cufflinks-2.2.1: 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 15:49:52 2017 -0500
Changeset:	97118ec373ad5a4f13c25f75c0efc212c3a24926

Modified Files:
	cufflinks-2.2.1/Makefile
	cufflinks-2.2.1/distinfo
	cufflinks-2.2.1/patches/patch-configure
	cufflinks-2.2.1/patches/patch-src_bundles.cpp

Log Message:
cufflinks-2.2.1: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=97118ec373ad5a4f13c25f75c0efc212c3a24926

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

diffstat:
 cufflinks-2.2.1/Makefile                      | 13 +++++++------
 cufflinks-2.2.1/distinfo                      |  4 ++--
 cufflinks-2.2.1/patches/patch-configure       |  1 +
 cufflinks-2.2.1/patches/patch-src_bundles.cpp |  1 +
 4 files changed, 11 insertions(+), 8 deletions(-)

diffs:
diff --git a/cufflinks-2.2.1/Makefile b/cufflinks-2.2.1/Makefile
index d6ce28370b..1bf7a4b8f6 100644
--- a/cufflinks-2.2.1/Makefile
+++ b/cufflinks-2.2.1/Makefile
@@ -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@localhost
+MAINTAINER=	bacon4000%gmail.com@localhost
 
 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"
diff --git a/cufflinks-2.2.1/distinfo b/cufflinks-2.2.1/distinfo
index dd715127b4..757d2db4d4 100644
--- a/cufflinks-2.2.1/distinfo
+++ b/cufflinks-2.2.1/distinfo
@@ -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
diff --git a/cufflinks-2.2.1/patches/patch-configure b/cufflinks-2.2.1/patches/patch-configure
index ba09a47d4e..24dc2b508e 100644
--- a/cufflinks-2.2.1/patches/patch-configure
+++ b/cufflinks-2.2.1/patches/patch-configure
@@ -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"
diff --git a/cufflinks-2.2.1/patches/patch-src_bundles.cpp b/cufflinks-2.2.1/patches/patch-src_bundles.cpp
index a3bc28123a..a309d1e2d6 100644
--- a/cufflinks-2.2.1/patches/patch-src_bundles.cpp
+++ b/cufflinks-2.2.1/patches/patch-src_bundles.cpp
@@ -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