[med-svn] r21858 - in trunk/packages/ffindex/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sat May 7 22:53:31 UTC 2016
Author: tille
Date: 2016-05-07 22:53:31 +0000 (Sat, 07 May 2016)
New Revision: 21858
Modified:
trunk/packages/ffindex/trunk/debian/changelog
trunk/packages/ffindex/trunk/debian/control
trunk/packages/ffindex/trunk/debian/patches/Makefile.patch
trunk/packages/ffindex/trunk/debian/patches/basename.patch
trunk/packages/ffindex/trunk/debian/rules
Log:
* New upstream version
* cme fix dpkg-control
* enable mpi
Modified: trunk/packages/ffindex/trunk/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog 2016-05-05 05:48:58 UTC (rev 21857)
+++ trunk/packages/ffindex/trunk/debian/changelog 2016-05-07 22:53:31 UTC (rev 21858)
@@ -1,3 +1,11 @@
+ffindex (0.9.9.7-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * enable mpi
+
+ -- Andreas Tille <tille at debian.org> Sun, 08 May 2016 00:43:21 +0200
+
ffindex (0.9.9.6-2) unstable; urgency=medium
* Install ffindex_posix_search.h (see #802076)
Modified: trunk/packages/ffindex/trunk/debian/control
===================================================================
--- trunk/packages/ffindex/trunk/debian/control 2016-05-05 05:48:58 UTC (rev 21857)
+++ trunk/packages/ffindex/trunk/debian/control 2016-05-07 22:53:31 UTC (rev 21858)
@@ -6,10 +6,10 @@
Priority: optional
Build-Depends: debhelper (>= 9),
help2man,
-# libopenmpi-dev,
-# openmpi-bin ... needs another Build-Depends to create the manpage - but which one?
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ffindex/trunk/
+ libopenmpi-dev,
+ openmpi-bin
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/ffindex/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ffindex/trunk/
Homepage: http://www.splashground.de/~andy/programs/FFindex/
Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile.patch 2016-05-05 05:48:58 UTC (rev 21857)
+++ trunk/packages/ffindex/trunk/debian/patches/Makefile.patch 2016-05-07 22:53:31 UTC (rev 21858)
@@ -18,7 +18,7 @@
LANG=C
#CC=musl-gcc
#OMPI_CC=musl-gcc
-@@ -7,7 +8,11 @@ CC=gcc
+@@ -7,11 +8,15 @@ LANG=C
#CC=icc
#CC=clang
CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I.
@@ -31,41 +31,30 @@
OS:= $(shell uname)
-@@ -15,7 +20,7 @@ ifdef FFINDEX_STATIC
- LDFLAGS+=-static
- FFINDEX_OBJECTS=libffindex.a
- else
-- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1
-+ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION)
- endif
+-FFINDEX_LIBS=libffindex.so libffindex.so.0.1 libffindex.a
++FFINDEX_LIBS=libffindex.so libffindex.so.$(SOVERSION) libffindex.a
- OBJECTS=ffindex_apply ffindex_from_fasta ffindex_get ffindex_build ffindex_modify libffindex.a libffindex.so ffindex_unpack ffindex_from_tsv
-@@ -35,10 +40,10 @@ ffindex_apply.o: ffindex_apply_mpi.c ffi
- $(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@
+ FFINDEX_HEADERS=ffindex.h ffindex_posix_search.h ffutil.h
+ FFINDEX_OBJECTS=$(FFINDEX_HEADERS:.h=.o)
+@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS)
+ ar rcs libffindex.a $^
- ffindex_apply: $(FFINDEX_OBJECTS) ffindex_apply.o ffindex.h
-- $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS)
-+ $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -L. -lffindex
-
- ffindex_apply_mpi: $(FFINDEX_OBJECTS) ffindex_apply_mpi.o ffindex.h
-- mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS)
-+ mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex
-
- ffindex_apply_mpi.o: ffindex_apply_mpi.c ffindex.h
- mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@
-@@ -68,20 +73,20 @@ ffindex_unpack: $(FFINDEX_OBJECTS) ffind
- $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex
-
ifeq ($(OS), Darwin)
--libffindex.so.0.1: ffindex.o ffutil.o ffindex_posix_search.o ext/fmemopen.o
+-libffindex.so.0.1: $(FFINDEX_OBJECTS) ext/fmemopen.o
- $(CC) -shared -o libffindex.so.0.1 $^
-+libffindex.so.$(SOVERSION): ffindex.o ffutil.o ffindex_posix_search.o ext/fmemopen.o
++libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS) ext/fmemopen.o
+ $(CC) -shared -o libffindex.so.$(SOVERSION) $^
else
--libffindex.so.0.1: ffindex.o ffutil.o ffindex_posix_search.o
+
+ ifdef FFINDEX_STATIC
+ STATIC=-static
+ endif
+
+-libffindex.so.0.1: $(FFINDEX_OBJECTS)
- $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.0.1 -shared -o libffindex.so.0.1 $^
-+libffindex.so.$(SOVERSION): ffindex.o ffutil.o ffindex_posix_search.o
-+ $(CC) $(LDFLAGS) -Wl,-z,defstack -Wl,-soname,libffindex.so.$(SOVERSION) -shared -o libffindex.so.$(SOVERSION) $^
++libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS)
++ $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.$(SOVERSION) -shared -o libffindex.so.$(SOVERSION) $^
+
endif
-libffindex.so: libffindex.so.0.1
@@ -73,30 +62,66 @@
+libffindex.so: libffindex.so.$(SOVERSION)
+ ln -sf libffindex.so.$(SOVERSION) libffindex.so
- libffindex.a: ffindex.o ffutil.o ffindex_posix_search.o
- ar rcs libffindex.a $^
+ ffindex_apply.o: ffindex_apply_mpi.c $(FFINDEX_LIBS)
+ $(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@
+ ffindex_apply: ffindex_apply.o $(FFINDEX_LIBS)
+- $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) $(STATIC)
++ $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -L. -lffindex
+
+ ffindex_apply_mpi: ffindex_apply_mpi.o $(FFINDEX_LIBS)
+- mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS)
++ mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex
+
+ 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 $(LDFLAGS) -L. -lffindex
+
-test:
+check:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
-@@ -101,10 +106,11 @@ time:
- LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" zsh -c "time ./ffindex_get ../test_big/nr20_11Jan10_a3m_db ../test_big/nr20_11Jan10_a3m_db.ffindex BABBAMIBA.a3m KARDUZEBA.a3m HARPAQIBA.a3m WOQQATEBA.a3m BEBRAQIBA.a3m GIRSAKEBA.a3m NAQTIFIBA.a3m BIWCIQABA.a3m > /dev/null"
+@@ -107,9 +112,10 @@ time:
clean:
-- rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 \
-+ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOVERSION) \
- ffindex_modify ffindex_modify.o libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o \
- ffindex_apply.o ffindex_apply ffindex_from_tsv ffindex_khget ffindex_unpack ffindex_from_tsv.o ffindex_unpack.o \
-- ffindex_posix_search.o
-+ ffindex_posix_search.o \
+ rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \
+- libffindex.so libffindex.so.0.1 libffindex.a \
++ libffindex.so libffindex.so.$(SOVERSION) libffindex.a \
+ ffindex_build.o ffindex_get.o ffindex_modify.o ffindex_from_fasta.o ffindex_apply_mpi.o \
+- ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o
++ ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o \
+ $(OBJECTS) $(OBJECTS:%=%.o)
install:
mkdir -p $(INSTALL_DIR)/bin
-@@ -116,9 +122,10 @@ install:
- install ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_fasta
+@@ -122,9 +128,10 @@ 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
- install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
@@ -107,13 +132,13 @@
+ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so
install ffindex.h $(INSTALL_DIR)/include/ffindex.h
install ffutil.h $(INSTALL_DIR)/include/ffutil.h
- ifdef HAVE_MPI
-@@ -127,7 +134,7 @@ endif
+ install ffindex_posix_search.h $(INSTALL_DIR)/include/ffindex_posix_search.h
+@@ -134,7 +141,7 @@ endif
deinstall:
rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \
- $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.a \
+ $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.a \
$(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h\
- $(INSTALL_DIR)/bin/ffindex_from_fasta
+ $(INSTALL_DIR)/include/ffindex_posix_search.h $(INSTALL_DIR)/bin/ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_tsv
rmdir $(INSTALL_DIR)/bin || true
Modified: trunk/packages/ffindex/trunk/debian/patches/basename.patch
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/basename.patch 2016-05-05 05:48:58 UTC (rev 21857)
+++ trunk/packages/ffindex/trunk/debian/patches/basename.patch 2016-05-07 22:53:31 UTC (rev 21858)
@@ -10,17 +10,17 @@
--- a/src/ffindex_build.c
+++ b/src/ffindex_build.c
-@@ -40,6 +40,8 @@ void usage(char *program_name)
- "\t-s\t\tsort index file, so that the index can queried.\n"
+@@ -41,6 +41,8 @@ void usage(char *program_name)
"\t\t\tAnother append operations can be done without sorting.\n"
"\t-v\t\tprint version and other info then exit\n"
+ "\t-h\t\tdisplay this help message\n"
+ "ENVIRONMENT\n"
+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
"\nEXAMPLES:\n"
"\tCreate a new ffindex containing all files from the \"bar/\" directory containing\n"
"\tsay myfile1.txt, myfile2.txt and sort (-s) it so that e.g. ffindex_get can use it.\n"
-@@ -52,7 +54,7 @@ void usage(char *program_name)
- "\tMaximum key/filename length is %d and maximum entries are by default %d\n"
+@@ -54,7 +56,7 @@ void usage(char *program_name)
+ "\tdefault maximum entries %d.\n"
"\tThis can be changed in the sources.\n"
FFINDEX_COPYRIGHT,
- program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
@@ -59,21 +59,10 @@
return -1;
}
char *data_filename = argv[1];
---- a/src/ffindex.c
-+++ b/src/ffindex.c
-@@ -307,7 +307,7 @@ ffindex_entry_t* ffindex_bsearch_get_ent
- ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
- {
- if(num_max_entries == 0)
-- num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
-+ num_max_entries = ffindex_max_index_entries();
- size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
- ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
- if(index == NULL)
--- a/src/ffindex.h
+++ b/src/ffindex.h
@@ -24,6 +24,8 @@
- #define FFINDEX_VERSION 0.996
+ #define FFINDEX_VERSION 0.997
#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.
@@ -81,7 +70,7 @@
#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000
#define FFINDEX_MAX_ENTRY_NAME_LENTH 63
-@@ -71,6 +73,8 @@ ffindex_db_t * ffindex_index_db_open(ffi
+@@ -76,6 +78,8 @@ int ffindex_index_close(ffindex_index_t*
/* return *out_data_file, *out_index_file, out_offset. */
int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset);
@@ -105,9 +94,9 @@
}
--- a/src/ffindex_get.c
+++ b/src/ffindex_get.c
-@@ -27,8 +27,10 @@ void usage(char* program_name)
- fprintf(stderr, "USAGE: %s data_filename index_filename entry name(s)\n"
+@@ -28,8 +28,10 @@ void usage(char* program_name)
"\t-f FILE\t\tfile containing a list of file names, one per line\n"
+ "\t-h\t\tdisplay this help message\n"
"\t-n\t\tuse index of entry instead of entry name\n"
+ "ENVIRONMENT\n"
+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
@@ -128,3 +117,14 @@
}
int main(int argn, char **argv)
+--- a/src/ffindex.c
++++ b/src/ffindex.c
+@@ -373,7 +373,7 @@ ffindex_entry_t* ffindex_bsearch_get_ent
+ ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
+ {
+ if(num_max_entries == 0)
+- num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
++ num_max_entries = ffindex_max_index_entries();
+
+ size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
+ ffindex_index_t *index = (ffindex_index_t *)mmap(0, nbytes, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0);
Modified: trunk/packages/ffindex/trunk/debian/rules
===================================================================
--- trunk/packages/ffindex/trunk/debian/rules 2016-05-05 05:48:58 UTC (rev 21857)
+++ trunk/packages/ffindex/trunk/debian/rules 2016-05-07 22:53:31 UTC (rev 21858)
@@ -6,8 +6,10 @@
# lkajan: work in progress, enable this in next upstream release, after speaking to upstream
# tille at d.o: If enabled only ffindex_apply_mpi and for creating the manpage another (not yet
# known) Build-Depends is needed.
-# export HAVE_MPI:=1
+export HAVE_MPI:=1
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
%:
dh $@ --parallel
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