samtools: Clean up patches, eliminate bin subdirectory

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: samtools: Clean up patches, eliminate bin subdirectory
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Fri, 19 May 2017 13:46:32 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri May 19 08:46:32 2017 -0500
Changeset:	663f74fbc384ec79c5826bbcff57752edc8dc5f8

Modified Files:
	samtools/Makefile
	samtools/PLIST
	samtools/distinfo
	samtools/patches/patch-Makefile
	samtools/patches/patch-configure.ac
Removed Files:
	samtools/patches/patch-test_test.pl

Log Message:
samtools: Clean up patches, eliminate bin subdirectory

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=663f74fbc384ec79c5826bbcff57752edc8dc5f8

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

diffstat:
 samtools/Makefile                   | 13 ---------
 samtools/PLIST                      | 40 +++++++++++++--------------
 samtools/distinfo                   |  5 ++--
 samtools/patches/patch-Makefile     | 54 ++++++++++++++++++++++++-------------
 samtools/patches/patch-configure.ac |  4 +--
 samtools/patches/patch-test_test.pl | 33 -----------------------
 6 files changed, 59 insertions(+), 90 deletions(-)

diffs:
diff --git a/samtools/Makefile b/samtools/Makefile
index c2c8be3e1d..800eea9cb9 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -17,24 +17,11 @@ COMMENT=	Tools for manipulating next-generation sequencing data
 
 LICENSE=	mit
 
-#USE_LANGUAGES=	c c++
 USE_TOOLS+=	autoconf automake autoreconf gmake perl
 GNU_CONFIGURE=	yes
 REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
 REPLACE_PYTHON=	misc/*.py
 
-SUBST_CLASSES+=		version
-SUBST_STAGE.version=	post-patch
-SUBST_SED.version+=	-e 's|@PORTVERSION@|${PORTVERSION}|g'
-SUBST_FILES.version+=	${WRKSRC}/configure.ac
-
-CPPFLAGS+=	-I${PREFIX}/include
-MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
-		INSTALL_DATA="${INSTALL_DATA}" \
-		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
-		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
-		INSTALL_DIR="${MKDIR}"
-
 PORTVERSION=	1.3.1
 
 post-patch:
diff --git a/samtools/PLIST b/samtools/PLIST
index 114d658330..5ab65fe32e 100644
--- a/samtools/PLIST
+++ b/samtools/PLIST
@@ -1,24 +1,24 @@
 @comment $NetBSD$
+bin/ace2sam
+bin/blast2sam.pl
+bin/bowtie2sam.pl
+bin/export2sam.pl
+bin/interpolate_sam.pl
+bin/maq2sam-long
+bin/maq2sam-short
+bin/md5fa
+bin/md5sum-lite
+bin/novo2sam.pl
+bin/plot-bamstats
+bin/psl2sam.pl
+bin/sam2vcf.pl
 bin/samtools
-bin/samtools_misc/ace2sam
-bin/samtools_misc/blast2sam.pl
-bin/samtools_misc/bowtie2sam.pl
-bin/samtools_misc/export2sam.pl
-bin/samtools_misc/interpolate_sam.pl
-bin/samtools_misc/maq2sam-long
-bin/samtools_misc/maq2sam-short
-bin/samtools_misc/md5fa
-bin/samtools_misc/md5sum-lite
-bin/samtools_misc/novo2sam.pl
-bin/samtools_misc/plot-bamstats
-bin/samtools_misc/psl2sam.pl
-bin/samtools_misc/sam2vcf.pl
-bin/samtools_misc/samtools.pl
-bin/samtools_misc/seq_cache_populate.pl
-bin/samtools_misc/soap2sam.pl
-bin/samtools_misc/varfilter.py
-bin/samtools_misc/wgsim
-bin/samtools_misc/wgsim_eval.pl
-bin/samtools_misc/zoom2sam.pl
+bin/samtools.pl
+bin/seq_cache_populate.pl
+bin/soap2sam.pl
+bin/varfilter.py
+bin/wgsim
+bin/wgsim_eval.pl
+bin/zoom2sam.pl
 man/man1/samtools.1
 man/man1/wgsim.1
diff --git a/samtools/distinfo b/samtools/distinfo
index 45ccfb0afe..1639e69314 100644
--- a/samtools/distinfo
+++ b/samtools/distinfo
@@ -4,6 +4,5 @@ SHA1 (samtools-1.3.1.tar.gz) = 1d5d2bca1742115ed0bc950b9c21132e9872768d
 RMD160 (samtools-1.3.1.tar.gz) = 8c559e3e4e548e8b8858e10b05ecf59e6d370101
 SHA512 (samtools-1.3.1.tar.gz) = 9ad5a7e25db73454c7f7661ebbfba372cfaa86f543d57302736a0021adefe068e6571d8095e13d0faa37a63c2051636b7ac232463117540b0d7571391af7cfb1
 Size (samtools-1.3.1.tar.gz) = 3757176 bytes
-SHA1 (patch-Makefile) = 25cc57e96740a2d209db1e1b358f692c2ae9ff6f
-SHA1 (patch-configure.ac) = 990c8588e07ce03b74821a634c27b70c055a2a84
-SHA1 (patch-test_test.pl) = 3245d783901f98ba19f90253a15e455cd52dfd26
+SHA1 (patch-Makefile) = bf0bd9cbce2f5c5c91f0c704fd7dc1aa1f12e61a
+SHA1 (patch-configure.ac) = 8a37d938d49f7def394dd3f73a41e139151cad4a
diff --git a/samtools/patches/patch-Makefile b/samtools/patches/patch-Makefile
index fb8a59c3af..287273644a 100644
--- a/samtools/patches/patch-Makefile
+++ b/samtools/patches/patch-Makefile
@@ -3,17 +3,32 @@ $NetBSD$
 # Respect build env
 --- Makefile.orig	2016-04-22 09:22:44.000000000 +0000
 +++ Makefile
-@@ -38,18 +38,18 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
+@@ -21,10 +21,10 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC       = gcc
+-CPPFLAGS =
+-CFLAGS   = -g -Wall -O2
+-LDFLAGS  =
++CC       ?= gcc
++CPPFLAGS ?=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  ?=
+ LIBS     =
+ 
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+@@ -38,20 +38,13 @@ AOBJS=      bam_index.o bam_plcmd.o sam_
              bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
              bam_quickcheck.o bam_addrprg.o
  
 -prefix      = /usr/local
-+prefix      = ${STAGEDIR}${PREFIX}
++prefix      = $(STAGEDIR)$(PREFIX)
  exec_prefix = $(prefix)
  bindir      = $(exec_prefix)/bin
  datarootdir = $(prefix)/share
 -mandir      = $(datarootdir)/man
-+mandir      = $(prefix)/man
++mandir      = $(PKGMANDIR)/man
  man1dir     = $(mandir)/man1
  
 -MKDIR_P = mkdir -p
@@ -21,15 +36,12 @@ $NetBSD$
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
-+#MKDIR_P = mkdir -p
-+#INSTALL = install -p
-+#INSTALL_PROGRAM = $(INSTALL)
-+#INSTALL_DATA    = $(INSTALL) -m 644
-+#INSTALL_DIR     = $(MKDIR_P) -m 755
- 
- 
+-
+-
  PROGRAMS = samtools
-@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
+ 
+ BUILT_MISC_PROGRAMS = \
+@@ -59,7 +52,6 @@ BUILT_MISC_PROGRAMS = \
  	misc/md5fa misc/md5sum-lite misc/wgsim
  
  MISC_PROGRAMS = \
@@ -37,7 +49,7 @@ $NetBSD$
  	misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
  	misc/interpolate_sam.pl misc/novo2sam.pl \
  	misc/plot-bamstats misc/psl2sam.pl \
-@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
+@@ -82,7 +74,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) 
  # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
  ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
  ALL_LDFLAGS  = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
@@ -46,16 +58,20 @@ $NetBSD$
  
  # Usually config.mk and config.h are generated by running configure
  # or config.status, but if those aren't used create defaults here.
-@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
+@@ -280,10 +272,12 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
  
  
  install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
 -	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
 -	$(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) 
-+	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
-+	$(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
-+	$(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
- 	$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
- 
+-	$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
+-
++	$(BSD_INSTALL_PROGRAM_DIR) $(DESTDIR)$(bindir)
++	$(BSD_INSTALL_MAN_DIR) $(DESTDIR)$(man1dir) 
++	$(BSD_INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
++	$(BSD_INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)
++	$(BSD_INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
++	$(BSD_INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
  
+ testclean:
+ 	-rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
diff --git a/samtools/patches/patch-configure.ac b/samtools/patches/patch-configure.ac
index d6432d7d10..33645329cf 100644
--- a/samtools/patches/patch-configure.ac
+++ b/samtools/patches/patch-configure.ac
@@ -1,6 +1,6 @@
 $NetBSD$
 
-# Fix version check and add deps to configure script
+# Replace non-portable version check and add deps to configure script
 --- configure.ac.orig	2015-12-15 21:26:20 UTC
 +++ configure.ac
 @@ -23,12 +23,15 @@
@@ -8,7 +8,7 @@ $NetBSD$
  
  dnl Process this file with autoconf to produce a configure script
 -AC_INIT([Samtools], m4_esyscmd_s([make print-version]),
-+AC_INIT([Samtools], [1.3],
++AC_INIT([Samtools], [1.3.1],
          [samtools-help%lists.sourceforge.net@localhost], [], [http://www.htslib.org/])
  AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
  AC_CONFIG_SRCDIR([bamtk.c])
diff --git a/samtools/patches/patch-test_test.pl b/samtools/patches/patch-test_test.pl
deleted file mode 100644
index 2c965f6d4e..0000000000
--- a/samtools/patches/patch-test_test.pl
+++ /dev/null
@@ -1,33 +0,0 @@
-$NetBSD$
-
-# Fix hard-coded paths
-# FIXME: FreeBSD-specific: Use a SUBST for this instead
---- test/test.pl.orig	2015-12-22 22:43:15 UTC
-+++ test/test.pl
-@@ -136,7 +136,7 @@ sub _cmd
-     else
-     {
-         # child
--        exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
-+        exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!");
-     }
- }
- sub cmd
-@@ -560,7 +560,7 @@ sub test_usage
-     my $command = $args{cmd};
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
--    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
-+    if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
- 
-     my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
- 
-@@ -615,7 +615,7 @@ sub test_usage_subcommand
-     my $commandpath = $$opts{bin}."/".$command;
-     my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
- 
--    if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
-+    if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
- 
-     if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }
-
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