From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/embassy-domalign/Manifest | 6 ++ .../embassy-domalign-0.1.660.ebuild | 15 +++ ...embassy-domalign-0.1.650_fix-build-system.patch | 101 +++++++++++++++++++++ sci-biology/embassy-domalign/metadata.xml | 11 +++ 4 files changed, 133 insertions(+) create mode 100644 sci-biology/embassy-domalign/Manifest create mode 100644 sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild create mode 100644 sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch create mode 100644 sci-biology/embassy-domalign/metadata.xml (limited to 'sci-biology/embassy-domalign') diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest new file mode 100644 index 000000000000..330ea4156ac7 --- /dev/null +++ b/sci-biology/embassy-domalign/Manifest @@ -0,0 +1,6 @@ +AUX embassy-domalign-0.1.650_fix-build-system.patch 2908 SHA256 3c4b3c8187942d52b5605f83cb2430cebb050fb7d6180e2784a041a4fe332d48 SHA512 5cd02b39812adc44d9b877cca8902b6a66e79c90975b50233a4f8f84392026ffad25d57665e68e5db533f28935f444b4dc75b7120bafd910e415b75737686ad2 WHIRLPOOL 0a7ddde136f33cb2618957ddfc5f7d7d62f1352e4902b700d1b22c636b0424bdbca28fb6946d97095d75ba5ce61b21b93647c10920ebe8e4539fba5751efca32 +DIST embassy-domalign-0.1.660.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37 +EBUILD embassy-domalign-0.1.660.ebuild 343 SHA256 af35754f603a88b67066c06f5d740c70558110c4a2d8e46eea840243c11880bf SHA512 bdc0f0bf6a006d2091f98c3a3258e402b522a743866db74324333c5ec9d14df181561b0beb75baa6aaec130636e1e866184e5c4ed414ceb4e8365e13801df84c WHIRLPOOL 99c14523285090460bb9a0f5a0cc5a2486ea34588ec8109844427a868fa66eaf755b6ba8debf619aca90af867115025573330bcf52fd6af79b3dc03956e8417e +MISC ChangeLog 3713 SHA256 de038347386131ea00279d8e2ff4296cdc7584894e5314125f9836f396c11730 SHA512 9294affdf27cf379fa512089b072d3bd8ee3b26d96e7d2f8f53138a5f5a101bf7ab22f2f9cbb311bd8ff2163312f7c996f5612b04e86810a0e65b738dc569519 WHIRLPOOL 9a463e64b8885abef98b97691b8a9b1164d2e164676bf0611e310129de59f6c07ff8d9292fc925bc156e6a1de55548a6d9afd6f53b6669e50ce131abdf201fec +MISC ChangeLog-2015 3920 SHA256 2c6a86ba92e5d72702153e3133653d4b169c16f3fcbe1bbc53407f2e47f94567 SHA512 d72ddff0bf2c5cd0076c6814bbbe724bcd86e373faec3b8484226049b29e4477b6fd2256aac247a9828c7f88633a16d9c40da799c80e3d306f7595353581a373 WHIRLPOOL 03a28fea0444fc3c68b3dc37f94c98465d4b96a34e6bd7712ee32bf6b3e9a309af5a69749fe1cc77578814c39f94877de01e50d7ca6a2c14fb6e069858c53285 +MISC metadata.xml 347 SHA256 52f98c83739517e0c387d292abce08592cc91f49f0ca6961830adce541004cb2 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e WHIRLPOOL 1e331531e26a30418ce16d219ba8f2869d88279d42b5a2808e371276f18a56bcdd6b044f01f2a2c8489f1976293095f3a4c14e6c6672e7e7534438e4993b144b diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild new file mode 100644 index 000000000000..a897dba4b060 --- /dev/null +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.660.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +EBO_DESCRIPTION="Protein domain alignment add-on package" + +EBO_EAUTORECONF=1 + +inherit emboss-r2 + +KEYWORDS="~amd64 ~x86 ~x86-linux" + +S="${WORKDIR}/DOMALIGN-0.1.650" +PATCHES=( "${FILESDIR}"/${PN}-0.1.650_fix-build-system.patch ) diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..033ddf7b6535 --- /dev/null +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -0,0 +1,101 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 ++----- + 2 files changed, 9 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 693eb4d..dc0fda9 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-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${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 8785446..fe85f11 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${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 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../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 new file mode 100644 index 000000000000..d1b9a7602ec2 --- /dev/null +++ b/sci-biology/embassy-domalign/metadata.xml @@ -0,0 +1,11 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + emboss + + -- cgit v1.2.3