[med-svn] [bcftools] 04/08: Attempt to adapt patches - may be failed since several entries moved from Makefile to config.mk.in. Check seriously if something might fail.
Andreas Tille
tille at debian.org
Thu Jul 20 11:46:33 UTC 2017
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tille pushed a commit to branch master
in repository bcftools.
commit 3a7371b84473a0d7a1de08a301b20fee3b243319
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 20 13:25:54 2017 +0200
Attempt to adapt patches - may be failed since several entries moved from Makefile to config.mk.in. Check seriously if something might fail.
---
debian/patches/compiler-flags.patch | 24 ++++-----
debian/patches/destdir.patch | 22 ++++----
debian/patches/external-libs.patch | 94 +++++++++++++----------------------
debian/patches/tests-pluginpath.patch | 2 +-
4 files changed, 59 insertions(+), 83 deletions(-)
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
index 8623c25..0912d02 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -5,18 +5,18 @@ Description: Allow compiler flags to be passed through to build system
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
Last-Update: 2015-11-09
---- bcftools.orig/Makefile
-+++ bcftools/Makefile
-@@ -32,9 +32,9 @@
- BGZIP = /usr/bin/bgzip
- TABIX = /usr/bin/tabix
+--- a/config.mk.in
++++ b/config.mk.in
+@@ -34,9 +34,9 @@ bindir = @bindir@
+ datarootdir = @datarootdir@
+ mandir = @mandir@
--CC = gcc
--CPPFLAGS =
--CFLAGS = -g -Wall -Wc++-compat -O2
-+CC ?= gcc
-+CPPFLAGS ?=
-+CFLAGS += -g -Wall -Wc++-compat -O2
+-CC = @CC@
+-CPPFLAGS = @CPPFLAGS@
+-CFLAGS = @CFLAGS@
++CC ?= @CC@
++CPPFLAGS ?=
++CFLAGS += @CFLAGS@
LDFLAGS ?=
- LIBS += $(LDFLAGS) -lhts
+ LIBS = $(LDFLAGS) -lhts
diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch
index f524146..b3bb456 100644
--- a/debian/patches/destdir.patch
+++ b/debian/patches/destdir.patch
@@ -4,21 +4,23 @@ Forwarded: not-needed
Last-Update: 2015-11-03
--- a/Makefile
+++ b/Makefile
-@@ -70,7 +70,7 @@ ifdef USE_GPL
- GSL_LIBS = -lgsl -lgslcblas
- endif
+@@ -41,7 +41,7 @@ OBJS = main.o vcfindex.o tabix.o \
+ mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
+ ccall.o em.o prob1.o kmin.o # the original samtools calling
-prefix = /usr/local
+prefix = /usr
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
libdir = $(exec_prefix)/lib
-@@ -78,7 +78,7 @@ libexecdir = $(exec_prefix)/libexec
- mandir = $(prefix)/share/man
- man1dir = $(mandir)/man1
+--- a/config.mk.in
++++ b/config.mk.in
+@@ -47,7 +47,7 @@ GSL_LIBS = -lgsl -lgslcblas
--plugindir = $(libexecdir)/bcftools
-+plugindir ?= $(libexecdir)/bcftools
- pluginpath = $(plugindir)
+ PLATFORM = @PLATFORM@
+ PLUGINS_ENABLED = @enable_bcftools_plugins@
+-plugindir = @bcf_plugindir@
++plugindir ?= @bcf_plugindir@
+ PLUGIN_EXT = @PLUGIN_EXT@
- MKDIR_P = mkdir -p
+ @Hsource at BGZIP = /usr/bin/bgzip
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index a3f5f5f..3aaf337 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -2,64 +2,38 @@ Description: Use packaged libraries
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
Last-Update: 2015-11-03
---- a/Makefile
-+++ b/Makefile
-@@ -29,20 +29,14 @@ TEST_PROG= test/test-rbuf test/test-reg
- all: $(PROG) $(TEST_PROG)
-
- # Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = ../htslib
--include $(HTSDIR)/htslib.mk
--include $(HTSDIR)/htslib_static.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP = $(HTSDIR)/bgzip
--TABIX = $(HTSDIR)/tabix
--HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
--HTSLIB_LIBS = $(HTSLIB_static_LIBS)
-+BGZIP = /usr/bin/bgzip
-+TABIX = /usr/bin/tabix
-
- CC = gcc
- CPPFLAGS =
- CFLAGS = -g -Wall -Wc++-compat -O2
--LDFLAGS =
--LIBS =
+--- a/config.mk.in
++++ b/config.mk.in
+@@ -37,27 +37,21 @@ mandir = @mandir@
+ CC = @CC@
+ CPPFLAGS = @CPPFLAGS@
+ CFLAGS = @CFLAGS@
+-LDFLAGS = @LDFLAGS@
+-LIBS = @LIBS@
+LDFLAGS ?=
-+LIBS += $(LDFLAGS) -lhts
-
- ifeq "$(shell uname -s)" "Darwin"
- DYNAMIC_FLAGS = -Wl,-export_dynamic
-@@ -73,7 +67,7 @@ GSL_LIBS =
- ifdef USE_GPL
- EXTRA_CPPFLAGS += -DUSE_GPL
- OBJS += polysomy.o peakfit.o
-- GSL_LIBS = -lgsl -lcblas
-+ GSL_LIBS = -lgsl -lgslcblas
- endif
-
- prefix = /usr/local
-@@ -123,11 +117,11 @@ force:
- .c.o:
- $(CC) $(CFLAGS) $(EXTRA_CPPFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
-
--test: $(PROG) plugins test/test-rbuf test/test-regidx $(BGZIP) $(TABIX)
-+test: $(PROG) plugins test/test-rbuf test/test-regidx
- ./test/test-regidx
- ./test/test.pl --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
-
--test-plugins: $(PROG) plugins test/test-rbuf $(BGZIP) $(TABIX)
-+test-plugins: $(PROG) plugins test/test-rbuf
- ./test/test.pl --plugins --exec bgzip=$(BGZIP) --exec tabix=$(TABIX)
-
-
-@@ -217,8 +211,8 @@ test/test-regidx.o: test/test-regidx.c r
- test/test-regidx: test/test-regidx.o regidx.o $(HTSLIB)
- $(CC) $(ALL_LDFLAGS) -o $@ $^ $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(ALL_LIBS)
-
--bcftools: $(HTSLIB) $(OBJS)
-- $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
-+bcftools: $(OBJS)
-+ $(CC) $(ALL_LDFLAGS) -o $@ $(OBJS) -lpthread $(HTSLIB_LIBS) $(GSL_LIBS) $(ALL_LIBS)
-
- doc/bcftools.1: doc/bcftools.txt
- cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
++LIBS = $(LDFLAGS) -lhts
+
+ DYNAMIC_FLAGS = @CC_RDYNAMIC_OPT@
+
+ USE_GPL = @USE_GPL@
+-GSL_LIBS = @GSL_LIBS@
++GSL_LIBS = -lgsl -lgslcblas
+
+ PLATFORM = @PLATFORM@
+ PLUGINS_ENABLED = @enable_bcftools_plugins@
+ plugindir = @bcf_plugindir@
+ PLUGIN_EXT = @PLUGIN_EXT@
+
+- at Hsource@HTSDIR = @HTSDIR@
+- at Hsource@include $(HTSDIR)/htslib.mk
+- at Hsource@include $(HTSDIR)/htslib_static.mk
+- at Hsource@HTSLIB = $(HTSDIR)/libhts.a
+- at Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
+- at Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
+- at Hsource@BGZIP = $(HTSDIR)/bgzip
+- at Hsource@TABIX = $(HTSDIR)/tabix
++ at Hsource@BGZIP = /usr/bin/bgzip
++ at Hsource@TABIX = /usr/bin/tabix
+ HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
+ @Hinstall at HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
+ @Hinstall at HTSLIB_LIB = -lhts
diff --git a/debian/patches/tests-pluginpath.patch b/debian/patches/tests-pluginpath.patch
index 1c88cdf..4049da5 100644
--- a/debian/patches/tests-pluginpath.patch
+++ b/debian/patches/tests-pluginpath.patch
@@ -10,7 +10,7 @@ Forwarded: not-needed
Last-Update: 2015-11-09
--- a/test/test.pl
+++ b/test/test.pl
-@@ -859,7 +859,7 @@ sub test_vcf_plugin
+@@ -862,7 +862,7 @@ sub test_vcf_plugin
{
my ($opts,%args) = @_;
if ( !$$opts{test_plugins} ) { return; }
--
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