[med-svn] [htslib] 02/04: Remove add_largefile.patch, applied upstream.
Charles Plessy
plessy at moszumanska.debian.org
Mon Apr 25 12:27:01 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/unstable
in repository htslib.
commit 559f8b44bec042eaa7f09f0f4cd07d6cfaf9a016
Author: Charles Plessy <plessy at debian.org>
Date: Mon Apr 25 21:14:26 2016 +0900
Remove add_largefile.patch, applied upstream.
---
debian/patches/add_largefile.patch | 217 -------------------------------------
debian/patches/series | 1 -
2 files changed, 218 deletions(-)
diff --git a/debian/patches/add_largefile.patch b/debian/patches/add_largefile.patch
deleted file mode 100644
index 1ad46af..0000000
--- a/debian/patches/add_largefile.patch
+++ /dev/null
@@ -1,217 +0,0 @@
-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 eb7a4c1..3c1f11a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
-add_largefile.patch
define_PATH_MAX.patch
literal_version.patch
--
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