[med-svn] [htslib] 01/06: add upstream's patch for largefile issue
Sascha Steinbiss
sascha at steinbiss.name
Mon Feb 8 16:47:53 UTC 2016
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sascha-guest pushed a commit to branch debian/unstable
in repository htslib.
commit 59917d4f15b76213acf32f33fed9bb1e95a92b39
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Feb 8 16:01:46 2016 +0000
add upstream's patch for largefile issue
---
debian/patches/add_largefile.patch | 217 +++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 218 insertions(+)
diff --git a/debian/patches/add_largefile.patch b/debian/patches/add_largefile.patch
new file mode 100644
index 0000000..1ad46af
--- /dev/null
+++ b/debian/patches/add_largefile.patch
@@ -0,0 +1,217 @@
+Author: John Marshall <jm18 at sanger.ac.uk>
+Description: Add AC_SYS_LARGEFILE test
+ Defines _FILE_OFFSET_BITS in config.h as appropriate. Hat tip @trifud.
+ Now that config.h has ODR implications, add #include <config.h> to
+ absolutely all *.c source files (cf 5f5aa02bfeb3857e8671f12a85787404ef9fa799).
+ Most k*.c files differ from their klib upstream versions due to #include
+ path-related trivia anyway, and knetfile.c in particular needs to see the
+ newly-added definitions.
+ .
+ Picked from htslib's GitHub (f1327a703583bf61e2e7ffd11198487fee2a8422)
+diff --git a/Makefile b/Makefile
+index be2405e..1122fde 100644
+--- a/Makefile
++++ b/Makefile
+@@ -251,8 +251,8 @@ libhts.dylib: $(LIBHTS_OBJS)
+
+
+ bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h)
+-kstring.o kstring.pico: kstring.c $(htslib_kstring_h)
+-knetfile.o knetfile.pico: knetfile.c $(htslib_knetfile_h)
++kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
++knetfile.o knetfile.pico: knetfile.c config.h $(htslib_knetfile_h)
+ hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
+ hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
+ hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
+@@ -265,7 +265,7 @@ faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib
+ synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
+ vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
+ vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
+-kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h)
++kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
+ regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
+ md5.o md5.pico: md5.c config.h $(htslib_hts_h)
+ plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
+@@ -335,13 +335,13 @@ test/test-vcf-api: test/test-vcf-api.o libhts.a
+ test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
+ $(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
+
+-test/fieldarith.o: test/fieldarith.c $(htslib_sam_h)
+-test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h)
+-test/sam.o: test/sam.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
+-test/test-regidx.o: test/test-regidx.c $(htslib_regidx_h)
+-test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h)
+-test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
+-test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h)
++test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
++test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
++test/sam.o: test/sam.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
++test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h)
++test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
++test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
++test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
+
+
+ install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
+diff --git a/config.h.in b/config.h.in
+index 09b23ff..0397762 100644
+--- a/config.h.in
++++ b/config.h.in
+@@ -25,3 +25,14 @@
+
+ /* Define to 1 if you have a working `mmap' system call. */
+ #undef HAVE_MMAP
++
++/* Enable large inode numbers on Mac OS X 10.5. */
++#ifndef _DARWIN_USE_64_BIT_INODE
++# define _DARWIN_USE_64_BIT_INODE 1
++#endif
++
++/* Number of bits in a file offset, on hosts where this is settable. */
++#undef _FILE_OFFSET_BITS
++
++/* Define for large files, on AIX-style hosts. */
++#undef _LARGE_FILES
+diff --git a/configure.ac b/configure.ac
+index 27fa1f4..6f658a2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -38,6 +38,8 @@ redistribute it. There is NO WARRANTY, to the extent permitted by law.])
+ AC_PROG_CC
+ AC_PROG_RANLIB
+
++AC_SYS_LARGEFILE
++
+ need_crypto=no
+
+ AC_ARG_WITH([irods],
+diff --git a/kfunc.c b/kfunc.c
+index faa2ac5..323e70f 100644
+--- a/kfunc.c
++++ b/kfunc.c
+@@ -24,6 +24,8 @@
+ SOFTWARE.
+ */
+
++#include <config.h>
++
+ #include <math.h>
+ #include <stdlib.h>
+ #include "htslib/kfunc.h"
+diff --git a/knetfile.c b/knetfile.c
+index 28fe629..aa28858 100644
+--- a/knetfile.c
++++ b/knetfile.c
+@@ -28,6 +28,8 @@
+ therefore I decide to heavily annotate this file, for Linux and
+ Windows as well. -ac */
+
++#include <config.h>
++
+ #include <time.h>
+ #include <stdio.h>
+ #include <ctype.h>
+diff --git a/kstring.c b/kstring.c
+index b84ee2c..f43a982 100644
+--- a/kstring.c
++++ b/kstring.c
+@@ -23,6 +23,8 @@
+ SOFTWARE.
+ */
+
++#include <config.h>
++
+ #include <stdarg.h>
+ #include <stdio.h>
+ #include <ctype.h>
+diff --git a/test/fieldarith.c b/test/fieldarith.c
+index 6d871b7..3627a89 100644
+--- a/test/fieldarith.c
++++ b/test/fieldarith.c
+@@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdio.h>
+
+ #include "htslib/sam.h"
+diff --git a/test/hfile.c b/test/hfile.c
+index c4ba91c..180f2ff 100644
+--- a/test/hfile.c
++++ b/test/hfile.c
+@@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdarg.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+diff --git a/test/sam.c b/test/sam.c
+index d6610c0..2c85010 100644
+--- a/test/sam.c
++++ b/test/sam.c
+@@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdarg.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+diff --git a/test/test-regidx.c b/test/test-regidx.c
+index 0aea6b8..abb390b 100644
+--- a/test/test-regidx.c
++++ b/test/test-regidx.c
+@@ -23,6 +23,8 @@
+ THE SOFTWARE.
+ */
+
++#include <config.h>
++
+ #include <stdarg.h>
+ #include <stdlib.h>
+ #include <stdio.h>
+diff --git a/test/test-vcf-api.c b/test/test-vcf-api.c
+index 3e7623a..2df9b71 100644
+--- a/test/test-vcf-api.c
++++ b/test/test-vcf-api.c
+@@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdio.h>
+ #include <htslib/hts.h>
+ #include <htslib/vcf.h>
+diff --git a/test/test-vcf-sweep.c b/test/test-vcf-sweep.c
+index 57c47bc..44c2fb1 100644
+--- a/test/test-vcf-sweep.c
++++ b/test/test-vcf-sweep.c
+@@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdio.h>
+ #include <htslib/vcf_sweep.h>
+
+diff --git a/test/test_view.c b/test/test_view.c
+index 6dbef00..0b83bf5 100644
+--- a/test/test_view.c
++++ b/test/test_view.c
+@@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE. */
+
++#include <config.h>
++
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <stdlib.h>
diff --git a/debian/patches/series b/debian/patches/series
index 2339362..b0939db 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+add_largefile.patch
define_PATH_MAX.patch
--
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