassy-emnu/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/embassy-emnu
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.32 2011/10/20 08:54:43 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.33 2015/03/28 17:24:57 jlec Exp $
+
+*embassy-emnu-1.05.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-emnu-1.05.650.ebuild,
+  +files/embassy-emnu-1.05.650_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-emnu-1.05-r5.ebuild, embassy-emnu-1.05-r6.ebuild:
diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest
index b67930cc3c26..f21f17683ef2 100644
--- a/sci-biology/embassy-emnu/Manifest
+++ b/sci-biology/embassy-emnu/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
-DIST embassy-6.0.1-emnu-1.05.tar.gz 390229 RMD160 1d6bbb61cc22d72c130c90c33b4e6ecb14c89aab SHA1 06a57905af7fa7807825e000377b3d8626c99d2e SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
-DIST embassy-6.1.0-emnu-1.05.tar.gz 364956 RMD160 9b84bf7590200e0b386d9440016203c5e8e7048e SHA1 1f4ff9e592ab42557a16815c2ee3851f5b3bdc68 SHA256 cf02a8a30b3d84330279cf553488cb3f2fef63bab31dc01b6b9e69a97d619b2c
-EBUILD embassy-emnu-1.05-r5.ebuild 585 RMD160 a968573cff64d56fe76ce79367d4212753500177 SHA1 fd0688d9c4a8b966f52bc78b1d4e6f5d77072ccc SHA256 107017fa4db5806261142fca90ab67f8b37ad27d844676ebc868f5ab648d0c2d
-EBUILD embassy-emnu-1.05-r6.ebuild 609 RMD160 08aa13b892ea36c48e019996fda3b0312f7ef1b4 SHA1 e51b427f0e171c3eb12a485de5c1a4762507353b SHA256 3efb2f1f2a0c2f7cf0700708a9278769931937ea3a51e416f6c48fa09a63addc
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+AUX embassy-emnu-1.05.650_fix-build-system.patch 3455 SHA256 6f165662eb1e8d57eed8f51fa6c836b949f6be83327732bb7a7fa1b93373c763 SHA512 fd0a51d12009d3ccd25a0a60b0fd2133b22988594667b2c68498c987b9a41ac0ac75421996940d7480864912a2316f0d7a0ca4bd2bb777f16706d0a4907d6896 WHIRLPOOL ef04417248b83999c8c83769c7576acb4da71387904a83d7876d0a2a8be59032140aaf624b22b1c8c85ffb4e2ec63eb2d9ea6bca079a541f330a8f37842f9e15
+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-emnu-1.05.tar.gz 390229 SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
+DIST embassy-6.1.0-emnu-1.05.tar.gz 364956 SHA256 cf02a8a30b3d84330279cf553488cb3f2fef63bab31dc01b6b9e69a97d619b2c
+DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a
+EBUILD embassy-emnu-1.05-r5.ebuild 585 SHA256 107017fa4db5806261142fca90ab67f8b37ad27d844676ebc868f5ab648d0c2d SHA512 5007d4bb4f96210d0602ff489533d8a5deee8c6eed55fa6c745d85a9304a9b6f8dea18f4ba22519ab0f39c9d6c2d44c2bc30d30fa900255abe3ca36066c99153 WHIRLPOOL 4ff71bd1ba6025f335a4d1970ca0d5acfd0d2c545def98f8becc971deddb67e880ed379d3c6ec2a9250ccd3aa6b0e4ab3fcbff7ada7fd7bf890e51be0c04b4ed
+EBUILD embassy-emnu-1.05-r6.ebuild 609 SHA256 3efb2f1f2a0c2f7cf0700708a9278769931937ea3a51e416f6c48fa09a63addc SHA512 0682ac937318e4b8156d34df9a0b8fc254ec81cabea48b3ed6d1914bcc19a5d730299a48288f1fdeab66dd8382a49f43c41a8012b3d7947b8d2290b0865532bc WHIRLPOOL ec5648807dd813024fe03226e31075cbf580ddda15d033882612e7c87960992d505bbd1b91bf4cf912ef88d4986e0571e8052533b4da38af12f0b0f0347afcf2
+EBUILD embassy-emnu-1.05.650.ebuild 549 SHA256 23f388299bf4aec4355c2287a45c892f859a98d1ade2379174a764a77a3a25a9 SHA512 a47452aec70960e5ed562871980b6d84c6974ca01a6d48f5e3de2ff7f111e16ad1e0ea929b2be429e81524042d2de21ce473f30d397f5da91d7ed1d5e059f9e2 WHIRLPOOL ff4f4dbc5ddcc30c3e7d7871d8d5debaae2d78a93d7196bee076c52c7ff6bee754832b04cd04e3ca0d281650296120c57215693378856a72eda37a8174f0d925
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+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
new file mode 100644
index 000000000000..15daeda9d936
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild,v 1.1 2015/03/28 17:24:57 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Simple menu of EMBOSS applications"
+EBO_EXTRA_ECONF="$(use_enable ncurses curses)"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"
+IUSE+=" ncurses"
+
+RDEPEND+=" ncurses? ( sys-libs/ncurses )"
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
new file mode 100644
index 000000000000..e73eb7b170ce
--- /dev/null
+++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch
@@ -0,0 +1,127 @@
+--- EMNU-1.05.650/configure.ac
++++ EMNU-1.05.650/configure.ac
+@@ -635,33 +635,6 @@
+ 
+ 
+ 
+-dnl PCRE library definitions - see the MAJOR and MINOR values
+-dnl to see which version's configure.in these lines come from
+-
+-dnl Provide the current PCRE version information. Do not use numbers
+-dnl with leading zeros for the minor version, as they end up in a C
+-dnl macro, and may be treated as octal constants. Stick to single
+-dnl digits for minor numbers less than 10. There are unlikely to be
+-dnl that many releases anyway.
+-
+-PCRE_MAJOR="7"
+-PCRE_MINOR="9"
+-PCRE_DATE="11-Apr-2009"
+-PCRE_VERSION="${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"],
+@@ -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 +832,11 @@
+ 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
+@@ -899,20 +862,16 @@
+ 
+ 
+ dnl emnu and mse only: uses curses
+-dnl Test if --with-curses is given
+-AC_ARG_WITH([curses],
+-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])])
+-
+-AC_MSG_CHECKING([for curses])
+-
+-AS_IF([test "${with_curses}"],
+-[
+-  CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses"
+-  LDFLAGS="$LDFLAGS -L${with_curses}/lib"
++dnl Test if --enable-curses is given
++AC_ARG_ENABLE([curses],
++[AS_HELP_STRING([--enable-curses], [curses])])
++
++AS_IF([test "x$enable_curses" = "xyes"], [
++  PKG_CHECK_MODULES([NCURSES], [ncurses])
++  PKG_CHECK_MODULES([FORM], [form])
++  PKG_CHECK_MODULES([MENU], [menu])
+ ])
+ 
+-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"])
+-
+ 
+ 
+ 
+--- EMNU-1.05.650/src/Makefile.am
++++ EMNU-1.05.650/src/Makefile.am
+@@ -17,9 +17,8 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \
++	$(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -57,5 +56,5 @@
+ 	../../../plplot/libeplplot.la -lmenu -lform $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB)
++        -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB)
+ endif
+--- EMNU-1.05.650/emboss_acd/Makefile.am
++++ EMNU-1.05.650/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-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-emnu/metadata.xml
+++ b/sci-biology/embassy-emnu/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>