Update cufflinks from jb-wip

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Update cufflinks from jb-wip
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 11 May 2016 15:33:37 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 10:33:37 2016 -0500
Changeset:	4f49a5cb1d02c7b5fea9439220d24372bc76a622

Modified Files:
	cufflinks/DESCR
	cufflinks/Makefile
	cufflinks/PLIST
	cufflinks/distinfo
	cufflinks/patches/patch-configure
	cufflinks/patches/patch-src_bundles.cpp
Added Files:
	cufflinks/TODO

Log Message:
Update cufflinks from jb-wip

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4f49a5cb1d02c7b5fea9439220d24372bc76a622

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

diffstat:
 cufflinks/DESCR                         |   5 +-
 cufflinks/Makefile                      | 105 +++++++++++++++++++-------------
 cufflinks/PLIST                         |   4 +-
 cufflinks/TODO                          |   1 +
 cufflinks/distinfo                      |  13 ++--
 cufflinks/patches/patch-configure       |  32 +++++++++-
 cufflinks/patches/patch-src_bundles.cpp |   8 +--
 7 files changed, 105 insertions(+), 63 deletions(-)

diffs:
diff --git a/cufflinks/DESCR b/cufflinks/DESCR
index 4eecdb7..845dbab 100644
--- a/cufflinks/DESCR
+++ b/cufflinks/DESCR
@@ -1,4 +1 @@
-Cufflinks assembles transcripts, estimates their abundances, and tests for
-differential expression and regulation in RNA-Seq samples.
-
-WWW: http://port.home.page/
+[description of the port]
diff --git a/cufflinks/Makefile b/cufflinks/Makefile
index eeac0a3..8602955 100644
--- a/cufflinks/Makefile
+++ b/cufflinks/Makefile
@@ -1,62 +1,79 @@
-# $NetBSD: Makefile,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
-
+# $NetBSD$
+#
 ###########################################################
 #               Generated by fbsd2pkg                     #
 ###########################################################
+# Do not upgrade to 2.2.1 until crash bugs are worked out
 
-###################################
-# Unconverted FreeBSD port syntax:
-
-# # FIXME: Find logl somewhere instead of falling back to log
-# # FIXME: boost problem and hackaround: https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
-# post-patch:
-# 	${REINPLACE_CMD} \
-# 		-e 's|logl|log|g' \
-# 		-e 's|long double|double|g' \
-# 		${WRKSRC}/src/*.cpp \
-# 		${WRKSRC}/src/*.h
-# .include <bsd.port.mk>
-
-DISTNAME=	cufflinks-2.2.1
+DISTNAME=	cufflinks-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
 
-MAINTAINER=	jwbacon%tds.net@localhost
-
-COMMENT=	RNA transcript assembly, differential expression/regulation
+MAINTAINER=	dsiercks%uwm.edu@localhost
+HOMEPAGE=	http://port.home.page/
+COMMENT=	Transcript assembly, differential expression and regulation for RNA-Seq
 # LICENSE=	
 
-# Pessimistic assumption.  Test and change if possible.
-MAKE_JOBS_SAFE=	no
-
-# Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
+REPLACE_PYTHON=	src/cuffmerge
+
+# FIXME: boost problem with long double and hackaround: https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
+# Just using double instead for now
+SUBST_CLASSES+=		boost
+SUBST_STAGE.boost=	post-patch
+SUBST_SED.boost+=	-e 's|shared_ptr|boost::shared_ptr|g'
+SUBST_SED.boost+=	-e 's|boost::shared_ptr.hpp|shared_ptr.hpp|g'
+SUBST_SED.boost+=	-e 's|boost::boost::|boost::|g'
+SUBST_SED.boost+=	-e 's|^mutex|boost::mutex|g'
+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 \
+			${WRKSRC}/src/abundances.h \
+			${WRKSRC}/src/assemble.h \
+			${WRKSRC}/src/biascorrection.cpp \
+			${WRKSRC}/src/biascorrection.h \
+			${WRKSRC}/src/bundles.cpp \
+			${WRKSRC}/src/bundles.cpp.orig \
+			${WRKSRC}/src/bundles.h \
+			${WRKSRC}/src/clustering.cpp \
+			${WRKSRC}/src/common.h \
+			${WRKSRC}/src/compress_gtf.cpp \
+			${WRKSRC}/src/cuffdiff.cpp \
+			${WRKSRC}/src/cufflinks.cpp \
+			${WRKSRC}/src/differential.cpp \
+			${WRKSRC}/src/differential.h \
+			${WRKSRC}/src/filters.cpp \
+			${WRKSRC}/src/filters.h \
+			${WRKSRC}/src/gtf_to_sam.cpp \
+			${WRKSRC}/src/hits.h \
+			${WRKSRC}/src/replicates.cpp \
+			${WRKSRC}/src/replicates.h \
+			${WRKSRC}/src/scaffolds.cpp \
+			${WRKSRC}/src/scaffolds.h
 
-# Darwin
+SUBST_CLASSES+=		boolint
+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${LOCALBASE}/include/eigen3
-# These are getting left out on CentOS and Darwin in spite of buildlink
-LDFLAGS+=	-L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization
-
-# Darwin i386 Snow Leopard doesn't support /bin/arch or /usr/bin/arch -k
-SUBST_CLASSES+=		arch
-SUBST_STAGE.arch=	post-patch
-SUBST_FILES.arch=	configure
-SUBST_SED.arch=		'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'
-
-.include "../../wip/samtools/buildlink3.mk"
+LDFLAGS+=	-lboost_system -lboost_iostreams -lboost_thread
+
+PORTVERSION=	2.1.1
+
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/eigen3/buildlink3.mk"
 .include "../../devel/boost-libs/buildlink3.mk"
 .include "../../devel/boost-headers/buildlink3.mk"
 .include "../../devel/boost-jam/buildlink3.mk"
-# CentOS can't find libbam without this.  samtools buildlink issue?
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../math/eigen3/buildlink3.mk"
-.include "../../lang/python/application.mk"
+.include "../../wip/samtools0119/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/cufflinks/PLIST b/cufflinks/PLIST
index f9111cd..21e89aa 100644
--- a/cufflinks/PLIST
+++ b/cufflinks/PLIST
@@ -1,10 +1,8 @@
-@comment $NetBSD: PLIST,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+@comment $NetBSD$
 bin/compress_gtf
 bin/cuffcompare
 bin/cuffdiff
 bin/cufflinks
 bin/cuffmerge
-bin/cuffnorm
-bin/cuffquant
 bin/gffread
 bin/gtf_to_sam
diff --git a/cufflinks/TODO b/cufflinks/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/cufflinks/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/cufflinks/distinfo b/cufflinks/distinfo
index a48ab68..81e81fe 100644
--- a/cufflinks/distinfo
+++ b/cufflinks/distinfo
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+$NetBSD$
 
-SHA1 (cufflinks-2.2.1.tar.gz) = 2b1b3a8f12cd2821ffc74ffbdd55cb329f37cbbb
-RMD160 (cufflinks-2.2.1.tar.gz) = 6378571ecb06971d1dff5b6ef81a55b36a8be498
-Size (cufflinks-2.2.1.tar.gz) = 766280 bytes
-SHA1 (patch-configure) = 24e592c47e814f5c355a2351752473507ed9fca5
-SHA1 (patch-src_bundles.cpp) = 4240e40a3f16223e868a421248972f057b3a74f4
+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
diff --git a/cufflinks/patches/patch-configure b/cufflinks/patches/patch-configure
index ba09a47..feac27b 100644
--- a/cufflinks/patches/patch-configure
+++ b/cufflinks/patches/patch-configure
@@ -1,8 +1,8 @@
 $NetBSD$
 
---- configure.orig	2015-09-30 01:19:17.827123473 +0000
+--- configure.orig	2013-04-11 13:09:12.000000000 +0000
 +++ configure
-@@ -7592,7 +7592,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"
+@@ -6339,7 +6339,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"
  export LDFLAGS
  export EIGEN_CPPFLAGS
  
@@ -11,3 +11,31 @@ $NetBSD$
  
  
  cat >>confdefs.h <<\_ACEOF
+@@ -6974,7 +6974,7 @@ case "${host_cpu}-${host_os}" in
+   i*86-*linux*)
+ 	    ext_CFLAGS="-march=i686";;
+   i*86-darwin*)
+-	CFLAGS="-m64"
++	# CFLAGS="-m64"
+ 	cat >conftest.$ac_ext <<_ACEOF
+ /* confdefs.h.  */
+ _ACEOF
+@@ -7022,7 +7022,7 @@ rm -f conftest.err conftest.$ac_objext c
+   *)
+     echo "$as_me:$LINENO: checking if gcc accepts -m64" >&5
+ echo $ECHO_N "checking if gcc accepts -m64... $ECHO_C" >&6
+-    CFLAGS="-m64"
++    # CFLAGS="-m64"
+     cat >conftest.$ac_ext <<_ACEOF
+ /* confdefs.h.  */
+ _ACEOF
+@@ -7060,7 +7060,8 @@ if { (eval echo "$as_me:$LINENO: \"$ac_c
+   ac_status=$?
+   echo "$as_me:$LINENO: \$? = $ac_status" >&5
+   (exit $ac_status); }; }; then
+-  ext_CFLAGS="-m64"; echo "$as_me:$LINENO: result: yes" >&5
++  # ext_CFLAGS="-m64";
++echo "$as_me:$LINENO: result: yes" >&5
+ echo "${ECHO_T}yes" >&6
+ else
+   echo "$as_me: failed program was:" >&5
diff --git a/cufflinks/patches/patch-src_bundles.cpp b/cufflinks/patches/patch-src_bundles.cpp
index a3bc281..9b37ebf 100644
--- a/cufflinks/patches/patch-src_bundles.cpp
+++ b/cufflinks/patches/patch-src_bundles.cpp
@@ -1,13 +1,13 @@
-$NetBSD: patch-src_bundles.cpp,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+$NetBSD$
 
---- src/bundles.cpp.orig	2014-03-24 21:54:47.000000000 +0000
+--- src/bundles.cpp.orig	2013-04-04 14:41:19.000000000 +0000
 +++ src/bundles.cpp
-@@ -698,7 +698,7 @@ double BundleFactory::next_valid_alignme
+@@ -677,7 +677,7 @@ double BundleFactory::next_valid_alignme
          if (!_hit_fac->get_hit_from_buf(hit_buf, tmp, false))
              continue;
          
 -		if (tmp.ref_id() == 12638153115695167477)  // corresponds to SAM "*" under FNV hash. unaligned read record 
-+		if (tmp.ref_id() == 12638153115695167477ULL)  // corresponds to SAM "*" under FNV hash. unaligned read record 
++		if (tmp.ref_id() == 12638153115695167477LL)  // corresponds to SAM "*" under FNV hash. unaligned read record 
              continue;
          
  		raw_mass += tmp.mass();
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