cufflinks: Clean up

[Jason W. Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Tue Sep 5 15:39:02 2017 -0500
Changeset:	989b6819e56526b737eeef050d761fb58a063528

Modified Files:
	cufflinks/Makefile
	cufflinks/distinfo
	cufflinks/patches/patch-configure
	cufflinks/patches/patch-src_bundles.cpp

Log Message:
cufflinks: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=989b6819e56526b737eeef050d761fb58a063528

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 cufflinks/Makefile                      | 10 +++-------
 cufflinks/distinfo                      |  4 ++--
 cufflinks/patches/patch-configure       |  1 +
 cufflinks/patches/patch-src_bundles.cpp |  1 +
 4 files changed, 7 insertions(+), 9 deletions(-)

diffs:
diff --git a/cufflinks/Makefile b/cufflinks/Makefile
index 14a3d504bd..094f647ab3 100644
--- a/cufflinks/Makefile
+++ b/cufflinks/Makefile
@@ -11,8 +11,8 @@ MASTER_SITES=	http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
 
 MAINTAINER=	dsiercks%uwm.edu@localhost
 HOMEPAGE=	http://port.home.page/
-COMMENT=	Transcript assembly, differential expression and regulation for RNA-Seq
-# LICENSE=	
+COMMENT=	Transcript assembly, differential expression, regulation for RNA-Seq
+LICENSE=	boost-license
 
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
@@ -30,7 +30,6 @@ SUBST_SED.boost+=	-e 's|logl|log|g'
 SUBST_SED.boost+=	-e 's|long double|double|g'
 SUBST_SED.boost+=	-e 's|Lf|lf|g'
 SUBST_SED.boost+=	-e 's|Lg|lg|g'
-SUBST_MESSAGE.boost=	"Substituting for boost"
 SUBST_FILES.boost+=	${WRKSRC}/src/abundances.cpp
 SUBST_FILES.boost+=	${WRKSRC}/src/abundances.h
 SUBST_FILES.boost+=	${WRKSRC}/src/assemble.h
@@ -60,11 +59,8 @@ SUBST_STAGE.boolint=	post-patch
 SUBST_FILES.boolint=	${WRKSRC}/src/rounding.h
 SUBST_SED.boolint+=	-e 's|int& is_up|bool\& is_up|g'
 
-# CONFIGURE_ARGS are not linker flags.  Run configure --help to see
-# proper usage of --with-bam
 CONFIGURE_ARGS+=--with-bam=${PREFIX}/samtools0119 --with-boost
-# CONFIGURE_ARGS+=--with-bam="-L${PREFIX}/lib ${LINKER_RPATH_FLAG}${PREFIX}/lib"
-CFLAGS+=	-I${LOCALBASE}/include/eigen3
+CFLAGS+=	-I${PREFIX}/include/eigen3
 LDFLAGS+=	-lboost_system -lboost_iostreams -lboost_thread
 
 PORTVERSION=	2.1.1
diff --git a/cufflinks/distinfo b/cufflinks/distinfo
index 81e81fe708..af145bf68f 100644
--- a/cufflinks/distinfo
+++ b/cufflinks/distinfo
@@ -4,5 +4,5 @@ SHA1 (cufflinks-2.1.1.tar.gz) = 9c5bf3d3872e8dd358ba7d7407644ab2cbbfdcb6
 RMD160 (cufflinks-2.1.1.tar.gz) = 4a612f98be24d7d31520be0501f1f4bcd3e76e0f
 SHA512 (cufflinks-2.1.1.tar.gz) = 3a52852d356240eeb24bfc10e449524499f03e8b908133f35e7fcb6ccb5d3566bacd99aa752082081b601fcd2872f5335473ccecb2cd1cb9a9224af41b224c29
 Size (cufflinks-2.1.1.tar.gz) = 705930 bytes
-SHA1 (patch-configure) = fa6121ad0abad7bfcc9cfc585b395999b107277c
-SHA1 (patch-src_bundles.cpp) = d90c68a2613c42b182e5dc4250f0609e55789c5b
+SHA1 (patch-configure) = 87a10d1d224f60370f6c42f901460529f57df59f
+SHA1 (patch-src_bundles.cpp) = fcb5e8ba79faa1d1fdebcbe96da0fbc54d959b6e
diff --git a/cufflinks/patches/patch-configure b/cufflinks/patches/patch-configure
index feac27b992..ba01890fdd 100644
--- a/cufflinks/patches/patch-configure
+++ b/cufflinks/patches/patch-configure
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Non-portable shell feature
 --- configure.orig	2013-04-11 13:09:12.000000000 +0000
 +++ configure
 @@ -6339,7 +6339,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"
diff --git a/cufflinks/patches/patch-src_bundles.cpp b/cufflinks/patches/patch-src_bundles.cpp
index 9b37ebfe38..d216a57160 100644
--- a/cufflinks/patches/patch-src_bundles.cpp
+++ b/cufflinks/patches/patch-src_bundles.cpp
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Constant too big for int on some systems
 --- src/bundles.cpp.orig	2013-04-04 14:41:19.000000000 +0000
 +++ src/bundles.cpp
 @@ -677,7 +677,7 @@ double BundleFactory::next_valid_alignme