diff options
Diffstat (limited to 'sci-biology/embassy-esim4')
| -rw-r--r-- | sci-biology/embassy-esim4/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-biology/embassy-esim4/Manifest | 51 | ||||
| -rw-r--r-- | sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch | 97 | ||||
| -rw-r--r-- | sci-biology/embassy-esim4/metadata.xml | 2 |
5 files changed, 148 insertions, 26 deletions
diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog index 549d86832d6f..c7243b02282c 100644 --- a/sci-biology/embassy-esim4/ChangeLog +++ b/sci-biology/embassy-esim4/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/embassy-esim4 -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.31 2011/10/20 08:54:22 xarthisius Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.32 2015/03/28 17:23:35 jlec Exp $ + +*embassy-esim4-1.0.0.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-esim4-1.0.0.650.ebuild, + +files/embassy-esim4-1.0.0.650_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-esim4-1.0.0-r6.ebuild, embassy-esim4-1.0.0-r5.ebuild: diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest index 466d29bb81a1..77980aa589b2 100644 --- a/sci-biology/embassy-esim4/Manifest +++ b/sci-biology/embassy-esim4/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-esim4-1.0.0.tar.gz 431898 RMD160 228f886fa5804e2558884e035c90e8837a6939be SHA1 10710ade8f85c7adf5ded862b211726d2c1000d5 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 -DIST embassy-6.1.0-esim4-1.0.0.tar.gz 405076 RMD160 7db28acb948de25501dd2428567e208376066e07 SHA1 853aaafb776270e607e5a4040fb6062280484a30 SHA256 ff4c01548a4a70f0e27b25df439588d25db417a6f80371590acc4254b3876b7c -EBUILD embassy-esim4-1.0.0-r5.ebuild 519 RMD160 5dd0458d94ef6da81069e7a10410daef12c74575 SHA1 87de3028bcfc8d3821b68302f79853192b1b02c3 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab -EBUILD embassy-esim4-1.0.0-r6.ebuild 543 RMD160 3c885a479d09f6f85e9ee317bf31b8327a0fd859 SHA1 a468266dd0ca9971e692341a3fc94192da700f13 SHA256 1d0c45a80b4a3ff5b53edb353ccacd2778e20d331ce7a31fc24214aecf0f6460 -MISC ChangeLog 4611 RMD160 3da98d80cb7b7e5d1506c728dc189e8db64ac44a SHA1 7fa545cee07344fcdfa974fe8dd9fa7809d28df7 SHA256 65363d052a21e0e3f79994eb19309834ffbc56babad2b9661c7fa80e4e9fb079 -MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 +AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2568 SHA256 b19e115c5e2585349cea1a67e10d2928eb57ec65d2d55d305145d942cf7592b3 SHA512 2205c7b6ddcbbb17be6ae7242ddc54240c8087f04be5b7b9b245ce5d14c16ac196e227589b579d9c10ec433eaef7d69af9acb0ba16795130f630ef4b597997c2 WHIRLPOOL 8e52232753759142512035c86753214bf40b1e4433bf643b6866e8802aa53125ec61b5c3387a259aa81cadb3ddc1854eaaf7e8d15e3ec4d68d5fa6209bd3b49d +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-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 +DIST embassy-6.1.0-esim4-1.0.0.tar.gz 405076 SHA256 ff4c01548a4a70f0e27b25df439588d25db417a6f80371590acc4254b3876b7c +DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 +EBUILD embassy-esim4-1.0.0-r5.ebuild 519 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab SHA512 23b41eea8b3c0dd1f41887305afa18596cc82e6853e83355399a81545932c95c661760df2d926b1fd295bb04554e471f3926669808c0a625813216dc3e3750c3 WHIRLPOOL 47d8e921988c76e15d5a77adafe5df01b655be2a9d60201a139a098b2b45252b81befc23f6e5b8813bf71a64c6c843f676c99f194a7b2cb9b5e5902fd1388771 +EBUILD embassy-esim4-1.0.0-r6.ebuild 543 SHA256 1d0c45a80b4a3ff5b53edb353ccacd2778e20d331ce7a31fc24214aecf0f6460 SHA512 13e8a52f313123b41ba178feb8e44aa7f8607cebb7c1a3a700b22e31a6f057980edf9aea09b55dc300d404b1731590c05f3f9e4dd5a52ee9cd8c5d65a138b5ac WHIRLPOOL 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51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.18 (GNU/Linux) +Version: GnuPG v2.0 -iQIcBAEBCAAGBQJOn+HGAAoJEF0huFKJUZL5/W0P/3eUZm3EHCJDUrvP7hKdtkPU -McJdHcSIQJ6k5YQnGpWxrX2XXIEyrpN/7roHTaiD5yNH031gonAfAYLVrr0pFZaz -g0UirRBnuqFz0AWhBf81B3oY2MrXgtcpF9GLWFOdTs/7nHotbRIoQgpO4rl4w9qw -EblP5pS+1+rHD3VpkJDBYpR66PnhqaxCUveXCMOXrp9j35Wt9OTHUmMFp/KFUT1T -mi10pAwhDwuNmkdAAixZMXp8xUSWOQ5q0rLmO0vADhseYi3o2m/hMVu5yiY65PB3 -4BjZLN+W4YBV+MicOKDybEuV7LgA4xdkSqEyQLQBIbQ1Exla9KO8jDLqXPM2TZGk -l0OGChWLh/fOPMPKd0PdKzasdVbZRIyGpJxXM+PdrtMlhiFLB94SENJD5Sw+DLiu -NvZIsYUIKfx2Vnsd3mK1v2cvHjKodm5jP99YCB7+vJSm6n3hGUhij6sesldi45uS -zhFncqKLhT8QX9LQhoLePH4SxK8fHLFbtCKk++5JJkKM2jXyhRoJu1q+jfzigsH0 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+X3ZEgwXb41oN+hLQzhYvB1Oq8sNJ1qv9CDXuSPVAUrhUbJbZ6kP+5RyNbBwdoIwe +C6ryK2RKmtYhNQBrTAsH +=MEEd -----END PGP SIGNATURE----- diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild new file mode 100644 index 000000000000..218b569b4a1c --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.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-esim4/embassy-esim4-1.0.0.650.ebuild,v 1.1 2015/03/28 17:23:35 jlec Exp $ + +EAPI=5 + +EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" + +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-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..8279071806c6 --- /dev/null +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -0,0 +1,97 @@ +--- ESIM4-1.0.0.650/configure.ac ++++ ESIM4-1.0.0.650/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${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +--- ESIM4-1.0.0.650/src/Makefile.am ++++ ESIM4-1.0.0.650/src/Makefile.am +@@ -17,9 +17,7 @@ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +61,5 @@ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif +--- ESIM4-1.0.0.650/emboss_acd/Makefile.am ++++ ESIM4-1.0.0.650/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-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml index d4648212cbad..f17a827e3101 100644 --- a/sci-biology/embassy-esim4/metadata.xml +++ b/sci-biology/embassy-esim4/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> |