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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]>, Charles Plessy <[email protected]> -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 <[email protected]> +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 <[email protected]> +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
