Call correct install function

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

diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog
index fd9e262347602ba6db35de3f8f746aab90e63e52..cf25c5266a7c0a9c3a823a6fee2052d7a07fa085 100644 (file)
--- a/sci-biology/embassy-domalign/ChangeLog
+++ b/sci-biology/embassy-domalign/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-domalign
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.23 2011/10/20 08:57:30 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.24 2015/03/28 17:30:41 jlec Exp $
+
+*embassy-domalign-0.1.650 (28 Mar 2015)
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-domalign-0.1.650.ebuild,
+  +files/embassy-domalign-0.1.650_fix-build-system.patch, metadata.xml:
+  Call correct install function
 
   20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org>
   embassy-domalign-0.1.0-r4.ebuild, embassy-domalign-0.1.0-r3.ebuild:
@@ -100,4 +106,3 @@
   07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +embassy-domalign-0.1.0.ebuild:
   Initial import. Part of EMBASSY 3.0.0.
-

diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest
index 88735b6a4c71863d07ab77611cdf8458636258ed..0d00775cb9018736de2e1fa3c9cea932f29c60f6 100644 (file)
--- a/sci-biology/embassy-domalign/Manifest
+++ b/sci-biology/embassy-domalign/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-domalign-0.1.0.tar.gz 462156 RMD160 ff7dbe964fc8aebafd0a0cff4e67cca21c0c44c8 SHA1 6b3c67a5d6327bc0b3e82636e9a02e8eb91f8cc5 SHA256 c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a
-DIST embassy-6.1.0-domalign-0.1.0.tar.gz 434640 RMD160 05645f883ab3a0550eb8bb4b9fffc1131e688d57 SHA1 c7cc721f6c6ec6c3bda5a2c28da89ed9df1e4136 SHA256 45ddc0ee932d2bc6387a0fef77a52b67dfa07c22e27a17481e7ef682d6145472
-EBUILD embassy-domalign-0.1.0-r3.ebuild 506 RMD160 62a9ca5619ded3e7310325f34e8666811dfd4a35 SHA1 839185010bab03c756e32d641fffe09bf395e9e0 SHA256 0316f829e9c9b1f3e481200222f9b1a509ef614e91480699f6cfacbca59bae70
-EBUILD embassy-domalign-0.1.0-r4.ebuild 530 RMD160 96d90882b2702dc730f1eeeea62116d348250e20 SHA1 8bef6654b0628310577cdb0a18bb1c3e4610ca53 SHA256 94f10bf15c970767b3dc146fdf4963b8b4db1300f57480860404613484cbf942
-MISC ChangeLog 3355 RMD160 bc574a239b23505e32f0ed3f1e86612250b86cc5 SHA1 863478f4d7d9c43217b544dfdbc5f407a675a656 SHA256 32de5fac06035d9d185a6f09fd889fa9915abcfe84ab2122d46daeb0746702f9
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+AUX embassy-domalign-0.1.650_fix-build-system.patch 2410 SHA256 b95188d2dd4490a4e32c0f0debc107500749c2a558472dbc0d7d655aab4b336a SHA512 be0368314c1317b0102c0ba910ff273a7db127e59d2e0ff94f4da4b42d59ddaf788369abc39aa82d90694f422ea1f9dce7153d414d20013bb4b36a10893eb2c2 WHIRLPOOL ad0e509a2a46d1b8fd027f6bc67fe08feeaa91fe7368011c18b2ff578cab367e6ced83fc13b63ffa3d6a59f8fd2282a10f594b95fb50ca8325d22d1a794c50a3
+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-domalign-0.1.0.tar.gz 462156 SHA256 c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a
+DIST embassy-6.1.0-domalign-0.1.0.tar.gz 434640 SHA256 45ddc0ee932d2bc6387a0fef77a52b67dfa07c22e27a17481e7ef682d6145472
+DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37
+EBUILD embassy-domalign-0.1.0-r3.ebuild 506 SHA256 0316f829e9c9b1f3e481200222f9b1a509ef614e91480699f6cfacbca59bae70 SHA512 d13cfc9e6210b00a51ff1c12fe3da9919d7e700226883668795095c85f50574f6eff10a18d19cbb2e48956edbc458b6ef7832d9c34c7ac3c4c397a35dc229e93 WHIRLPOOL b6ab4ca7cdfeaf19e7929f0ae5e2583f87809086d191dd09b823c3ce9c09014e77555e0a51a1a546819795e9ab4344abc7f6d7089460003069dc4dd0ced6f336
+EBUILD embassy-domalign-0.1.0-r4.ebuild 530 SHA256 94f10bf15c970767b3dc146fdf4963b8b4db1300f57480860404613484cbf942 SHA512 db2532efadfdf008aac1486f40dec18bed503bee3a0bbb47635cc1bd902ebc879863da250a90172c302b1383f06351e2ee6a1051200b648e8a58e9999acb8868 WHIRLPOOL 02f9614c00823666f921442f259da64d94b0f2375082317c6e10971194d7230c39a9279886065db4f4fa31c7fd572384ce4993d0713093b000c8d585af3009e3
+EBUILD embassy-domalign-0.1.650.ebuild 454 SHA256 edb69bfadc6834be718e9e261101a7bb3968e1d0d885c295b91c5d9c5863e354 SHA512 21930ab588009ce5a3d97dc44ff3027e0053c512c0432d768977ffff79afb462144ec3f3edb4b604d7839211ec5ce42969b82fc09a451789d24a869c70db1543 WHIRLPOOL fdfa4e1a116bca9c64aaacd6568a109de297a33c4f468daf34d68391d9945282b9056aabc068674a9696213bf4efecfa26cdd6d0d6b107da293d560731fb06c4
+MISC ChangeLog 3575 SHA256 30b96ceededcd911eb9a7eb64a5489c6ec069bda6c36098da43a0474a9c8036c SHA512 985228d17a156f5973b70bccb399cc0f040d6af74a58a4bc6489866cdc47543d42e4d66d38ff929f2716321dbce29f589e9395ca34434314db76cec86136544d WHIRLPOOL 78a7aa8af58cf55d9a1fdb489832adf2df19ff64ec2f5cf7c2b513f64b428c3f19ab57ce2d639058017d0ddcacf60885a2b695d6dcc35e424cbe92eb64b6540a
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0
 
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diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild
new file mode 100644 (file)
index 0000000..8152116
--- /dev/null
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.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-domalign/embassy-domalign-0.1.650.ebuild,v 1.1 2015/03/28 17:30:41 jlec Exp $
+
+EAPI=5
+
+EBO_DESCRIPTION="Protein domain alignment add-on package"
+
+PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch )
+AUTOTOOLS_AUTORECONF=1
+inherit emboss-r1
+
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos"

diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
new file mode 100644 (file)
index 0000000..d87bae3
--- /dev/null
+++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch
@@ -0,0 +1,92 @@
+--- DOMALIGN-0.1.650/configure.ac
++++ DOMALIGN-0.1.650/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${enable_systemlibs}" = "xyes"],
++[
++dnl using system libraries
++  PKG_CHECK_MODULES([PLPLOT], [plplotd])
++])
+ 
+ 
+ # Enable the purify tool: --enable-purify, sets CC and LIBTOOL
+--- DOMALIGN-0.1.650/src/Makefile.am
++++ DOMALIGN-0.1.650/src/Makefile.am
+@@ -17,10 +17,7 @@
+       -I../../../ajax/ensembl -I../../../ajax/ajaxdb \
+       -I../../../ajax/acd -I../../../plplot
+ else
+-AM_CPPFLAGS = -I../include -I${embprefix}/include \
+-      -I${embprefix}/include/eplplot \
+-      $(NLINCLUDES) \
+-      -I${embprefix}/include/epcre
++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS)
+ endif
+ 
+ if ISSHARED
+@@ -63,5 +60,5 @@
+       ../../../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-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml
index d4648212cbad546e8f10fb42efdcf38118469ccc..f17a827e310198336846040c3e61382ed748e991 100644 (file)
--- a/sci-biology/embassy-domalign/metadata.xml
+++ b/sci-biology/embassy-domalign/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>

diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog
index 08248221ea751c9998228df56a99b5e4cab4d329..601378dedd085de141c8ed30e6323206c740cbef 100644 (file)
--- a/sci-biology/embassy-mse/ChangeLog
+++ b/sci-biology/embassy-mse/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/embassy-mse
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.39 2015/03/28 17:14:17 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.40 2015/03/28 17:29:44 jlec Exp $
+
+  28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.650.ebuild:
+  Call correct install function
 
 *embassy-mse-3.0.0.650 (28 Mar 2015)
 

diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 00bd96e6004fe50973e4173dbaf1b8e9c1721767..17f678584c6f6753a6797ca69cfabcd1cd02adb3 100644 (file)
--- a/sci-biology/embassy-mse/Manifest
+++ b/sci-biology/embassy-mse/Manifest
@@ -9,25 +9,25 @@ DIST embassy-6.1.0-mse-1.0.0.tar.gz 424839 SHA256 916e6cc772c499cb0519e1fa19e1f6
 DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b
 EBUILD embassy-mse-1.0.0-r6.ebuild 598 SHA256 40ae8e6cb04fd32fcaa7d93c4a9b247d555f76fff212fb5b0ce2228ec46e4465 SHA512 fc8c501160f9d93eee5e5f72b2a3421fc8a290b66da5802f973c12102334050c8afb9727fd1a1598a1d8cefc6a05db926c1cd63ea94c82f6108959fa552989eb WHIRLPOOL e8368ff3f0e0d5f768964d84cc3c4934ecf6f45060a52e161030a93c160c88b848b0fa659ef84d10e2767f15b35dda53c263524cb3169d6b94f3adcda1d6c304
 EBUILD embassy-mse-1.0.0-r7.ebuild 622 SHA256 ba96c25c4e91946fc509113af0d4acca7409a293bb8ea757b3f8a63705736587 SHA512 bd742fee143508a9011a9a792f324af2fce01ef5d9c7d09d6165c305926a77df8aa21316ed04d914439aa134cc196b33e857de585f99aef4349b97f3d131c67a WHIRLPOOL 59eb19b7b117a13184da27d4e88ca48140f4ba0d51df291e37ca7298f23d16be768b3041a1384af898ab6c231fc7d166871b91d0c07abf89f769c97cd0410382
-EBUILD embassy-mse-3.0.0.650.ebuild 639 SHA256 2f82a102d42816ce5289649417b199f68a581e7f48c9c566a7b52fc565768910 SHA512 c0f9f3f41707f8e876d008cc0b4deba21b196e77eb42b8b353d621f39354d45e33777bcc6181e32b0cec38c8a28328796fa43a488a2fc2dcec8d26d8feb6b957 WHIRLPOOL 7c016efd1a5212834d880cd6bb0d7ee6c235551e19aa4ef267b7ec40f276c7677a2dea2f0d7e36fac8bfee826f99f4ae9c2cb86124434235e4c11ef64506968e
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+MISC ChangeLog 5921 SHA256 d61bd9839eb621d7c2614a6c0f7c693b814096b067c1fe963714932522c7ece8 SHA512 05526f9b1358ad784cddc9cbb7195d75dceabe75a699691a810f18ce280b56dc71308d6cb5e3272f3a9596cde0d87729b9b70c2e07e2bc4f003f0658161e1b5b WHIRLPOOL 8d8adf6c627b8a41b5507f305097e255b83e277e21cdcb0f27bc6c982622608fc7cc1e46dcbf964e1f1bcec0ef55a2905f6a5ad77846de5200f824a2c9a57030
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
index 6b5725be73c3922704cb36e272353ab68e46fb9c..7cde055b231049cb1889411a49ddb30875b3d661 100644 (file)
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild,v 1.1 2015/03/28 17:14:17 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild,v 1.2 2015/03/28 17:29:44 jlec Exp $
 
 EAPI=5
 
@@ -17,7 +17,7 @@ IUSE+=" ncurses"
 RDEPEND+=" ncurses? ( sys-libs/ncurses )"
 
 src_install() {
-       emboss-r1_src_install
+       autotools-utils_src_install
        insinto /usr/include/emboss/mse
        doins h/*.h
 }