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cufflinks-2.2.1: Clean up

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This commit is contained in:
Jason W. Bacon 2017-09-05 15:49:52 -05:00
parent 989b6819e5
commit 97118ec373
4 changed files with 11 additions and 8 deletions
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13
cufflinks-2.2.1/Makefile
View file

@ -11,17 +11,17 @@ DISTNAME= cufflinks-2.2.1
CATEGORIES= biology
MASTER_SITES= http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
MAINTAINER= jwbacon@tds.net
MAINTAINER= bacon4000@gmail.com
COMMENT= RNA transcript assembly, differential expression/regulation
# LICENSE=
LICENSE= boost-license
USE_LANGUAGES= c c++
GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --with-bam=${PREFIX}/samtools0119
# Darwin
CFLAGS+= -I${LOCALBASE}/include/eigen3
CFLAGS+= -I${PREFIX}/include/eigen3
# These are getting left out on CentOS and Darwin in spite of buildlink
LDFLAGS+= -L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization
@ -29,18 +29,19 @@ LDFLAGS+= -L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization
SUBST_CLASSES+= arch
SUBST_STAGE.arch= post-patch
SUBST_FILES.arch= configure
SUBST_SED.arch= 's|arch -k|arch|g'
SUBST_SED.arch= -e 's|arch -k|arch|g'
# Allow compiling on i386
SUBST_CLASSES+= cflags
SUBST_STAGE.cflags= post-patch
SUBST_FILES.cflags= configure
SUBST_SED.cflags= 's|-arch x86_64||g'
SUBST_SED.cflags= -e 's|-arch x86_64||g'
SUBST_CLASSES+= ldouble
SUBST_STAGE.ldouble= post-patch
SUBST_FILES.ldouble= ${WRKSRC}/src/*.cpp ${WRKSRC}/src/*.h
SUBST_SED.ldouble= -e 's|logl|log|g' -e 's|long double|double|g'
SUBST_SED.ldouble= -e 's|logl|log|g'
SUBST_SED.ldouble+= -e 's|long double|double|g'
.include "../../wip/samtools0119/buildlink3.mk"
.include "../../devel/boost-libs/buildlink3.mk"

4
cufflinks-2.2.1/distinfo
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@ -4,5 +4,5 @@ SHA1 (cufflinks-2.2.1.tar.gz) = 2b1b3a8f12cd2821ffc74ffbdd55cb329f37cbbb
RMD160 (cufflinks-2.2.1.tar.gz) = 6378571ecb06971d1dff5b6ef81a55b36a8be498
SHA512 (cufflinks-2.2.1.tar.gz) = 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
Size (cufflinks-2.2.1.tar.gz) = 766280 bytes
SHA1 (patch-configure) = 24e592c47e814f5c355a2351752473507ed9fca5
SHA1 (patch-src_bundles.cpp) = 4240e40a3f16223e868a421248972f057b3a74f4
SHA1 (patch-configure) = 3ed0a4c440baaf059f0c947612d6e722b5d3a6c8
SHA1 (patch-src_bundles.cpp) = 365ca5a444b2394191a5fbd5064583ec8329edb2

1
cufflinks-2.2.1/patches/patch-configure
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@ -1,5 +1,6 @@
$NetBSD$
# Non-portable shell feature
--- configure.orig 2015-09-30 01:19:17.827123473 +0000
+++ configure
@@ -7592,7 +7592,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"

1
cufflinks-2.2.1/patches/patch-src_bundles.cpp
View file

@ -1,5 +1,6 @@
$NetBSD: patch-src_bundles.cpp,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
# Const too big for int on some systems
--- src/bundles.cpp.orig 2014-03-24 21:54:47.000000000 +0000
+++ src/bundles.cpp
@@ -698,7 +698,7 @@ double BundleFactory::next_valid_alignme