[med-svn] r6055 - in trunk/packages/ncbi-epcr/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Tue Feb 22 10:49:47 UTC 2011 

Author: tille
Date: 2011-02-22 10:49:46 +0000 (Tue, 22 Feb 2011)
New Revision: 6055

Added:
   trunk/packages/ncbi-epcr/trunk/debian/patches/ensure_build_options.patch
Modified:
   trunk/packages/ncbi-epcr/trunk/debian/changelog
   trunk/packages/ncbi-epcr/trunk/debian/control
   trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch
   trunk/packages/ncbi-epcr/trunk/debian/patches/series
   trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
Fix Build system and use debhelper instead of cdbs whic seems to be simpler to implement 


Modified: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog	2011-02-22 10:43:06 UTC (rev 6054)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog	2011-02-22 10:49:46 UTC (rev 6055)
@@ -2,7 +2,9 @@
 
   * debian/source/format: 3.0 (quilt)
   * Standards-Version: 3.9.1 (no changes needed)
-  * debian/patches: Fix location of includes
+  * debian/rules: Implementation of upstream build systems seems to
+    be simpler with short dh rules file
+  * debian/patches: Ensure Build options will be propagated properly
     Closes: 614482
 
  -- Andreas Tille <tille at debian.org>  Tue, 22 Feb 2011 09:09:21 +0100

Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control	2011-02-22 10:43:06 UTC (rev 6054)
+++ trunk/packages/ncbi-epcr/trunk/debian/control	2011-02-22 10:49:46 UTC (rev 6055)
@@ -6,7 +6,7 @@
 Uploaders: Steffen Moeller <moeller at debian.org>,
  Andreas Tille <tille at debian.org>,
  Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), cdbs, quilt
+Build-Depends: debhelper (>= 7.1), quilt (>= 0.47)
 Standards-Version: 3.9.1
 Homepage: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-epcr/trunk/?rev=0&sc=0

Added: trunk/packages/ncbi-epcr/trunk/debian/patches/ensure_build_options.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/ensure_build_options.patch	                        (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/ensure_build_options.patch	2011-02-22 10:49:46 UTC (rev 6055)
@@ -0,0 +1,11 @@
+--- e-PCR-2.3.12.orig/Makefile
++++ e-PCR-2.3.12/Makefile
+@@ -29,7 +29,7 @@
+ 
+ all links dirs clean dist clean-all install install-lib dist-clean depend: 	
+ 	for i in $(LIBS:%=lib%) $(BINS) ; do \
+-		$(MAKE) -ef $(srcdir)/stand/Makefile.$$i $@ ; \
++		$(MAKE) -ef $(srcdir)/stand/Makefile.$$i CXXFLAGS='$(CFLAGS)' $@ ; \
+ 	done
+ 
+ #

Modified: trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch	2011-02-22 10:43:06 UTC (rev 6054)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch	2011-02-22 10:49:46 UTC (rev 6055)
@@ -4,15 +4,9 @@
 
 --- epcr-2.3.12.orig/faread.cpp
 +++ epcr-2.3.12/faread.cpp
-@@ -27,11 +27,12 @@
-  *
-  * ========================================================================= */
+@@ -31,7 +31,8 @@
+ #include <epcr/bin-io.hpp>
  
--#include <epcr/faread.hpp>
--#include <epcr/bin-io.hpp>
-+#include "faread.hpp"
-+#include "bin-io.hpp"
- 
  #include <stdexcept>
 -#include <string.h>
 +#include <string>
@@ -20,449 +14,3 @@
  #include <ctype.h>
  #include <errno.h>
  
---- epcr-2.3.12.orig/faread.hpp
-+++ epcr-2.3.12/faread.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_FAREAD__HPP
- #define EPCR_FAREAD__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- #include <stdexcept>
- 
- BEGIN_NCBI_SCOPE
---- epcr-2.3.12.orig/e-PCR_main.cpp
-+++ epcr-2.3.12/e-PCR_main.cpp
-@@ -27,10 +27,10 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/defaults.h>
--#include <epcr/faread.hpp>
-+#include "defaults.h"
-+#include "faread.hpp"
- 
--#include <epcr/stsmatch.hpp>
-+#include "stsmatch.hpp"
- 
- #include <assert.h>
- #include <errno.h>
---- epcr-2.3.12.orig/re-PCR_main.cpp
-+++ epcr-2.3.12/re-PCR_main.cpp
-@@ -27,11 +27,11 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/defaults.h>
--#include <epcr/stsmatch.hpp>
--#include <epcr/fahash.hpp>
--#include <epcr/align.hpp>
--#include <epcr/sts.hpp>
-+#include "defaults.h"
-+#include "stsmatch.hpp"
-+#include "fahash.hpp"
-+#include "align.hpp"
-+#include "sts.hpp"
- 
- //#include <unistd.h>
- #include <errno.h>
---- epcr-2.3.12.orig/bin-io.hpp
-+++ epcr-2.3.12/bin-io.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_BIN_IO__HPP
- #define EPCR_BIN_IO__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- 
- #include <stdio.h>
- #include <errno.h>
---- epcr-2.3.12.orig/stsmatch.hpp
-+++ epcr-2.3.12/stsmatch.hpp
-@@ -30,9 +30,9 @@
- #ifndef EPCR_STSMATCH__HPP
- #define EPCR_STSMATCH__HPP
- 
--#include <epcr/build_cfg.h>
--#include <epcr/stsmatch_m.hpp>
--#include <epcr/defaults.h>
-+#include "build_cfg.h"
-+#include "stsmatch_m.hpp"
-+#include "defaults.h"
- 
- 
- BEGIN_NCBI_SCOPE
---- epcr-2.3.12.orig/stsmatch_i.hpp
-+++ epcr-2.3.12/stsmatch_i.hpp
-@@ -30,10 +30,10 @@
- #ifndef EPCR_STSMATCH_I__HPP
- #define EPCR_STSMATCH_I__HPP
- 
--#include <epcr/build_cfg.h>
--#include <epcr/hashset.hpp>
--#include <epcr/sts_i.hpp>
--#include <epcr/align.hpp>
-+#include "build_cfg.h"
-+#include "hashset.hpp"
-+#include "sts_i.hpp"
-+#include "align.hpp"
- 
- #include <stdexcept>
- #include <vector>
---- epcr-2.3.12.orig/stsmatch_m.hpp
-+++ epcr-2.3.12/stsmatch_m.hpp
-@@ -30,8 +30,8 @@
- #ifndef EPCR_STSMATCH_M__HPP
- #define EPCR_STSMATCH_M__HPP
- 
--#include <epcr/build_cfg.h>
--#include <epcr/stsmatch_i.hpp>
-+#include "build_cfg.h"
-+#include "stsmatch_i.hpp"
- #include <stdexcept>
- 
- BEGIN_NCBI_SCOPE
---- epcr-2.3.12.orig/stsmatch.cpp
-+++ epcr-2.3.12/stsmatch.cpp
-@@ -27,9 +27,9 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/defaults.h>
--#include <epcr/hashset.hpp>
--#include <epcr/stsmatch.hpp>
-+#include "defaults.h"
-+#include "hashset.hpp"
-+#include "stsmatch.hpp"
- 
- #include <errno.h>
- #include <ctype.h>
---- epcr-2.3.12.orig/stsmatch_i.cpp
-+++ epcr-2.3.12/stsmatch_i.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/hashset.hpp>
--#include <epcr/stsmatch_i.hpp>
-+#include "hashset.hpp"
-+#include "stsmatch_i.hpp"
- 
- #include <stdexcept>
- 
---- epcr-2.3.12.orig/stsmatch_m.cpp
-+++ epcr-2.3.12/stsmatch_m.cpp
-@@ -27,10 +27,10 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/defaults.h>
--#include <epcr/align.hpp>
--#include <epcr/hashset.hpp>
--#include <epcr/stsmatch_m.hpp>
-+#include "defaults.h"
-+#include "align.hpp"
-+#include "hashset.hpp"
-+#include "stsmatch_m.hpp"
- 
- #include <sys/types.h>
- #include <sys/stat.h>
---- epcr-2.3.12.orig/strref.hpp
-+++ epcr-2.3.12/strref.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_STRREF__HPP
- #define EPCR_STRREF__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- #include <cstring>
- #include <string>
- 
---- epcr-2.3.12.orig/sts.hpp
-+++ epcr-2.3.12/sts.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_STS__HPP
- #define EPCR_STS__HPP
- 
--#include <epcr/sts_i.hpp>
-+#include "sts_i.hpp"
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- epcr-2.3.12.orig/sts_i.hpp
-+++ epcr-2.3.12/sts_i.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_STS_I__HPP
- #define EPCR_STS_I__HPP
- 
--#include <epcr/strref.hpp>
-+#include "strref.hpp"
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- epcr-2.3.12.orig/stsfilter.cpp
-+++ epcr-2.3.12/stsfilter.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/hashset.hpp>
--#include <epcr/stsmatch_i.hpp>
-+#include "hashset.hpp"
-+#include "stsmatch_i.hpp"
- 
- #include <stdexcept>
- 
---- epcr-2.3.12.orig/hashset.cpp
-+++ epcr-2.3.12/hashset.cpp
-@@ -27,7 +27,7 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/hashset.hpp>
-+#include "hashset.hpp"
- #include <string.h>
- 
- USING_NCBI_SCOPE;
---- epcr-2.3.12.orig/hashset.hpp
-+++ epcr-2.3.12/hashset.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_HASHSET__HPP
- #define EPCR_HASHSET__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- epcr-2.3.12.orig/minilcs.hpp
-+++ epcr-2.3.12/minilcs.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_MINILCS__HPP
- #define EPCR_MINILCS__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- #include <stdexcept>
- #include <algorithm>
- #include <vector>
---- epcr-2.3.12.orig/mmap.cpp
-+++ epcr-2.3.12/mmap.cpp
-@@ -27,7 +27,7 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/mmap.hpp>
-+#include "mmap.hpp"
- 
- #include <stdexcept>
- //#include <sstream>
---- epcr-2.3.12.orig/mmap.hpp
-+++ epcr-2.3.12/mmap.hpp
-@@ -30,7 +30,7 @@
- #ifndef EPCR_MMAP__HPP
- #define EPCR_MMAP__HPP
- 
--#include <epcr/build_cfg.h>
-+#include "build_cfg.h"
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- epcr-2.3.12.orig/seqcmp_main.cpp
-+++ epcr-2.3.12/seqcmp_main.cpp
-@@ -27,7 +27,7 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/align.hpp>
-+#include "align.hpp"
- #include <stdexcept>
- #include <string.h>
- #include <errno.h>
---- epcr-2.3.12.orig/align.cpp
-+++ epcr-2.3.12/align.cpp
-@@ -27,10 +27,10 @@
-  *
-  * ========================================================================= */
- 
--//#include <epcr/hashset.hpp>
--//#include <epcr/stsmatch_i.hpp>
-+//#include "hashset.hpp"
-+//#include "stsmatch_i.hpp"
- 
--#include <epcr/align.hpp>
-+#include "align.hpp"
- #include <stdio.h>
- #include <string.h>
- 
---- epcr-2.3.12.orig/align.hpp
-+++ epcr-2.3.12/align.hpp
-@@ -30,8 +30,8 @@
- #ifndef EPCR_ALIGN__HPP
- #define EPCR_ALIGN__HPP
- 
--#include <epcr/build_cfg.h>
--#include <epcr/minilcs.hpp>
-+#include "build_cfg.h"
-+#include "minilcs.hpp"
- 
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- epcr-2.3.12.orig/build_cfg.h
-+++ epcr-2.3.12/build_cfg.h
-@@ -46,7 +46,7 @@
- #define USING_NCBI_SCOPE USING_SCOPE(ncbi)
- 
- #ifdef _WIN32
--#include <epcr/mswin.h>
-+#include "mswin.h"
- #define FILE_BINARY "b"
- #define FILE_TEXT   "t"
- //#warning "Using Borland C/C++ Builder config"
-@@ -79,7 +79,7 @@
- #include <sys/fcntl.h>
- 
- #ifdef NATIVE_LARGEFILES
--#include <epcr/native64.h>
-+#include "native64.h"
- #endif // NATIVE_LARGEFILES
- 
- #include <stdint.h>
---- epcr-2.3.12.orig/fahash_create.cpp
-+++ epcr-2.3.12/fahash_create.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fahash.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fahash.hpp"
-+#include "bin-io.hpp"
- #include "fahash_defines.h"
- 
- #include <stdexcept>
---- epcr-2.3.12.orig/fahash_create1.cpp
-+++ epcr-2.3.12/fahash_create1.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fahash.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fahash.hpp"
-+#include "bin-io.hpp"
- #include "fahash_defines.h"
- 
- #include <stdexcept>
---- epcr-2.3.12.orig/fahash_create2.cpp
-+++ epcr-2.3.12/fahash_create2.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fahash.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fahash.hpp"
-+#include "bin-io.hpp"
- #include "fahash_defines.h"
- 
- #include <iostream>
---- epcr-2.3.12.orig/fahash.hpp
-+++ epcr-2.3.12/fahash.hpp
-@@ -30,10 +30,10 @@
- #ifndef EPCR_HASH__HPP
- #define EPCR_HASH__HPP
- 
--#include <epcr/fast_seqio.hpp>
--#include <epcr/hashset.hpp>
--#include <epcr/sts_i.hpp>
--#include <epcr/align.hpp>
-+#include "fast_seqio.hpp"
-+#include "hashset.hpp"
-+#include "sts_i.hpp"
-+#include "align.hpp"
- 
- #include <list>
- #include <map>
---- epcr-2.3.12.orig/fahash_lookup.cpp
-+++ epcr-2.3.12/fahash_lookup.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fahash.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fahash.hpp"
-+#include "bin-io.hpp"
- #include "fahash_defines.h"
- 
- #include <stdexcept>
---- epcr-2.3.12.orig/fahash_main.cpp
-+++ epcr-2.3.12/fahash_main.cpp
-@@ -27,10 +27,10 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/defaults.h>
--#include <epcr/stsmatch.hpp>
--#include <epcr/fahash.hpp>
--#include <epcr/sts.hpp>
-+#include "defaults.h"
-+#include "stsmatch.hpp"
-+#include "fahash.hpp"
-+#include "sts.hpp"
- 
- //#include <unistd.h>
- #include <errno.h>
---- epcr-2.3.12.orig/fast_seqio.hpp
-+++ epcr-2.3.12/fast_seqio.hpp
-@@ -30,9 +30,9 @@
- #ifndef EPCR_FAST_SEQIO__HPP
- #define EPCR_FAST_SEQIO__HPP
- 
--#include <epcr/build_cfg.h>
--#include <epcr/faread.hpp>
--#include <epcr/mmap.hpp>
-+#include "build_cfg.h"
-+#include "faread.hpp"
-+#include "mmap.hpp"
- #include <string>
- #include <vector>
- 
---- epcr-2.3.12.orig/fast_seqio_read.cpp
-+++ epcr-2.3.12/fast_seqio_read.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fast_seqio.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fast_seqio.hpp"
-+#include "bin-io.hpp"
- 
- #include <stdexcept>
- #include <sys/types.h>
---- epcr-2.3.12.orig/famap_main.cpp
-+++ epcr-2.3.12/famap_main.cpp
-@@ -27,7 +27,7 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fast_seqio.hpp>
-+#include "fast_seqio.hpp"
- #include <stdexcept>
- #include <cstdio>
- #include <cstdlib>
---- epcr-2.3.12.orig/fast_seqio_write.cpp
-+++ epcr-2.3.12/fast_seqio_write.cpp
-@@ -27,8 +27,8 @@
-  *
-  * ========================================================================= */
- 
--#include <epcr/fast_seqio.hpp>
--#include <epcr/bin-io.hpp>
-+#include "fast_seqio.hpp"
-+#include "bin-io.hpp"
- 
- #include <stdexcept>
- #include <string.h>

Modified: trunk/packages/ncbi-epcr/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/series	2011-02-22 10:43:06 UTC (rev 6054)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/series	2011-02-22 10:49:46 UTC (rev 6055)
@@ -1,2 +1,3 @@
 fix_clean_target.patch
 fix_header_location.patch
+ensure_build_options.patch

Modified: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules	2011-02-22 10:43:06 UTC (rev 6054)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules	2011-02-22 10:49:46 UTC (rev 6055)
@@ -1,17 +1,16 @@
 #!/usr/bin/make -f
-# debian/rules for ncbi-epcr using cdbs
+# debian/rules for ncbi-epcr using
 # Andreas Tille <tille at debian.org>, GPL
 
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+%:
+	dh $@ --with quilt
 
-DEB_MAKE_CLEAN_TARGET := clean
-clean::
-	rm -f epcr
-	rm -f libepcr.a
+override_dh_auto_clean:
+	rm -fr epcr
+	rm -f *_depend.mk
+	rm -f libepcr.a *.o
 	rm -f e-PCR famap fahash re-PCR
 
-DEB_OPT_FLAG += -I. -g2 -DDEALLOCATE=0 `getconf LFS_CFLAGS` -DVERSION=\\\"2.3.12\\\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1
-
-LDFLAGS += `getconf LFS_LDFLAGS` `getconf LFS_LIBS`  -L.
+override_dh_auto_build:
+	$(MAKE) links depend all OPTIMIZE=6 \
+	    CFLAGS='-I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.12\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=12 -DSTANDALONE=1'

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