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, 149 insertions, 27 deletions

diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog
index d282ee0ce54f..d58acceadb12 100644
--- a/sci-biology/embassy-iprscan/ChangeLog
+++ b/sci-biology/embassy-iprscan/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/embassy-iprscan
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.7 2011/10/20 08:53:38 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.8 2015/03/28 17:20:18 jlec Exp $
+
+*embassy-iprscan-4.3.1.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +embassy-iprscan-4.3.1.650.ebuild,
+  +files/embassy-iprscan-4.3.1.650_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-iprscan-4.3.1-r1.ebuild, embassy-iprscan-4.3.1.ebuild:
@@ -32,4 +40,3 @@
   27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +embassy-iprscan-4.3.1.ebuild:
   Initial import for EMBASSY 6.0.1.
-
diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest
index c1907f316f0d..b246d609c6f0 100644
--- a/sci-biology/embassy-iprscan/Manifest
+++ b/sci-biology/embassy-iprscan/Manifest
@@ -1,28 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
-DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
-DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
-DIST embassy-6.0.1-iprscan-4.3.1.tar.gz 339939 RMD160 bdedabd2b86cbf4cc33ebfb4e55650faadffa0aa SHA1 cf3de395e0642126e1a9e23fdad0288f80e0e7e0 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
-DIST embassy-6.1.0-iprscan-4.3.1.tar.gz 343265 RMD160 6c7afbe8fbafc01eacf9634d44f0e38659e2b06c SHA1 8eaf9bf518ff770ae58bed6ba89985fa01bb2099 SHA256 a98c08136d98dcbaa45e61714c3598c1ce705fd3a1578a85c94674f41ff1b3ba
-EBUILD embassy-iprscan-4.3.1-r1.ebuild 545 RMD160 d8828e08dd0b2802091bd6272bd9b2251488541a SHA1 6003c53e5d5fb6124c7058d30bdb96f5e7382edd SHA256 c785cbed3440f0391eca0f5bfda4d382b2994cf50adfafde5e801dc27a4591e0
-EBUILD embassy-iprscan-4.3.1.ebuild 505 RMD160 e9b6d9f077e2ba156257e0029f7bce26d5a72d40 SHA1 36c205a0a1bab91a1b0ff9b581633b76c76094b4 SHA256 f64afda1a967a295c3468100fa61f6961695af1ff8c760356dc15c4ae137897d
-MISC ChangeLog 1204 RMD160 2700bd7fd4ee1edbac81617c5c4f024cedc6582c SHA1 6dcde1fa70747fb0657446a7b991bb638cdee14a SHA256 37bf46afd396e8714db21867dbdf553d8dc7aef1b162c802014aecaa37017c4b
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2580 SHA256 8027ce9bd9b318fc6bce543770ab59fc8bd50237a68b959bc05274cdb3caa282 SHA512 de367b404d1f772276f4ca8f51c031ba148db6b80a480a4594f5e4151594eefae49ade820c145ae2b2feb5d7bd32bbb4196c82b3e809bc160ab88ce3a7b74913 WHIRLPOOL 71fb4928262df5669d828d945d47fa22f963c928e0dd0b24e1962191e63f803f354a15093c604caf7a1c8372a9b329c0183791c4577f456f634cdb5bdb6062bc
+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-iprscan-4.3.1.tar.gz 339939 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
+DIST embassy-6.1.0-iprscan-4.3.1.tar.gz 343265 SHA256 a98c08136d98dcbaa45e61714c3598c1ce705fd3a1578a85c94674f41ff1b3ba
+DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8
+EBUILD embassy-iprscan-4.3.1-r1.ebuild 545 SHA256 c785cbed3440f0391eca0f5bfda4d382b2994cf50adfafde5e801dc27a4591e0 SHA512 a845734ed8f1ca811c62149d811715d17189fc05f67e5c44d538ca3b69ce29b7e893b4afc1160036e56526cb72afea9b57ae2ddc3350a2adf2aedea17bdcc3da WHIRLPOOL 540f9237ba980962a99492183ca355e869d8d123a25948a4554e45453e7369edef49cfcd1d0b56bc9122bed210be8959ed78d4bbdc8c1256f2b958dfde98e22d
+EBUILD embassy-iprscan-4.3.1.650.ebuild 471 SHA256 3ec77ba7ebed4d0cc94a846f65c78b91d5d424b8403e4fac8384ff5b4f2d4dd3 SHA512 08b1345f41f7213e445d30b048285c7a303cf07d237295bd69b7ddc718b5986e4ef458d18b5a41466cc8e84025235865100846733e543c68c89fcf8e5393b810 WHIRLPOOL 8ec24e16e6858f4bcfd5407143a3bf96d0cea0428c00ee1cbcb805113cda6041fef73a5f87279a46e3ea1c0f14c4757549089805529edd33aadd5a5326ee5596
+EBUILD embassy-iprscan-4.3.1.ebuild 505 SHA256 f64afda1a967a295c3468100fa61f6961695af1ff8c760356dc15c4ae137897d SHA512 0d48b41756575422adfa44c1303b35f41a7b36953b47997f4b7748471c4e95e8d31c16be9c6b21af0eecce643eb2f65f8a5a6dd140ae698cc70e03bb5f0b0696 WHIRLPOOL a1a54ad6ea1f29ac6b1482fb7f9ecbe0db24db6d08eedc310c8fbaad046eb6e7f40fd6cbe06e7c11a53dbd33fdad4f0ee7a03fb4de4161f4a2bf598f68f62551
+MISC ChangeLog 1493 SHA256 e2d973289f80af17a9388df77e3e0b2cf81fff2baa638671b991fbda7da8e7e8 SHA512 cafa77c87dd604614953707704402595d36303261a299c1c335dd4e4552bfb6d6481e49ef248f11eea2a59fd0dfabe860ff1ffd3c9805d0492ed7e73517fa895 WHIRLPOOL 2d70f04ca2efe69059487851e6838375e2f667907fd6a9e78f7fd93a7f96845f1f7249f6c24efe7232a2ad9ed226f9a0c610bb536fbd022582e88c7d99bf05cd
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0
 
-iQIcBAEBCAAGBQJOn+GaAAoJEF0huFKJUZL5ctMP/2QrS3rz0SaZmyYCz/RurtJL
-VOQwCchSniTeQt0g9537u/EduUx24cEFpSobH3Q0IRVqaJ68HvgBp1ezaYbtdKgQ
-ecuptVPvFCznvb7sTAEE17q6wvHcEaDNsEZh85ygPfAC2Fryx8cnUqlsMaAfMEm+
-GiEVr1kaE55xqrrxqbOsaE3bWIJPJxRnHSD19F241DVmS2ukjsJvv/DEkCVDk+nK
-NK6Kls+sLFLjXz8c2NuYMr2H4Pe2KgKyReKIQevINDC3ZkgGb025PuxonQnP+0Fd
-TDpadlrJGCb65FRxZdQ0LK602A5m8p3C2yWJd/fB8biVqh9ubVCtQQKIrNb0S6TU
-mhsctACqmN3YAFMsoCEuWUKqJQuxkacY8YFoordvYRXrnbTdr29mh2i66UZyGo92
-Gc6KDhpgYxUqD95AkZTKa/5RHTC1eN2dZMKIO8BtfGJNU8bmvxo8jhEfdROL26vX
-KICdbwKzSN0bDfMDJ0SHlN+8P5iPWQNTw9K+fHilXPTRWf3f6whn9o0wmFxhzl2/
-4npUDn+eE0xSsaAdLuG5oLV6Ln6w5GIv9lnrptv1+Ipvt9Wgsoldbs6DU0UYXLLs
-MGlUoqI76ntcpE82uwqliK8gd2BOIVP2p43uMGQPDoW3Fl6p8o8NdPjEo1pZzILb
-5KhLPklyrqv6AOk1PdIF
-=QLil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+=I025
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
new file mode 100644
index 000000000000..48ee401e232b
--- /dev/null
+++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild,v 1.1 2015/03/28 17:20:18 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="InterProScan motif detection add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
new file mode 100644
index 000000000000..955005d51211
--- /dev/null
+++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch
@@ -0,0 +1,97 @@
+--- IPRSCAN-4.3.1.650/configure.ac
++++ IPRSCAN-4.3.1.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- IPRSCAN-4.3.1.650/src/Makefile.am
++++ IPRSCAN-4.3.1.650/src/Makefile.am
+@@ -17,9 +17,7 @@
+ 	-I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+ 	-I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \
+-	$(NLINCLUDES) \
+-	-I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -58,5 +56,5 @@
+ 	$(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
++        -lajax $(NLADD) $(XLIB)
+ endif
+--- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am
++++ IPRSCAN-4.3.1.650/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-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
index d4648212cbad..f17a827e3101 100644
--- a/sci-biology/embassy-iprscan/metadata.xml
+++ b/sci-biology/embassy-iprscan/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>