[med-svn] [Git][med-team/ffindex][master] 5 commits: New upstream version 0.9.9.9
Andreas Tille
gitlab at salsa.debian.org
Mon Jan 28 18:08:13 GMT 2019
Andreas Tille pushed to branch master at Debian Med / ffindex
Commits:
4d1c7063 by Andreas Tille at 2019-01-28T17:58:43Z
New upstream version 0.9.9.9
- - - - -
d1bfeb1f by Andreas Tille at 2019-01-28T17:58:43Z
Update upstream source from tag 'upstream/0.9.9.9'
Update to upstream version '0.9.9.9'
with Debian dir 00673ee18cbf3db83d37b4df3da11b5887ba0a0f
- - - - -
0c045eb2 by Andreas Tille at 2019-01-28T17:58:43Z
New upstream version
- - - - -
901ebcc8 by Andreas Tille at 2019-01-28T18:06:09Z
Adapt patches
- - - - -
6599a15d by Andreas Tille at 2019-01-28T18:07:14Z
Upload to unstable
- - - - -
22 changed files:
- LICENSE
- README
- RELEASE_NOTES
- VERSION
- debian/changelog
- debian/patches/Makefile.patch
- debian/patches/basename.patch
- rpm/ffindex.spec
- src/Makefile
- src/ffindex.c
- src/ffindex.h
- src/ffindex_apply_mpi.c
- src/ffindex_apply_mpi_spawn.c
- src/ffindex_build.c
- src/ffindex_from_fasta.c
- src/ffindex_from_tsv.c
- src/ffindex_get.c
- src/ffindex_modify.c
- src/ffindex_optimize.c
- src/ffindex_unpack.c
- src/ffutil.c
- src/ffutil.h
Changes:
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LICENSE
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@@ -1,346 +1,428 @@
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+ License.
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+ terms or conditions communicated by You unless expressly agreed.
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+ Licensed Material not stated herein are separate from and
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+ conditions on any use of the Licensed Material that could lawfully
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+=======================================================================
+
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+public licenses is dedicated to the public domain under the CC0 Public
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+the avoidance of doubt, this paragraph does not form part of the
+public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
=====================================
README
=====================================
@@ -1,13 +1,13 @@
* Copyright
-FFindex was written by Andreas Hauser <andy at splpashground.de>.
+FFindex was written by Andreas Hauser <Andreas.Hauser at LMU.de>.
Please add your name here if you distribute modified versions.
-FFindex is provided under the Create Commons license "Attribution-ShareAlike 3.0",
+FFindex is provided under the Create Commons license "Attribution-ShareAlike 4.0",
which basically captures the spirit of the Gnu Public License (GPL).
See:
-http://creativecommons.org/licenses/by-sa/3.0/
+http://creativecommons.org/licenses/by-sa/4.0/
* Thanks
=====================================
RELEASE_NOTES
=====================================
@@ -1,3 +1,6 @@
+For updated version, please see public git log.
+
+
0.9.9.6
- Fix OS X builds and integrate Makefile.osx
=====================================
VERSION
=====================================
@@ -1 +1 @@
-0.9.9.8
+0.9.9.9
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+ffindex (0.9.9.9-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Jan 2019 19:03:23 +0100
+
ffindex (0.9.9.8-1) unstable; urgency=medium
* Revert again to original code which now added the interface for
=====================================
debian/patches/Makefile.patch
=====================================
@@ -40,7 +40,7 @@ Last-Update: 2017-06-29
FFINDEX_HEADERS=ffindex.h ffindex_posix_search.h ffutil.h
FFINDEX_OBJECTS=$(FFINDEX_HEADERS:.h=.o)
-@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS)
+@@ -34,30 +39,29 @@ libffindex.a: $(FFINDEX_OBJECTS)
ar rcs libffindex.a $^
ifeq ($(OS), Darwin)
@@ -50,9 +50,11 @@ Last-Update: 2017-06-29
+ $(CC) -shared -o libffindex.so.$(SOVERSION) $^
else
- ifdef FFINDEX_STATIC
- STATIC=-static
- endif
+- ifdef FFINDEX_STATIC
+-STATIC=-static
+- endif
++# Hack in needed linker options into unneeded variable STATIC
++STATIC=-L. -lffindex
-libffindex.so.0.1: $(FFINDEX_OBJECTS)
- $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.0.1 -shared -o libffindex.so.0.1 $^
@@ -79,39 +81,16 @@ Last-Update: 2017-06-29
ffindex_apply_mpi.o: ffindex_apply_mpi.c $(FFINDEX_HEADERS)
mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@
-@@ -69,24 +74,24 @@ ffindex_apply_mpi_spawn.o: ffindex_apply
- mpicc $(CFLAGS) -c ffindex_apply_mpi_spawn.c -o $@
-
- ffindex_from_fasta: ffindex_from_fasta.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex
-
- ffindex_from_tsv: ffindex_from_tsv.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) -L. -lffindex
-
- ffindex_get: ffindex_get.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_get.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex
-
- ffindex_build: ffindex_build.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_build.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex
-
- ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_modify.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
-
- ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS)
-- $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
-+ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex
+@@ -89,7 +93,7 @@ ffindex_unpack: ffindex_unpack.o $(FFIND
+ ffindex_order: ffindex_order.o $(FFINDEX_LIBS)
+ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
-test:
+check:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
-@@ -107,9 +112,10 @@ time:
+@@ -110,9 +114,10 @@ time:
clean:
rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \
@@ -124,7 +103,7 @@ Last-Update: 2017-06-29
install:
mkdir -p $(INSTALL_DIR)/bin
-@@ -122,9 +128,10 @@ install:
+@@ -125,9 +130,10 @@ install:
install ffindex_from_tsv $(INSTALL_DIR)/bin/ffindex_from_tsv
install ffindex_apply $(INSTALL_DIR)/bin/ffindex_apply
install ffindex_unpack $(INSTALL_DIR)/bin/ffindex_unpack
@@ -137,7 +116,7 @@ Last-Update: 2017-06-29
install ffindex.h $(INSTALL_DIR)/include/ffindex.h
install ffutil.h $(INSTALL_DIR)/include/ffutil.h
install ffindex_posix_search.h $(INSTALL_DIR)/include/ffindex_posix_search.h
-@@ -134,7 +141,7 @@ endif
+@@ -137,7 +143,7 @@ endif
deinstall:
rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \
=====================================
debian/patches/basename.patch
=====================================
@@ -48,21 +48,10 @@ Forwarded: yes
-/* vim: ts=2 sw=2 et: */
+// vim: ts=2 sw=2 et:
---- a/src/ffindex_unpack.c
-+++ b/src/ffindex_unpack.c
-@@ -37,7 +37,7 @@ int main(int argn, char **argv)
- fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
- "\n\tPlease note that a huge number of files might be created!\n"
- FFINDEX_COPYRIGHT,
-- argv[0]);
-+ basename(argv[0]));
- return -1;
- }
- char *data_filename = argv[1];
--- a/src/ffindex.h
+++ b/src/ffindex.h
@@ -24,6 +24,8 @@
- #define FFINDEX_VERSION 0.998
+ #define FFINDEX_VERSION 0.999
#define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy at splashground.de>.\n"
+// lkajan: the below makes a default allocation over 2G. malloc in ffindex.c:225 fails on a machine with 'only' 2G of RAM.
@@ -79,19 +68,6 @@ Forwarded: yes
int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name);
int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name);
---- a/src/ffindex_apply_mpi.c
-+++ b/src/ffindex_apply_mpi.c
-@@ -214,8 +214,8 @@ int main(int argn, char **argv)
- "\t-d\tFFDATA output file, stdout of program will be captured\n"
- "\t-i\tFFINDEX output file, entries get the same name as input entry\n"
- FFINDEX_COPYRIGHT,
-- argv[0],
-- argv[0]);
-+ basename(argv[0]),
-+ basename(argv[0]));
- errno = EINVAL;
- goto EXCEPTION;
- }
--- a/src/ffindex_get.c
+++ b/src/ffindex_get.c
@@ -29,8 +29,10 @@ void usage(char* program_name)
=====================================
rpm/ffindex.spec
=====================================
@@ -1,10 +1,10 @@
Summary: FFindex is a very simple index/database for huge amounts of small files.
Name: ffindex
-Version: 0.9.9.8
+Version: 0.9.9.9
Release: 1
License: Create Commons license "Attribution-ShareAlike 3.0"
Group: Utilities/System
-Source: https://github.com/ahcm/ffindex/archive/0.9.9.8.tar.gz
+Source: https://github.com/ahcm/ffindex/archive/0.9.9.9.tar.gz
%description
FFindex is a very simple index/database for huge amounts of small files. The
files are stored concatenated in one big data file, seperated by '\0'. A second
=====================================
src/Makefile
=====================================
@@ -86,6 +86,9 @@ ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS)
ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS)
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
+ffindex_order: ffindex_order.o $(FFINDEX_LIBS)
+ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
+
test:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
=====================================
src/ffindex.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex.h
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
@@ -21,7 +21,7 @@
#include <stdio.h>
-#define FFINDEX_VERSION 0.998
+#define FFINDEX_VERSION 0.999
#define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy at splashground.de>.\n"
#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000
=====================================
src/ffindex_apply_mpi.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
@@ -214,8 +214,8 @@ int main(int argn, char **argv)
"\t-d\tFFDATA output file, stdout of program will be captured\n"
"\t-i\tFFINDEX output file, entries get the same name as input entry\n"
FFINDEX_COPYRIGHT,
- argv[0],
- argv[0]);
+ basename(argv[0]),
+ basename(argv[0]));
errno = EINVAL;
goto EXCEPTION;
}
=====================================
src/ffindex_apply_mpi_spawn.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
=====================================
src/ffindex_build.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_from_fasta.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -60,7 +60,7 @@ int main(int argn, char **argv)
version = 1;
break;
default:
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
@@ -74,7 +74,7 @@ int main(int argn, char **argv)
if(argn - optind < 3)
{
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
=====================================
src/ffindex_from_tsv.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_get.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -70,6 +70,7 @@ int main(int argn, char **argv)
ffindex_db->ffdata_filename = data_filename;
ffindex_db->ffindex_filename = index_filename;
ffindex_db->mode[0] = 'r';
+ ffindex_db->num_max_entries = ffcount_lines(index_filename);
ffindex_db = ffindex_index_db_open(ffindex_db);
if(!ffindex_db)
=====================================
src/ffindex_modify.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -71,7 +71,7 @@ int main(int argn, char **argv)
break;
default:
fprintf(stderr, "Option %c not recognized\n", opt);
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
=====================================
src/ffindex_optimize.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_unpack.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
@@ -37,7 +37,7 @@ int main(int argn, char **argv)
fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
"\n\tPlease note that a huge number of files might be created!\n"
FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
return -1;
}
char *data_filename = argv[1];
=====================================
src/ffutil.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
=====================================
src/ffutil.h
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
View it on GitLab: https://salsa.debian.org/med-team/ffindex/compare/de9335a06f050b61516042789a8d61dd003dcb61...6599a15d42077411cc4c6a858a73655f6fd1b761
--
View it on GitLab: https://salsa.debian.org/med-team/ffindex/compare/de9335a06f050b61516042789a8d61dd003dcb61...6599a15d42077411cc4c6a858a73655f6fd1b761
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