[med-svn] r20074 - in trunk/packages/ffindex/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-09-18 20:23:09 +0000 (Fri, 18 Sep 2015)
New Revision: 20074

Modified:
   trunk/packages/ffindex/trunk/debian/changelog
   trunk/packages/ffindex/trunk/debian/control
   trunk/packages/ffindex/trunk/debian/ffindex.manpages
   trunk/packages/ffindex/trunk/debian/patches/Makefile.patch
   trunk/packages/ffindex/trunk/debian/rules
Log:
Tried to enable MPI but failed - leave some comments


Modified: trunk/packages/ffindex/trunk/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog	2015-09-17 08:32:11 UTC (rev 20073)
+++ trunk/packages/ffindex/trunk/debian/changelog	2015-09-18 20:23:09 UTC (rev 20074)
@@ -1,11 +1,11 @@
-ffindex (0.9.9.6-1) UNRELEASED; urgency=medium
+ffindex (0.9.9.6-1) unstable; urgency=medium
 
   * New upstream version
   * Remove symbols file
   * DEP5
   * cme fix dpkg-control
 
- -- Andreas Tille <tille at debian.org>  Mon, 14 Sep 2015 15:09:02 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 15 Sep 2015 08:09:23 +0200
 
 ffindex (0.9.9.3-2) unstable; urgency=medium
 

Modified: trunk/packages/ffindex/trunk/debian/control
===================================================================
--- trunk/packages/ffindex/trunk/debian/control	2015-09-17 08:32:11 UTC (rev 20073)
+++ trunk/packages/ffindex/trunk/debian/control	2015-09-18 20:23:09 UTC (rev 20074)
@@ -5,7 +5,9 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               help2man
+               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/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ffindex/trunk/

Modified: trunk/packages/ffindex/trunk/debian/ffindex.manpages
===================================================================
--- trunk/packages/ffindex/trunk/debian/ffindex.manpages	2015-09-17 08:32:11 UTC (rev 20073)
+++ trunk/packages/ffindex/trunk/debian/ffindex.manpages	2015-09-18 20:23:09 UTC (rev 20074)
@@ -1,6 +1 @@
-ffindex_apply.1
-ffindex_build.1
-ffindex_from_fasta.1
-ffindex_get.1
-ffindex_modify.1
-ffindex_unpack.1
+*.1

Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile.patch	2015-09-17 08:32:11 UTC (rev 20073)
+++ trunk/packages/ffindex/trunk/debian/patches/Makefile.patch	2015-09-18 20:23:09 UTC (rev 20074)
@@ -40,7 +40,7 @@
  endif
  
  OBJECTS=ffindex_apply ffindex_from_fasta ffindex_get ffindex_build ffindex_modify libffindex.a libffindex.so ffindex_unpack ffindex_from_tsv
-@@ -35,7 +40,7 @@ ffindex_apply.o: ffindex_apply_mpi.c ffi
+@@ -35,10 +40,10 @@ ffindex_apply.o: ffindex_apply_mpi.c ffi
  	$(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@ 
  
  ffindex_apply: $(FFINDEX_OBJECTS) ffindex_apply.o ffindex.h
@@ -48,7 +48,11 @@
 +	$(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)
++	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
  

Modified: trunk/packages/ffindex/trunk/debian/rules
===================================================================
--- trunk/packages/ffindex/trunk/debian/rules	2015-09-17 08:32:11 UTC (rev 20073)
+++ trunk/packages/ffindex/trunk/debian/rules	2015-09-18 20:23:09 UTC (rev 20074)
@@ -3,19 +3,16 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
-export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
-export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-
 # lkajan: work in progress, enable this in next upstream release, after speaking to upstream
-#export HAVE_MPI:=1
+# 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
 
 %:
 	dh $@ --parallel
 
 FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1
-.PHONY: ffmanpages
+# ffindex_apply_mpi.1
 ffmanpages: $(FFMANPAGES)
 BINNAMES =	\
 		ffindex_apply="apply a program to each FFindex entry";\
@@ -24,26 +21,23 @@
 		ffindex_get="retrieve entries from file index";\
 		ffindex_modify="modify file index entries";\
 		ffindex_unpack="unpack file index entries";
+#		ffindex_apply_mpi="apply a program to each FFindex entry (mpi enhanced)";\
 
-.PHONY: override_dh_installman
 override_dh_installman: $(FFMANPAGES)
 	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" '$<' -o '$@' --include debian/man_notes.nroff
 
-.PHONY: override_dh_clean
 override_dh_clean:
 	rm -f $(FFMANPAGES)
 	dh_clean
 
-.PHONY: override_dh_strip
 override_dh_strip:
 	dh_strip --dbg-package=ffindex-dbg
 
 # [Laszlo Kajan <lkajan at rostlab.org>]
 # ffindex has an overly large default for FFINDEX_MAX_INDEX_ENTRIES (40000000). In order to require less RAM for testing the package (make check), a more modest value is set below.
-.PHONY: override_dh_auto_test
 override_dh_auto_test:
 	dh_auto_test -- FFINDEX_MAX_INDEX_ENTRIES=20000 check