[med-svn] r6053 - in trunk/packages/ncbi-epcr/trunk/debian: . patches source
Andreas Tille
tille at alioth.debian.org
Tue Feb 22 08:43:58 UTC 2011
Author: tille
Date: 2011-02-22 08:43:36 +0000 (Tue, 22 Feb 2011)
New Revision: 6053
Added:
trunk/packages/ncbi-epcr/trunk/debian/patches/
trunk/packages/ncbi-epcr/trunk/debian/patches/fix_clean_target.patch
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/source/
trunk/packages/ncbi-epcr/trunk/debian/source/format
Modified:
trunk/packages/ncbi-epcr/trunk/debian/changelog
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
First try to fix #614482, some more C++ hacking is needed
Modified: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog 2011-02-21 21:10:06 UTC (rev 6052)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog 2011-02-22 08:43:36 UTC (rev 6053)
@@ -1,3 +1,12 @@
+epcr (2.3.12-2) UNRELEASED; urgency=low
+
+ * debian/source/format: 3.0 (quilt)
+ * Standards-Version: 3.9.1 (no changes needed)
+ * debian/patches: Fix location of includes
+ Closes: 614482
+
+ -- Andreas Tille <tille at debian.org> Tue, 22 Feb 2011 09:09:21 +0100
+
epcr (2.3.12-1) unstable; urgency=low
* New upstream release buildable with GCC 4.4 (Closes: #504849)
Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control 2011-02-21 21:10:06 UTC (rev 6052)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2011-02-22 08:43:36 UTC (rev 6053)
@@ -6,8 +6,8 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), cdbs
-Standards-Version: 3.8.2
+Build-Depends: debhelper (>= 7), cdbs, quilt
+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
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-epcr/trunk/
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/fix_clean_target.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/fix_clean_target.patch (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/fix_clean_target.patch 2011-02-22 08:43:36 UTC (rev 6053)
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 22 Feb 2011 09:09:21 +0100
+Description: Do not let clean target fail if there is nothing to clean
+
+--- epcr-2.3.12.orig/stand/config.mk
++++ epcr-2.3.12/stand/config.mk
+@@ -94,13 +94,13 @@
+ done
+
+ clean:
+- -rm $(OBJ) $(HDR:%=%~) $(SRC:%=%~)
++ -rm -f $(OBJ) $(HDR:%=%~) $(SRC:%=%~)
+
+ clean-all: clean
+- -rm $(TARGET)
++ -rm -f $(TARGET)
+
+ dist-clean: clean-all
+- -rm *~
++ -rm -f *~
+ -test -L $(LIBNAME) && rm $(LIBNAME)
+
+ $(objdir)/%.o: $(srcdir)/%.cpp
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/fix_header_location.patch 2011-02-22 08:43:36 UTC (rev 6053)
@@ -0,0 +1,468 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 22 Feb 2011 09:09:21 +0100
+Description: Fix path of includes
+
+--- epcr-2.3.12.orig/faread.cpp
++++ epcr-2.3.12/faread.cpp
+@@ -27,11 +27,12 @@
+ *
+ * ========================================================================= */
+
+-#include <epcr/faread.hpp>
+-#include <epcr/bin-io.hpp>
++#include "faread.hpp"
++#include "bin-io.hpp"
+
+ #include <stdexcept>
+-#include <string.h>
++#include <string>
++#include <cstdio>
+ #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>
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/series (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/series 2011-02-22 08:43:36 UTC (rev 6053)
@@ -0,0 +1,2 @@
+fix_clean_target.patch
+fix_header_location.patch
Modified: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules 2011-02-21 21:10:06 UTC (rev 6052)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules 2011-02-22 08:43:36 UTC (rev 6053)
@@ -4,6 +4,7 @@
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
DEB_MAKE_CLEAN_TARGET := clean
clean::
Added: trunk/packages/ncbi-epcr/trunk/debian/source/format
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/source/format (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/source/format 2011-02-22 08:43:36 UTC (rev 6053)
@@ -0,0 +1 @@
+3.0 (quilt)
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