diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-libs/libmuscle | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-libs/libmuscle')
| -rw-r--r-- | sci-libs/libmuscle/Manifest | 7 | ||||
| -rw-r--r-- | sci-libs/libmuscle/files/3.7-bufferoverflow.patch | 22 | ||||
| -rw-r--r-- | sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch | 21 | ||||
| -rw-r--r-- | sci-libs/libmuscle/libmuscle-3.7-r3.ebuild | 40 | ||||
| -rw-r--r-- | sci-libs/libmuscle/metadata.xml | 8 |
5 files changed, 98 insertions, 0 deletions
diff --git a/sci-libs/libmuscle/Manifest b/sci-libs/libmuscle/Manifest new file mode 100644 index 000000000000..12c92ff9ebdd --- /dev/null +++ b/sci-libs/libmuscle/Manifest @@ -0,0 +1,7 @@ +AUX 3.7-bufferoverflow.patch 447 SHA256 cffb273380ae1793dd470b52461bff1475280918e5121927fa5b0fece2bba659 SHA512 09dd1fca3e75eb753a820c2f2957422c9433698af5bcbc572d48e437052d76522bac0b68923d296346d654f5e9130c15839180c4a635d9247e1ddf51993bcce6 WHIRLPOOL 1b7f8ab7fa0f0a03759c85ec6cb61944ff28603ed2dd90b69de0f5ffe609ee4bec65cb9137b0a88ad52c9ddb41b467fa9de1486d1cc1ba0e67459891ae398231 +AUX libmuscle-3.7-fix-build-system.patch 918 SHA256 a1caad44919835c335a4a06185df50512979a8cc80f7ef0f0ec50c7019abe2f0 SHA512 bb1590e8a9980de3a92fba16ce3e45a04a1cdf2f2a7fbbaedeba48f3d08f398e03bb6be7a9c9c0ba39a8772bc24d844480e9b57dce0f391d92b2f595e09677e0 WHIRLPOOL 75f812304ffd7f803281aa20b0f728a402ccc771b428389149d752497536110858f71f447286efe17fddc992fab0b5fe2928a1d3df7140e1b0f4df0596813cd7 +DIST libmuscle-3.7-r1.tar.bz2 458852 SHA256 3c0df6aeb8ea86bcd92e61f509486244176cee22c9bd7239ff16a51e1d046a14 SHA512 3031070dcd888c327b023eeb225a291bf36ec0c6fa8046fb1d945929305692bcdb3bc9623b02dfd753e086d3524bb7f10b9b011f663e38c71b17f6f516c0ac62 WHIRLPOOL d40edcebe7481565cec0efd390c9f545277fcccfc9ef9b3c051c5357bcaa0141c22e7efba794d9ca376724aaf0310c1e75dcd3e3f4bafa983f1692198a6dc51a +EBUILD libmuscle-3.7-r3.ebuild 726 SHA256 c50fb8e9d478960d46d73f7ce4be7078bed506e074bb129df71117e83a035b60 SHA512 97027e93ed6569e302644b76dbdc84cb5d0464b09e3940645a898f779bcead4c9fa029ca2a527623a591f5717442cc505836df2130bfd3bb816a32e262f788ce WHIRLPOOL d7a6aa0b57bd078bdc973fd285cfac88b193eb82765dc54cb101d707bfab428ce2219b2909bbce91799992b40bc72695a47677874aeda70c3cc21cff999c2a5c +MISC ChangeLog 2773 SHA256 e7eda55c3b9c918bb2ea370ac95383a1e91ad2507cb2dbd90799384e1bc13346 SHA512 92c5783a3588662be503cf525659612b1d71449ce425b9474caf47548ff64bf6f17591a84a5b255e0124ce413241d79a871261b830f5d727d410de1ca97b840d WHIRLPOOL c062973779edee12bcd7a0fbaad8653ae4dc1b67dcfcadb82c12fb0f630c253319bd590642135873c6561b9d375f551f29f647a78772de074e0d4d6e830dae76 +MISC ChangeLog-2015 881 SHA256 24dd90b3c5c29f55cf5f32c23012bfec9f11c833738a212aa5774a7a5423c2af SHA512 38106430a2a5c35eee8786a5a4bdf0ae35fd031876a5c7742536078ba9d0793b7b25d55663a6b589b75e0ccdff0629c8389fc833dad4723eb51a99c51d80321d WHIRLPOOL 7ba5b3efcf6aeee8a12c006db5e0a91f1be51aace8e263b3086b628cb5932b0df75f20529d3ac00dd872213e1e99fd3c7af72deac08eb3595c16f94a3af148cc +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-libs/libmuscle/files/3.7-bufferoverflow.patch b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch new file mode 100644 index 000000000000..384f17acfbf4 --- /dev/null +++ b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch @@ -0,0 +1,22 @@ +--- a/libMUSCLE/globalslinux.cpp ++++ b/libMUSCLE/globalslinux.cpp +@@ -159,7 +159,7 @@ + }
+ return DEFAULT_RAM;
+ }
+- int Bytes = atoi(pMem+9)*1000;
++ long Bytes = atol(pMem+9)*1000;
+ return ((double) Bytes)/1e6;
+ }
+
+--- a/libMUSCLE/progress.cpp ++++ b/libMUSCLE/progress.cpp +@@ -48,7 +48,7 @@ + if (MB < 0)
+ return "";
+
+- static char Str[9];
++ static char Str[11];
+ static double MaxMB = 0;
+ static double RAMMB = 0;
+
diff --git a/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch new file mode 100644 index 000000000000..2b2c28c8132a --- /dev/null +++ b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch @@ -0,0 +1,21 @@ +* Make build system parallel buildable +* Remove -funroll-loops and friends + +--- a/libMUSCLE/Makefile.am ++++ b/libMUSCLE/Makefile.am +@@ -1,6 +1,4 @@ +-OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations +-AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@ +-AM_LDFLAGS = $(OPTIMIZATION) ++AM_CXXFLAGS = -DNDEBUG=1 @OPENMP_CXXFLAGS@ + + LIBMUSCLE_H = \ + alpha.h cluster.h clust.h clustsetdf.h clustset.h clustsetmsa.h diaglist.h distcalc.h distfunc.h dpregionlist.h dpreglist.h edgelist.h enumopts.h enums.h estring.h gapscoredimer.h gonnet.h intmath.h msadist.h msa.h muscle.h objscore.h params.h profile.h pwpath.h refine.h scorehistory.h seq.h seqvect.h textfile.h timing.h tree.h types.h unixio.h threadstorage.h +@@ -36,6 +34,6 @@ + + + muscle_SOURCES = main.cpp +-muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la ++muscle_LDADD = libMUSCLE-3.7.la + + diff --git a/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild new file mode 100644 index 000000000000..d3a8107c1052 --- /dev/null +++ b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="mirror://gentoo/${P}-r1.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc static-libs" + +RDEPEND="!sci-biology/muscle" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${PV}-bufferoverflow.patch + "${FILESDIR}"/${PN}-3.7-fix-build-system.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + + # package provides .pc file + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libmuscle/metadata.xml b/sci-libs/libmuscle/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-libs/libmuscle/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |