[med-svn] r11478 - in trunk/packages/ffindex/trunk/debian: . patches

Laszlo Kajan lkajan-guest at alioth.debian.org
Tue Jun 26 12:57:56 UTC 2012 

Author: lkajan-guest
Date: 2012-06-26 12:57:56 +0000 (Tue, 26 Jun 2012)
New Revision: 11478

Added:
   trunk/packages/ffindex/trunk/debian/man_notes.nroff
Modified:
   trunk/packages/ffindex/trunk/debian/changelog
   trunk/packages/ffindex/trunk/debian/ffindex.manpages
   trunk/packages/ffindex/trunk/debian/patches/Makefile
   trunk/packages/ffindex/trunk/debian/rules
Log:
New upstream release.

Modified: trunk/packages/ffindex/trunk/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog	2012-06-26 09:39:18 UTC (rev 11477)
+++ trunk/packages/ffindex/trunk/debian/changelog	2012-06-26 12:57:56 UTC (rev 11478)
@@ -1,3 +1,9 @@
+ffindex (0.9.6.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Laszlo Kajan <lkajan at rostlab.org>  Tue, 26 Jun 2012 11:43:41 +0200
+
 ffindex (0.9.3-2) unstable; urgency=low
 
   * Included full text of CC-BY-SA-3.0 license (Closes: #667698)

Modified: trunk/packages/ffindex/trunk/debian/ffindex.manpages
===================================================================
--- trunk/packages/ffindex/trunk/debian/ffindex.manpages	2012-06-26 09:39:18 UTC (rev 11477)
+++ trunk/packages/ffindex/trunk/debian/ffindex.manpages	2012-06-26 12:57:56 UTC (rev 11478)
@@ -1,3 +1,5 @@
+ffindex_apply.1
 ffindex_build.1
+ffindex_from_fasta.1
 ffindex_get.1
 ffindex_modify.1

Added: trunk/packages/ffindex/trunk/debian/man_notes.nroff
===================================================================
--- trunk/packages/ffindex/trunk/debian/man_notes.nroff	                        (rev 0)
+++ trunk/packages/ffindex/trunk/debian/man_notes.nroff	2012-06-26 12:57:56 UTC (rev 11478)
@@ -0,0 +1,4 @@
+[BUGS]
+User feedback is welcome, especially bugs, performance issues and last but not least convenience of the programs and \s-1API\s0.
+.PP
+Email Andreas Hauser hauser at genzentrum.lmu.de.

Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile	2012-06-26 09:39:18 UTC (rev 11477)
+++ trunk/packages/ffindex/trunk/debian/patches/Makefile	2012-06-26 12:57:56 UTC (rev 11478)
@@ -1,10 +1,8 @@
 * make Makefile DESTDIR-aware
 * deinstall -> uninstall
 * fix issues where the path in help pages is taken from the build-time location of the executables
-Index: ffindex-0.9.3/Makefile
-===================================================================
---- ffindex-0.9.3.orig/Makefile	2012-02-24 11:51:44.275044508 +0100
-+++ ffindex-0.9.3/Makefile	2012-02-24 11:57:11.291044574 +0100
+--- a/Makefile
++++ b/Makefile
 @@ -6,15 +6,8 @@
  MFILE=Makefile
  endif
@@ -24,17 +22,23 @@
 -	$(MAKE) -C src clean
 +%:
 +	$(MAKE) -C src -f $(MFILE) $@
-Index: ffindex-0.9.3/src/Makefile
-===================================================================
---- ffindex-0.9.3.orig/src/Makefile	2012-02-24 11:51:44.303044506 +0100
-+++ ffindex-0.9.3/src/Makefile	2012-02-24 14:29:50.919044571 +0100
-@@ -1,12 +1,14 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,15 +1,19 @@
 -INSTALL_DIR?=..
 -libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
 +PREFIX?=/usr
++INSTALL_DIR=$(DESTDIR)$(PREFIX)
 +libdir=lib
  LANG=C
- CFLAGS+=-std=c99 -openmp -g -fPIC -Wall
+-CC=gcc -fopenmp
+-#CC=icc -openmp
++CC=gcc
+ CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic
+-LDFLAGS=-lffindex -L.
++CFLAGS+=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security
++CPPFLAGS+=-D_FORTIFY_SOURCE=2
++LDFLAGS+=-Wl,-z,relro
 +SOCURRENT=0
 +SOVERSION=$(SOCURRENT).1.0
  ifdef FFINDEX_STATIC
@@ -46,14 +50,36 @@
  endif
  
  #-Wl,--version-script=libffindex.map
-@@ -24,16 +26,17 @@
+@@ -25,33 +29,34 @@
+ ffindex_apply: $(FFINDEX_OBJECTS) ffindex_apply.o ffindex.h
+ 
+ ffindex_apply_mpi: $(FFINDEX_OBJECTS) ffindex_apply_mpi.o ffindex.h
+-	mpicc $(CFLAGS) -I $(MPI_INCLUDE) -o $@  ffindex_apply_mpi.o $(LDFLAGS)
++	mpicc $(CFLAGS) -I $(MPI_INCLUDE) -o $@  ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex
+ 
+ ffindex_apply_mpi.o: ffindex_apply_mpi.c ffindex.h
+ 	mpicc $(CFLAGS) -I $(MPI_INCLUDE) -c ffindex_apply_mpi.c -o $@ 
+ 
+ ffindex_from_fasta: $(FFINDEX_OBJECTS) ffindex_from_fasta.o ffindex.h
+-	$(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex
+ 
+ ffindex_get: $(FFINDEX_OBJECTS) ffindex_get.o ffindex.h
+-	$(CC) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex
+ 
+ ffindex_build: $(FFINDEX_OBJECTS) ffindex_build.o ffindex.h
+-	$(CC) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex
+ 
  ffindex_modify: $(FFINDEX_OBJECTS) ffindex_modify.o ffindex.h
- 	$(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
+-	$(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
++	$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
  
 -libffindex.so.0.1: ffindex.o ffutil.o
 -	$(CC) -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o libffindex.so.0.1 ffindex.o ffutil.o -lc
 +libffindex.so.$(SOVERSION): ffindex.o ffutil.o
-+	$(CC) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc
  
 -libffindex.so: libffindex.so.0.1
 -	ln -sf libffindex.so.0.1 libffindex.so
@@ -69,59 +95,34 @@
  	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
-@@ -53,25 +56,28 @@
+@@ -71,9 +76,11 @@
  	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"
  
  clean:
--	rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 ffindex_modify ffindex_modify.o libffindex.a
-+	rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOCURRENT) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o libffindex.a
+-	rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 ffindex_modify ffindex_modify.o \
++	rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOCURRENT) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o \
+ 		libffindex.a  ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o ffindex_apply.o
+ 
++distclean: clean
 +
-+distclean: clean
- 
  install:
--	mkdir -p $(INSTALL_DIR)/bin
--	mkdir -p $(INSTALL_DIR)/$(libdir)
--	mkdir -p $(INSTALL_DIR)/include
--	install ffindex_get $(INSTALL_DIR)/bin/ffindex_get
--	install ffindex_build $(INSTALL_DIR)/bin/ffindex_build
--	install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify
+ 	mkdir -p $(INSTALL_DIR)/bin
+ 	mkdir -p $(INSTALL_DIR)/$(libdir)
+@@ -83,9 +90,10 @@
+ 	install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify
+ 	install ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_fasta
+ 	install ffindex_apply $(INSTALL_DIR)/bin/ffindex_apply
 -	install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
--	install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a
++	install libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION)
+ 	install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a
 -	ln -sf libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so
--	install ffindex.h $(INSTALL_DIR)/include/ffindex.h
--	install ffutil.h $(INSTALL_DIR)/include/ffutil.h
--
--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 $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h
--	rmdir $(INSTALL_DIR)/bin || true
--	rmdir $(INSTALL_DIR)/$(libdir) || true
--	rmdir $(INSTALL_DIR)/include || true
-+	mkdir -p $(DESTDIR)$(PREFIX)/bin
-+	mkdir -p $(DESTDIR)$(PREFIX)/$(libdir)
-+	mkdir -p $(DESTDIR)$(PREFIX)/include
-+	install ffindex_get $(DESTDIR)$(PREFIX)/bin/ffindex_get
-+	install ffindex_build $(DESTDIR)$(PREFIX)/bin/ffindex_build
-+	install ffindex_modify $(DESTDIR)$(PREFIX)/bin/ffindex_modify
-+	install libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so.$(SOVERSION)
-+	install libffindex.a $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.a
-+	ln -sf libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so.$(SOCURRENT)
-+	ln -sf libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so
-+	install ffindex.h $(DESTDIR)$(PREFIX)/include/ffindex.h
-+	install ffutil.h $(DESTDIR)$(PREFIX)/include/ffutil.h
-+
-+uninstall:
-+	rm -f $(PREFIX)/bin/ffindex_get $(PREFIX)/bin/ffindex_build $(PREFIX)/bin/ffindex_modify \
-+		$(PREFIX)/$(libdir)/libffindex.so.$(SOVERSION) $(PREFIX)/$(libdir)/libffindex.a \
-+		$(PREFIX)/$(libdir)/libffindex.so.$(SOCURRENT) $(PREFIX)/$(libdir)/libffindex.so $(PREFIX)/include/ffindex.h $(PREFIX)/include/ffutil.h
-+	rmdir $(PREFIX)/bin || true
-+	rmdir $(PREFIX)/$(libdir) || true
-+	rmdir $(PREFIX)/include || true
-Index: ffindex-0.9.3/src/ffindex_build.c
-===================================================================
---- ffindex-0.9.3.orig/src/ffindex_build.c	2012-02-24 11:49:40.279044528 +0100
-+++ ffindex-0.9.3/src/ffindex_build.c	2012-02-24 11:51:49.663044720 +0100
++	ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT)
++	ln -sf libffindex.so.$(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
+--- a/src/ffindex_build.c
++++ b/src/ffindex_build.c
 @@ -31,7 +31,7 @@
  
  void usage(char *program_name)
@@ -140,26 +141,8 @@
  }
  
  int main(int argn, char **argv)
-Index: ffindex-0.9.3/src/ffindex_get.c
-===================================================================
---- ffindex-0.9.3.orig/src/ffindex_get.c	2012-02-24 11:49:40.299044548 +0100
-+++ ffindex-0.9.3/src/ffindex_get.c	2012-02-24 11:51:49.671044437 +0100
-@@ -26,9 +26,8 @@
- {
-   if(argn < 3)
-   {
--    fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n"
--                    "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
--                    argv[0]);
-+    fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n"
-+                    "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n");
-     return -1;
-   }
-   char *data_filename  = argv[1];
-Index: ffindex-0.9.3/src/ffindex_modify.c
-===================================================================
---- ffindex-0.9.3.orig/src/ffindex_modify.c	2012-02-24 11:49:40.331044474 +0100
-+++ ffindex-0.9.3/src/ffindex_modify.c	2012-02-24 12:53:15.362982150 +0100
+--- a/src/ffindex_modify.c
++++ b/src/ffindex_modify.c
 @@ -30,7 +30,7 @@
  
  void usage(char *program_name)
@@ -194,3 +177,48 @@
      }
    }
  
+--- a/src/ffindex_get.c
++++ b/src/ffindex_get.c
+@@ -26,9 +26,8 @@
+ {
+   if(argn < 3)
+   {
+-    fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n"
+-                    "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
+-                    argv[0]);
++    fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n"
++                    "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n");
+     return -1;
+   }
+   char *data_filename  = argv[1];
+--- a/src/ffindex.h
++++ b/src/ffindex.h
+@@ -18,7 +18,8 @@
+ #include <stdio.h>
+ 
+ #define FFINDEX_VERSION 0.961
+-#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 40000000
++// lkajan: with 72 bytes per entry, the below makes a default allocation over 2G. malloc in ffindex.c:225 fails with hardening flags. Let's give a value for approx. 256MB.
++#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 3728270
+ #define FFINDEX_MAX_ENTRY_NAME_LENTH 56
+ 
+ enum ffindex_type { PLAIN_FILE, SORTED_FILE, SORTED_ARRAY, TREE };
+--- a/src/ffindex.c
++++ b/src/ffindex.c
+@@ -223,13 +223,14 @@
+     num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
+   size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
+   ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
+-  index->num_max_entries = num_max_entries;
+   if(index == NULL)
+   {
+-    fferror_print(__FILE__, __LINE__, __func__, "malloc failed");
++    char buf[2048]; snprintf( buf, 2048, "malloc failed to allocate %ld bytes: %s", nbytes, strerror(errno) );
++    fferror_print(__FILE__, __LINE__, __func__, buf );
+     return NULL;
+   }
+ 
++  index->num_max_entries = num_max_entries;
+   index->file = index_file;
+   index->index_data = ffindex_mmap_data(index_file, &(index->index_data_size));
+   if(index->index_data_size == 0)

Modified: trunk/packages/ffindex/trunk/debian/rules
===================================================================
--- trunk/packages/ffindex/trunk/debian/rules	2012-06-26 09:39:18 UTC (rev 11477)
+++ trunk/packages/ffindex/trunk/debian/rules	2012-06-26 12:57:56 UTC (rev 11478)
@@ -6,8 +6,13 @@
 %:
 	dh $@ --parallel
 
-FFMANPAGES = ffindex_build.1 ffindex_get.1 ffindex_modify.1
-BINNAMES =	ffindex_build="build file index from files in directories";\
+FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1
+.PHONY: ffmanpages
+ffmanpages: $(FFMANPAGES)
+BINNAMES =	\
+		ffindex_apply="apply a program to each FFindex entry";\
+		ffindex_build="build file index from files in directories";\
+		ffindex_from_fasta="populate index from FASTA file";\
 		ffindex_get="retrieve entries from file index";\
 		ffindex_modify="modify file index entries";\
 
@@ -16,7 +21,7 @@
 	dh_installman
 
 $(FFMANPAGES): %.1 : debian/tmp/usr/bin/%
-	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@'
+	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@' --include debian/man_notes.nroff
 
 .PHONY: override_dh_clean
 override_dh_clean:

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