svn commit: r404398 - in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files
Jason Unovitch
junovitch at FreeBSD.org
Fri Dec 25 01:31:12 UTC 2015
Author: junovitch
Date: Fri Dec 25 01:31:09 2015
New Revision: 404398
URL: https://svnweb.freebsd.org/changeset/ports/404398
Log:
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3
- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's
PR: 205524
PR: 205525
PR: 205526
Submitted by: cartwright at asu.edu (maintainer)
Added:
head/biology/bcftools/files/patch-test_test.pl (contents, props changed)
head/biology/htslib/files/patch-hfile__libcurl.c (contents, props changed)
head/biology/samtools/files/ax_with_curses.m4 (contents, props changed)
head/biology/samtools/files/ax_with_htslib.m4 (contents, props changed)
head/biology/samtools/files/patch-configure.ac (contents, props changed)
head/biology/samtools/files/patch-dict.c (contents, props changed)
head/biology/samtools/files/patch-test_test.pl (contents, props changed)
Deleted:
head/biology/bcftools/files/patch-plugins_fixploidy.mk
head/biology/bcftools/files/patch-plugins_vcf2sex.mk
head/biology/htslib/files/patch-cram_cram__io.c
Modified:
head/biology/bcftools/Makefile
head/biology/bcftools/distinfo
head/biology/bcftools/files/patch-Makefile
head/biology/bcftools/files/patch-prob1.c
head/biology/bcftools/files/pkg-message.in
head/biology/bcftools/pkg-plist
head/biology/htslib/Makefile
head/biology/htslib/distinfo
head/biology/htslib/files/patch-Makefile
head/biology/htslib/files/patch-configure.ac
head/biology/htslib/pkg-plist
head/biology/samtools/Makefile
head/biology/samtools/distinfo
head/biology/samtools/files/patch-Makefile
head/biology/samtools/files/patch-errmod.c
head/biology/samtools/files/pkg-message.in
head/biology/samtools/pkg-plist
Modified: head/biology/bcftools/Makefile
==============================================================================
--- head/biology/bcftools/Makefile Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/Makefile Fri Dec 25 01:31:09 2015 (r404398)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= bcftools
-PORTVERSION= 1.2
+PORTVERSION= 1.3
CATEGORIES= biology
MAINTAINER= cartwright at asu.edu
@@ -11,15 +11,17 @@ COMMENT= Tools for manipulating next-gen
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
-BUILD_DEPENDS= htslib>=1.2:${PORTSDIR}/biology/htslib
+BUILD_DEPENDS= htslib>=1.3:${PORTSDIR}/biology/htslib
LIB_DEPENDS= libhts.so:${PORTSDIR}/biology/htslib
+TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
USE_GITHUB= yes
GH_ACCOUNT= samtools
-USES= gmake shebangfix
+USES= gmake perl5 shebangfix
+USE_PERL5= test
SUB_FILES= pkg-message
-SHEBANG_FILES= vcfutils.pl
+SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
OPTIONS_DEFINE= GPL
GPL_DESC= Enable modules that rely on GPL code
@@ -33,10 +35,10 @@ CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
- INSTALL_DATA="${INSTALL_DATA}" \
- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
- INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
- INSTALL_DIR="${MKDIR}"
+ INSTALL_DATA="${INSTALL_DATA}" \
+ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+ INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
+ INSTALL_DIR="${MKDIR}"
.if ${PORT_OPTIONS:MGPL}
MAKE_ENV+= USE_GPL=1
@@ -45,4 +47,6 @@ LICENSE= GPLv3
PLIST_SUB= PORTVERSION="${PORTVERSION}"
+TEST_TARGET= test
+
.include <bsd.port.mk>
Modified: head/biology/bcftools/distinfo
==============================================================================
--- head/biology/bcftools/distinfo Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/distinfo Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,2 +1,2 @@
-SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba
-SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625
+SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8
+SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041
Modified: head/biology/bcftools/files/patch-Makefile
==============================================================================
--- head/biology/bcftools/files/patch-Makefile Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/files/patch-Makefile Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,84 +1,78 @@
---- Makefile.orig 2015-02-02 15:40:17 UTC
+--- Makefile.orig 2015-12-15 21:42:34 UTC
+++ Makefile
-@@ -29,14 +29,13 @@ TEST_PROG= test/test-rbuf
+@@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf
all: $(PROG) $(TEST_PROG)
# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = ../htslib
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
+-BGZIP = $(HTSDIR)/bgzip
+-TABIX = $(HTSDIR)/tabix
+HTSDIR = $(prefix)/include
+HTSLIB = -lhts
- BGZIP = $(HTSDIR)/bgzip
- TABIX = $(HTSDIR)/tabix
++BGZIP = $(HTSDIR)/../bin/bgzip
++TABIX = $(HTSDIR)/../bin/tabix
-CC = gcc
+-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
-+CC ?= cc
-+CFLAGS += -Wall
- DFLAGS =
+-LDFLAGS =
++CC ?= cc
++CPPFLAGS +=
++CFLAGS += -Wall
++LDFLAGS +=
+ LIBS =
+
OBJS = main.o vcfindex.o tabix.o \
- vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
-@@ -52,22 +51,15 @@ INCLUDES = -I. -I$(HTSDIR)
+@@ -57,26 +56,20 @@ GSL_LIBS =
ifdef USE_GPL
- CFLAGS += -DUSE_GPL
- OBJS += polysomy.o
-- LDLIBS = -lgsl -lcblas
-+ LDLIBS += -lgsl -lgslcblas
+ EXTRA_CPPFLAGS += -DUSE_GPL
+ OBJS += polysomy.o peakfit.o
+- GSL_LIBS = -lgsl -lcblas
++ GSL_LIBS = -lgsl -lgslcblas
endif
-prefix = /usr/local
+prefix = ${STAGEDIR}${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
+ libdir = $(exec_prefix)/lib
+ libexecdir = $(exec_prefix)/libexec
-mandir = $(prefix)/share/man
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
+ plugindir = $(libexecdir)/bcftools
+ pluginpath = $(plugindir)
+
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-
--
+ MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
+
all:$(PROG) plugins
+@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
+ $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
- # See htslib/Makefile
-@@ -102,8 +94,8 @@ PLUGINC = $(foreach dir, plugins, $(wild
- PLUGINS = $(PLUGINC:.c=.so)
- PLUGINM = $(PLUGINC:.c=.mk)
-
--%.so: %.c version.h version.c $(HTSDIR)/libhts.so
-- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
-+%.so: %.c version.h version.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -lhts
-
- -include $(PLUGINM)
-
-@@ -156,10 +148,10 @@ version.o: version.h version.c
- test/test-rbuf.o: test/test-rbuf.c rbuf.h
-
- test/test-rbuf: test/test-rbuf.o
-- $(CC) $(CFLAGS) -o $@ -lm -ldl $<
-+ $(CC) $(CFLAGS) -o $@ -lm $<
-
--bcftools: $(HTSLIB) $(OBJS)
-- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
-+bcftools: $(OBJS)
-+ $(CC) -pthread $(CFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lz -lm $(LDLIBS)
+ bcftools: $(HTSLIB) $(OBJS)
+- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
++ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
-@@ -170,8 +162,9 @@ doc/bcftools.html: doc/bcftools.txt
- docs: doc/bcftools.1 doc/bcftools.html
-
- install: $(PROG) doc/bcftools.1
-- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
-- $(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
-+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
+@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
+ # Since there is no make dependency, bcftools.1 can be out-of-date and
+ # make docs can be run to update if asciidoc is available
+ install: $(PROG)
+- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+- $(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
++ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+ $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
-+ $(INSTALL_SCRIPT) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)/samtools_misc
++ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
+ $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
- clean: testclean clean-plugins
Modified: head/biology/bcftools/files/patch-prob1.c
==============================================================================
--- head/biology/bcftools/files/patch-prob1.c Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/files/patch-prob1.c Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,15 +1,13 @@
---- prob1.c.orig 2015-04-28 01:28:23 UTC
+--- prob1.c.orig 2015-12-15 21:42:34 UTC
+++ prob1.c
-@@ -33,6 +33,14 @@ THE SOFTWARE. */
+@@ -33,6 +33,12 @@ THE SOFTWARE. */
#include <zlib.h>
#include "prob1.h"
+#include <sys/param.h>
-+#ifdef __FreeBSD__
-+# if __FreeBSD_version < 1000034
-+# define logl(x) log(x)
-+# define expl(x) exp(x)
-+# endif
++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
++# define logl(x) log(x)
++# define expl(x) exp(x)
+#endif
+
// #include "kstring.h"
Added: head/biology/bcftools/files/patch-test_test.pl
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bcftools/files/patch-test_test.pl Fri Dec 25 01:31:09 2015 (r404398)
@@ -0,0 +1,29 @@
+--- test/test.pl.orig 2015-12-22 22:45:13 UTC
++++ test/test.pl
+@@ -290,7 +290,7 @@ sub _cmd
+ else
+ {
+ # child
+- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
++ exec('/usr/local/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!");
+ }
+ return ($? >> 8, join('', at out));
+ }
+@@ -657,7 +657,7 @@ sub test_usage
+ my $command = $args{cmd};
+ my $commandpath = $$opts{bin}."/".$command;
+ my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
+- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
++ if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
+
+ my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
+
+@@ -708,7 +708,7 @@ sub test_usage_subcommand
+ my $subcommand = $args{subcmd};
+ my $commandpath = $$opts{bin}."/".$command;
+ my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
+- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
++ if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
+
+ my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
+
Modified: head/biology/bcftools/files/pkg-message.in
==============================================================================
--- head/biology/bcftools/files/pkg-message.in Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/files/pkg-message.in Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,2 +1,7 @@
+The miscellaneous tools included with Bcftools have been installed to
+%%PREFIX%%/bin/samtools_misc
-Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
+Add that directory to your path if you want to use these tools.
+
+Some of these tools depend on Perl5, and it will need to be installed to
+use them.
Modified: head/biology/bcftools/pkg-plist
==============================================================================
--- head/biology/bcftools/pkg-plist Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/bcftools/pkg-plist Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,4 +1,18 @@
bin/bcftools
+bin/samtools_misc/color-chrs.pl
bin/samtools_misc/plot-vcfstats
bin/samtools_misc/vcfutils.pl
+libexec/bcftools/color-chrs.so
+libexec/bcftools/counts.so
+libexec/bcftools/dosage.so
+libexec/bcftools/fill-AN-AC.so
+libexec/bcftools/fill-tags.so
+libexec/bcftools/fixploidy.so
+libexec/bcftools/frameshifts.so
+libexec/bcftools/impute-info.so
+libexec/bcftools/mendelian.so
+libexec/bcftools/missing2ref.so
+libexec/bcftools/setGT.so
+libexec/bcftools/tag2tag.so
+libexec/bcftools/vcf2sex.so
man/man1/bcftools.1.gz
Modified: head/biology/htslib/Makefile
==============================================================================
--- head/biology/htslib/Makefile Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/htslib/Makefile Fri Dec 25 01:31:09 2015 (r404398)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
-PORTVERSION= 1.2.1
+PORTVERSION= 1.3
CATEGORIES= biology devel
MAINTAINER= cartwright at asu.edu
@@ -12,13 +12,26 @@ LICENSE= BSD3CLAUSE MIT
LICENSE_COMB= multi
LICENSE_FILE= ${WRKSRC}/LICENSE
+TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
+
USE_GITHUB= yes
GH_ACCOUNT= samtools
-USES= gmake
+USES= autoreconf gmake perl5 shebangfix
+USE_PERL5= test
USE_LDCONFIG= yes
-USE_AUTOTOOLS= autoconf
-GNU_CONFIGURE=yes
+GNU_CONFIGURE= yes
+SHEBANG_FILES= test/compare_sam.pl test/test.pl test/test_view.pl
+
+OPTIONS_DEFINE= CURL
+OPTIONS_DEFAULT= CURL
+
+CURL_DESC= Use libcurl for network file access (HTTPS and S3 support).
+CURL_LIB_DEPENDS= libcurl.so:${PORTSDIR}/ftp/curl
+CURL_CONFIGURE_ENABLE= libcurl
+
+CPPFLAGS+= -I${LOCALBASE}/include
+LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
INSTALL_DATA="${INSTALL_DATA}" \
@@ -27,6 +40,8 @@ MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
PLIST_SUB= PORTVERSION="${PORTVERSION}"
+TEST_TARGET= test
+
post-patch:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
Modified: head/biology/htslib/distinfo
==============================================================================
--- head/biology/htslib/distinfo Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/htslib/distinfo Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,2 +1,2 @@
-SHA256 (samtools-htslib-1.2.1_GH0.tar.gz) = 4f67f0fc73ae86f3ed4336d8d8f6da3c12066e9cb5f142b685622dd6b8f9ae42
-SIZE (samtools-htslib-1.2.1_GH0.tar.gz) = 997625
+SHA256 (samtools-htslib-1.3_GH0.tar.gz) = 291a54090df3bc367b509890e1cfa34d53b1ee9be42c5fa6c2b1e2ec8f8b13af
+SIZE (samtools-htslib-1.3_GH0.tar.gz) = 1042953
Modified: head/biology/htslib/files/patch-Makefile
==============================================================================
--- head/biology/htslib/files/patch-Makefile Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/htslib/files/patch-Makefile Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,6 +1,6 @@
---- Makefile.orig 2015-02-03 16:22:23 UTC
+--- Makefile.orig 2015-12-15 16:34:33 UTC
+++ Makefile
-@@ -22,16 +22,9 @@
+@@ -22,16 +22,7 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
@@ -8,19 +8,18 @@
-AR = ar
-RANLIB = ranlib
-
--CPPFLAGS = -I.
-+CPPFLAGS += -I.
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-CPPFLAGS =
+-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
--LDLIBS =
+-LIBS =
# For now these don't work too well as samtools also needs to know to
# add -lbz2 and -llzma if linking against the static libhts.a library.
-@@ -57,16 +50,10 @@ bindir = $(exec_prefix)/bin
- includedir = $(prefix)/include
+@@ -58,16 +49,10 @@ includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
+ libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
-mandir = $(datarootdir)/man
+mandir = $(prefix)/man
@@ -35,18 +34,18 @@
-INSTALL_DIR = $(MKDIR_P) -m 755
+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
- BUILT_PROGRAMS = \
- bgzip \
-@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
+ # Set by config.mk if plugins are enabled
+ plugindir =
+@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
test/test-vcf-api \
test/test-vcf-sweep
--all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
-+all: lib-static lib-shared $(BUILT_PROGRAMS)
+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
HTSPREFIX =
include htslib_vars.mk
-@@ -332,7 +319,7 @@ installdirs:
+@@ -361,7 +346,7 @@ installdirs:
# and libhts.so.NN (used by client executables at runtime).
install-so: libhts.so installdirs
Modified: head/biology/htslib/files/patch-configure.ac
==============================================================================
--- head/biology/htslib/files/patch-configure.ac Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/htslib/files/patch-configure.ac Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,11 +1,11 @@
---- configure.ac.orig 2015-02-03 16:22:23 UTC
+--- configure.ac.orig 2015-12-15 16:34:33 UTC
+++ configure.ac
@@ -23,7 +23,7 @@
# DEALINGS IN THE SOFTWARE.
dnl Process this file with autoconf to produce a configure script
-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
-+AC_INIT([HTSlib], [@PORTVERSION@],
++AC_INIT([HTSlib], [1.3],
[samtools-help at lists.sourceforge.net], [], [http://www.htslib.org/])
AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
AC_CONFIG_SRCDIR(hts.c)
Added: head/biology/htslib/files/patch-hfile__libcurl.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/htslib/files/patch-hfile__libcurl.c Fri Dec 25 01:31:09 2015 (r404398)
@@ -0,0 +1,14 @@
+--- hfile_libcurl.c.orig 2015-12-22 22:35:42 UTC
++++ hfile_libcurl.c
+@@ -39,6 +39,11 @@ DEALINGS IN THE SOFTWARE. */
+
+ #include <curl/curl.h>
+
++#include <sys/param.h>
++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000033) && !defined(ENOTRECOVERABLE)
++# define ENOTRECOVERABLE EIO
++#endif
++
+ typedef struct {
+ hFILE base;
+ CURL *easy;
Modified: head/biology/htslib/pkg-plist
==============================================================================
--- head/biology/htslib/pkg-plist Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/htslib/pkg-plist Fri Dec 25 01:31:09 2015 (r404398)
@@ -2,10 +2,12 @@ bin/bgzip
bin/htsfile
bin/tabix
include/htslib/bgzf.h
+include/htslib/cram.h
include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
+include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h
include/htslib/khash_str2int.h
Modified: head/biology/samtools/Makefile
==============================================================================
--- head/biology/samtools/Makefile Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/samtools/Makefile Fri Dec 25 01:31:09 2015 (r404398)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= samtools
-PORTVERSION= 1.2
+PORTVERSION= 1.3
CATEGORIES= biology
MAINTAINER= cartwright at asu.edu
@@ -11,13 +11,17 @@ COMMENT= Tools for manipulating next-gen
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
-BUILD_DEPENDS= htslib>=1.2:${PORTSDIR}/biology/htslib
+BUILD_DEPENDS= htslib>=1.3:${PORTSDIR}/biology/htslib
LIB_DEPENDS= libhts.so:${PORTSDIR}/biology/htslib
+TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
USE_GITHUB= yes
-USES= gmake
+USES= autoreconf gmake perl5 shebangfix
+USE_PERL5= test
+GNU_CONFIGURE= yes
SUB_FILES= pkg-message
+SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
@@ -30,4 +34,11 @@ MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
PLIST_SUB= PORTVERSION="${PORTVERSION}"
+TEST_TARGET= test
+
+post-patch:
+ @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
+ ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
+ ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/
+
.include <bsd.port.mk>
Modified: head/biology/samtools/distinfo
==============================================================================
--- head/biology/samtools/distinfo Fri Dec 25 00:55:30 2015 (r404397)
+++ head/biology/samtools/distinfo Fri Dec 25 01:31:09 2015 (r404398)
@@ -1,2 +1,2 @@
-SHA256 (samtools-samtools-1.2_GH0.tar.gz) = e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47
-SIZE (samtools-samtools-1.2_GH0.tar.gz) = 4318615
+SHA256 (samtools-samtools-1.3_GH0.tar.gz) = f1eee9a217d547d9b483098519738ef351ec454f4a85cdb1e77ae8892fe858b5
+SIZE (samtools-samtools-1.3_GH0.tar.gz) = 3742904
Added: head/biology/samtools/files/ax_with_curses.m4
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/samtools/files/ax_with_curses.m4 Fri Dec 25 01:31:09 2015 (r404398)
@@ -0,0 +1,518 @@
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_WITH_CURSES
+#
+# DESCRIPTION
+#
+# This macro checks whether a SysV or X/Open-compatible Curses library is
+# present, along with the associated header file. The NcursesW
+# (wide-character) library is searched for first, followed by Ncurses,
+# then the system-default plain Curses. The first library found is the
+# one returned.
+#
+# The following options are understood: --with-ncursesw, --with-ncurses,
+# --without-ncursesw, --without-ncurses. The "--with" options force the
+# macro to use that particular library, terminating with an error if not
+# found. The "--without" options simply skip the check for that library.
+# The effect on the search pattern is:
+#
+# (no options) - NcursesW, Ncurses, Curses
+# --with-ncurses --with-ncursesw - NcursesW only [*]
+# --without-ncurses --with-ncursesw - NcursesW only [*]
+# --with-ncursesw - NcursesW only [*]
+# --with-ncurses --without-ncursesw - Ncurses only [*]
+# --with-ncurses - NcursesW, Ncurses [**]
+# --without-ncurses --without-ncursesw - Curses only
+# --without-ncursesw - Ncurses, Curses
+# --without-ncurses - NcursesW, Curses
+#
+# [*] If the library is not found, abort the configure script.
+#
+# [**] If the second library (Ncurses) is not found, abort configure.
+#
+# The following preprocessor symbols may be defined by this macro if the
+# appropriate conditions are met:
+#
+# HAVE_CURSES - if any SysV or X/Open Curses library found
+# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions
+# HAVE_CURSES_COLOR - if library supports color (enhanced functions)
+# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features
+# HAVE_NCURSESW - if NcursesW (wide char) library is to be used
+# HAVE_NCURSES - if the Ncurses library is to be used
+#
+# HAVE_CURSES_H - if <curses.h> is present and should be used
+# HAVE_NCURSESW_H - if <ncursesw.h> should be used
+# HAVE_NCURSES_H - if <ncurses.h> should be used
+# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used
+# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used
+#
+# (These preprocessor symbols are discussed later in this document.)
+#
+# The following output variable is defined by this macro; it is precious
+# and may be overridden on the ./configure command line:
+#
+# CURSES_LIB - library to add to xxx_LDADD
+#
+# The library listed in CURSES_LIB is NOT added to LIBS by default. You
+# need to add CURSES_LIB to the appropriate xxx_LDADD line in your
+# Makefile.am. For example:
+#
+# prog_LDADD = @CURSES_LIB@
+#
+# If CURSES_LIB is set on the configure command line (such as by running
+# "./configure CURSES_LIB=-lmycurses"), then the only header searched for
+# is <curses.h>. The user may use the CPPFLAGS precious variable to
+# override the standard #include search path. If the user needs to
+# specify an alternative path for a library (such as for a non-standard
+# NcurseW), the user should use the LDFLAGS variable.
+#
+# The following shell variables may be defined by this macro:
+#
+# ax_cv_curses - set to "yes" if any Curses library found
+# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present
+# ax_cv_curses_color - set to "yes" if color functions present
+# ax_cv_curses_obsolete - set to "yes" if obsolete features present
+#
+# ax_cv_ncursesw - set to "yes" if NcursesW library found
+# ax_cv_ncurses - set to "yes" if Ncurses library found
+# ax_cv_plaincurses - set to "yes" if plain Curses library found
+# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no"
+#
+# These variables can be used in your configure.ac to determine the level
+# of support you need from the Curses library. For example, if you must
+# have either Ncurses or NcursesW, you could include:
+#
+# AX_WITH_CURSES
+# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then
+# AC_MSG_ERROR([requires either NcursesW or Ncurses library])
+# fi
+#
+# If any Curses library will do (but one must be present and must support
+# color), you could use:
+#
+# AX_WITH_CURSES
+# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then
+# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color])
+# fi
+#
+# Certain preprocessor symbols and shell variables defined by this macro
+# can be used to determine various features of the Curses library. In
+# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses
+# library found conforms to the traditional SysV and/or X/Open Base Curses
+# definition. Any working Curses library conforms to this level.
+#
+# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the
+# library supports the X/Open Enhanced Curses definition. In particular,
+# the wide-character types attr_t, cchar_t and wint_t, the functions
+# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES
+# are checked. The Ncurses library does NOT conform to this definition,
+# although NcursesW does.
+#
+# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library
+# supports color functions and macros such as COLOR_PAIR, A_COLOR,
+# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the
+# X/Open Base Curses definition, but are part of the Enhanced set of
+# functions. The Ncurses library DOES support these functions, as does
+# NcursesW.
+#
+# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the
+# library supports certain features present in SysV and BSD Curses but not
+# defined in the X/Open definition. In particular, the functions
+# getattrs(), getcurx() and getmaxx() are checked.
+#
+# To use the HAVE_xxx_H preprocessor symbols, insert the following into
+# your system.h (or equivalent) header file:
+#
+# #if defined HAVE_NCURSESW_CURSES_H
+# # include <ncursesw/curses.h>
+# #elif defined HAVE_NCURSESW_H
+# # include <ncursesw.h>
+# #elif defined HAVE_NCURSES_CURSES_H
+# # include <ncurses/curses.h>
+# #elif defined HAVE_NCURSES_H
+# # include <ncurses.h>
+# #elif defined HAVE_CURSES_H
+# # include <curses.h>
+# #else
+# # error "SysV or X/Open-compatible Curses header file required"
+# #endif
+#
+# For previous users of this macro: you should not need to change anything
+# in your configure.ac or Makefile.am, as the previous (serial 10)
+# semantics are still valid. However, you should update your system.h (or
+# equivalent) header file to the fragment shown above. You are encouraged
+# also to make use of the extended functionality provided by this version
+# of AX_WITH_CURSES, as well as in the additional macros
+# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM.
+#
+# LICENSE
+#
+# Copyright (c) 2009 Mark Pulford <mark at kyne.com.au>
+# Copyright (c) 2009 Damian Pietras <daper at daper.net>
+# Copyright (c) 2012 Reuben Thomas <rrt at sc3d.org>
+# Copyright (c) 2011 John Zaitseff <J.Zaitseff at zap.org.au>
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception, the respective Autoconf Macro's copyright owner
+# gives unlimited permission to copy, distribute and modify the configure
+# scripts that are the output of Autoconf when processing the Macro. You
+# need not follow the terms of the GNU General Public License when using
+# or distributing such scripts, even though portions of the text of the
+# Macro appear in them. The GNU General Public License (GPL) does govern
+# all other use of the material that constitutes the Autoconf Macro.
+#
+# This special exception to the GPL applies to versions of the Autoconf
+# Macro released by the Autoconf Archive. When you make and distribute a
+# modified version of the Autoconf Macro, you may extend this special
+# exception to the GPL to apply to your modified version as well.
+
+#serial 15
+
+AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
+AC_DEFUN([AX_WITH_CURSES], [
+ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
+ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
+ [force the use of Ncurses or NcursesW])],
+ [], [with_ncurses=check])
+ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
+ [do not use NcursesW (wide character support)])],
+ [], [with_ncursesw=check])
+
+ ax_saved_LIBS=$LIBS
+ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes],
+ [ax_with_plaincurses=no], [ax_with_plaincurses=check])
+
+ ax_cv_curses_which=no
+
+ # Test for NcursesW
+
+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [
+ LIBS="$ax_saved_LIBS -lncursesw"
+
+ AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [
+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
+ [ax_cv_ncursesw=yes], [ax_cv_ncursesw=no])
+ ])
+ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [
+ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library])
+ ])
+
+ AS_IF([test "x$ax_cv_ncursesw" = xyes], [
+ ax_cv_curses=yes
+ ax_cv_curses_which=ncursesw
+ CURSES_LIB="-lncursesw"
+ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present])
+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
+
+ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@define _XOPEN_SOURCE_EXTENDED 1
+ @%:@include <ncursesw/curses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ attr_t d = WA_NORMAL;
+ cchar_t e;
+ wint_t f;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ wattr_set(stdscr, d, 0, NULL);
+ wget_wch(stdscr, &f);
+ ]])],
+ [ax_cv_header_ncursesw_curses_h=yes],
+ [ax_cv_header_ncursesw_curses_h=no])
+ ])
+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [
+ ax_cv_curses_enhanced=yes
+ ax_cv_curses_color=yes
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present])
+ ])
+
+ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@define _XOPEN_SOURCE_EXTENDED 1
+ @%:@include <ncursesw.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ attr_t d = WA_NORMAL;
+ cchar_t e;
+ wint_t f;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ wattr_set(stdscr, d, 0, NULL);
+ wget_wch(stdscr, &f);
+ ]])],
+ [ax_cv_header_ncursesw_h=yes],
+ [ax_cv_header_ncursesw_h=no])
+ ])
+ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [
+ ax_cv_curses_enhanced=yes
+ ax_cv_curses_color=yes
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present])
+ ])
+
+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@define _XOPEN_SOURCE_EXTENDED 1
+ @%:@include <ncurses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ attr_t d = WA_NORMAL;
+ cchar_t e;
+ wint_t f;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ wattr_set(stdscr, d, 0, NULL);
+ wget_wch(stdscr, &f);
+ ]])],
+ [ax_cv_header_ncurses_h_with_ncursesw=yes],
+ [ax_cv_header_ncurses_h_with_ncursesw=no])
+ ])
+ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [
+ ax_cv_curses_enhanced=yes
+ ax_cv_curses_color=yes
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
+ ])
+
+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [
+ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h])
+ ])
+ ])
+ ])
+
+ # Test for Ncurses
+
+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
+ LIBS="$ax_saved_LIBS -lncurses"
+
+ AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [
+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
+ [ax_cv_ncurses=yes], [ax_cv_ncurses=no])
+ ])
+ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [
+ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library])
+ ])
+
+ AS_IF([test "x$ax_cv_ncurses" = xyes], [
+ ax_cv_curses=yes
+ ax_cv_curses_which=ncurses
+ CURSES_LIB="-lncurses"
+ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present])
+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
+
+ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@include <ncurses/curses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ ]])],
+ [ax_cv_header_ncurses_curses_h=yes],
+ [ax_cv_header_ncurses_curses_h=no])
+ ])
+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [
+ ax_cv_curses_color=yes
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present])
+ ])
+
+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@include <ncurses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ ]])],
+ [ax_cv_header_ncurses_h=yes],
+ [ax_cv_header_ncurses_h=no])
+ ])
+ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [
+ ax_cv_curses_color=yes
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
+ ])
+
+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [
+ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h])
+ ])
+ ])
+ ])
+
+ # Test for plain Curses (or if CURSES_LIB was set by user)
+
+ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [
+ AS_IF([test "x$CURSES_LIB" != x], [
+ LIBS="$ax_saved_LIBS $CURSES_LIB"
+ ], [
+ LIBS="$ax_saved_LIBS -lcurses"
+ ])
+
+ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [
+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
+ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no])
+ ])
+
+ AS_IF([test "x$ax_cv_plaincurses" = xyes], [
+ ax_cv_curses=yes
+ ax_cv_curses_which=plaincurses
+ AS_IF([test "x$CURSES_LIB" = x], [
+ CURSES_LIB="-lcurses"
+ ])
+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
+
+ # Check for base conformance (and header file)
+
+ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@include <curses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ initscr();
+ ]])],
+ [ax_cv_header_curses_h=yes],
+ [ax_cv_header_curses_h=no])
+ ])
+ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [
+ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present])
+
+ # Check for X/Open Enhanced conformance
+
+ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@define _XOPEN_SOURCE_EXTENDED 1
+ @%:@include <curses.h>
+ @%:@ifndef _XOPEN_CURSES
+ @%:@error "this Curses library is not enhanced"
+ "this Curses library is not enhanced"
+ @%:@endif
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ attr_t d = WA_NORMAL;
+ cchar_t e;
+ wint_t f;
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ wattr_set(stdscr, d, 0, NULL);
+ wget_wch(stdscr, &f);
+ ]])],
+ [ax_cv_plaincurses_enhanced=yes],
+ [ax_cv_plaincurses_enhanced=no])
+ ])
+ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [
+ ax_cv_curses_enhanced=yes
+ ax_cv_curses_color=yes
+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ ])
+
+ # Check for color functions
+
+ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@define _XOPEN_SOURCE_EXTENDED 1
+ @%:@include <curses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ chtype c = COLOR_PAIR(1) & A_COLOR;
+ initscr();
+ init_pair(1, COLOR_WHITE, COLOR_RED);
+ ]])],
+ [ax_cv_plaincurses_color=yes],
+ [ax_cv_plaincurses_color=no])
+ ])
+ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [
+ ax_cv_curses_color=yes
+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
+ ])
+
+ # Check for obsolete functions
+
+ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[
+ @%:@include <curses.h>
+ ]], [[
+ chtype a = A_BOLD;
+ int b = KEY_LEFT;
+ int g = getattrs(stdscr);
+ int h = getcurx(stdscr) + getmaxx(stdscr);
+ initscr();
+ ]])],
+ [ax_cv_plaincurses_obsolete=yes],
+ [ax_cv_plaincurses_obsolete=no])
+ ])
+ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [
+ ax_cv_curses_obsolete=yes
+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
+ ])
+ ])
+
+ AS_IF([test "x$ax_cv_header_curses_h" = xno], [
*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
More information about the svn-ports-all
mailing list