[med-svn] r17004 - in trunk/packages/genometools/tags: . 1.5.2-4/debian 1.5.2-4/debian/patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat May 24 18:11:53 UTC 2014
Author: sascha-guest
Date: 2014-05-24 18:11:53 +0000 (Sat, 24 May 2014)
New Revision: 17004
Added:
trunk/packages/genometools/tags/1.5.2-4/
trunk/packages/genometools/tags/1.5.2-4/debian/changelog
trunk/packages/genometools/tags/1.5.2-4/debian/patches/series
trunk/packages/genometools/tags/1.5.2-4/debian/patches/typecheck-fixes
Removed:
trunk/packages/genometools/tags/1.5.2-4/debian/changelog
trunk/packages/genometools/tags/1.5.2-4/debian/patches/series
Log:
[svn-buildpackage] Tagging genometools 1.5.2-4
Deleted: trunk/packages/genometools/tags/1.5.2-4/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog 2014-05-22 12:04:26 UTC (rev 16999)
+++ trunk/packages/genometools/tags/1.5.2-4/debian/changelog 2014-05-24 18:11:53 UTC (rev 17004)
@@ -1,123 +0,0 @@
-genometools (1.5.2-3) unstable; urgency=low
-
- * Address building issues on s390x, powerpc and armhf
- * Don't use -m64 for arm64 (thanks to Logan Rosen)
- Closes: #748708
- * Build-depend on docbook-xsl to fix FTBFS while offline (thanks to
- Logan Rosen)
- Closes: #748709
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 19 May 2014 23:06:34 +0000
-
-genometools (1.5.2-2) unstable; urgency=low
-
- * Split manuals into separate documents to avoid strange LaTeX build issues.
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 23:23:20 +0000
-
-genometools (1.5.2-1) unstable; urgency=low
-
- * New upstream release.
- * Remove symbols file because private symbols are exported (next upstream
- version will properly control exported symbols and a new symbols file
- will be created and maintained)
- * Remove manpages from debian directory as they are now autogenerated on
- build
- * Fix some missing symbols problems
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 10:51:41 +0000
-
-genometools (1.5.1-3) unstable; urgency=low
-
- * debian/rules
- - Add basic tests to check whether cairo/pango linking works
- - Clean up indices created by tests to make repeated builds possible
- - Make sure bin/examples/sketch_parsed_with_* are built
- - Enable compiler optimization
- * debian/control
- - Move libgenometools0 package into libs section
- - Switch pango deps to new package
- - Add ruby builddep, required for the testsuite
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 06 Nov 2013 14:28:41 +0100
-
-genometools (1.5.1-2) unstable; urgency=low
-
- * debian/control
- - Add myself to Uploaders
- - cme fix dpkg-control
- - Follow liblua package name transition
- Closes: #728017
- - Remove depends from virtual package python-ctypes which is provided
- by python
- * provide symbols file
-
- -- Andreas Tille <tille at debian.org> Mon, 28 Oct 2013 08:17:04 +0100
-
-genometools (1.5.1-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 07 Mar 2013 14:08:05 +0100
-
-genometools (1.5.0-2) unstable; urgency=low
-
- * Patch manuals not to use includecomment/excludecomment
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 16 Feb 2013 16:58:11 +0100
-
-genometools (1.5.0-1) unstable; urgency=low
-
- * New upstream release
- * bugfixes and cleanups
- * development tool `gt sain' added to run an induced suffix array sorting
- algorithm
- * the -typecheck option in the `gt gff3` and `gt gff3validator` tools
- now also validates parent (part-of) relationships, see -help output for
- details
- * new option -encseq besides -seqfile(s) and -regionmapping to select a
- encseq index as a sequence source
- * GtBioseq backend switched to GtEncseq
- * GtSeqCol is now an interface, GtEncseqCol added
- * GtRankedList added
- * GtSNPAnnotatorStream and `gt snpper' tool added
- * node sorting code is now aware of MD5 hash presence
- * compatibility with old Pango versions inproved
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 05 Feb 2013 18:52:22 +0100
-
-genometools (1.4.2-4) unstable; urgency=low
-
- * Remove shlibs.local file
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 12:24:17 +0200
-
-genometools (1.4.2-3) unstable; urgency=low
-
- * Build with pbuilder to obtain reasonable libc dependency (>= 2.13)
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 10:04:34 +0200
-
-genometools (1.4.2-2) unstable; urgency=low
-
- * Fixed libpango-dev dependency
- * Updated manpages
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 08 Oct 2012 07:51:52 +0200
-
-genometools (1.4.2-1) unstable; urgency=low
-
- * New upstream release
- [ Sponsor Steffen Moeller ]
- * Update of policy to 3.9.4
- * Added DMUA flag
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Fri, 05 Oct 2012 15:47:56 +0200
-
-genometools (1.4.1-1) unstable; urgency=low
-
- * Initial release (Closes: #657923)
- * the GFF3 parser now handles children which are defined before their parents
- * many small improvements to the GFF3 parser
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 09 Jul 2012 14:10:23 +0100
Copied: trunk/packages/genometools/tags/1.5.2-4/debian/changelog (from rev 17003, trunk/packages/genometools/trunk/debian/changelog)
===================================================================
--- trunk/packages/genometools/tags/1.5.2-4/debian/changelog (rev 0)
+++ trunk/packages/genometools/tags/1.5.2-4/debian/changelog 2014-05-24 18:11:53 UTC (rev 17004)
@@ -0,0 +1,131 @@
+genometools (1.5.2-4) unstable; urgency=low
+
+ * Incorporate patches addressing type conversion errors (thanks to
+ Michael Tautschnig).
+ Closes: #748305
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 24 May 2014 18:57:45 +0000
+
+genometools (1.5.2-3) unstable; urgency=low
+
+ * Address building issues on s390x, powerpc and armhf
+ * Don't use -m64 for arm64 (thanks to Logan Rosen)
+ Closes: #748708
+ * Build-depend on docbook-xsl to fix FTBFS while offline (thanks to
+ Logan Rosen)
+ Closes: #748709
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 19 May 2014 23:06:34 +0000
+
+genometools (1.5.2-2) unstable; urgency=low
+
+ * Split manuals into separate documents to avoid strange LaTeX build issues.
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 23:23:20 +0000
+
+genometools (1.5.2-1) unstable; urgency=low
+
+ * New upstream release.
+ * Remove symbols file because private symbols are exported (next upstream
+ version will properly control exported symbols and a new symbols file
+ will be created and maintained)
+ * Remove manpages from debian directory as they are now autogenerated on
+ build
+ * Fix some missing symbols problems
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 10:51:41 +0000
+
+genometools (1.5.1-3) unstable; urgency=low
+
+ * debian/rules
+ - Add basic tests to check whether cairo/pango linking works
+ - Clean up indices created by tests to make repeated builds possible
+ - Make sure bin/examples/sketch_parsed_with_* are built
+ - Enable compiler optimization
+ * debian/control
+ - Move libgenometools0 package into libs section
+ - Switch pango deps to new package
+ - Add ruby builddep, required for the testsuite
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 06 Nov 2013 14:28:41 +0100
+
+genometools (1.5.1-2) unstable; urgency=low
+
+ * debian/control
+ - Add myself to Uploaders
+ - cme fix dpkg-control
+ - Follow liblua package name transition
+ Closes: #728017
+ - Remove depends from virtual package python-ctypes which is provided
+ by python
+ * provide symbols file
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Oct 2013 08:17:04 +0100
+
+genometools (1.5.1-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 07 Mar 2013 14:08:05 +0100
+
+genometools (1.5.0-2) unstable; urgency=low
+
+ * Patch manuals not to use includecomment/excludecomment
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 16 Feb 2013 16:58:11 +0100
+
+genometools (1.5.0-1) unstable; urgency=low
+
+ * New upstream release
+ * bugfixes and cleanups
+ * development tool `gt sain' added to run an induced suffix array sorting
+ algorithm
+ * the -typecheck option in the `gt gff3` and `gt gff3validator` tools
+ now also validates parent (part-of) relationships, see -help output for
+ details
+ * new option -encseq besides -seqfile(s) and -regionmapping to select a
+ encseq index as a sequence source
+ * GtBioseq backend switched to GtEncseq
+ * GtSeqCol is now an interface, GtEncseqCol added
+ * GtRankedList added
+ * GtSNPAnnotatorStream and `gt snpper' tool added
+ * node sorting code is now aware of MD5 hash presence
+ * compatibility with old Pango versions inproved
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 05 Feb 2013 18:52:22 +0100
+
+genometools (1.4.2-4) unstable; urgency=low
+
+ * Remove shlibs.local file
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 12:24:17 +0200
+
+genometools (1.4.2-3) unstable; urgency=low
+
+ * Build with pbuilder to obtain reasonable libc dependency (>= 2.13)
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 10:04:34 +0200
+
+genometools (1.4.2-2) unstable; urgency=low
+
+ * Fixed libpango-dev dependency
+ * Updated manpages
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 08 Oct 2012 07:51:52 +0200
+
+genometools (1.4.2-1) unstable; urgency=low
+
+ * New upstream release
+ [ Sponsor Steffen Moeller ]
+ * Update of policy to 3.9.4
+ * Added DMUA flag
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Fri, 05 Oct 2012 15:47:56 +0200
+
+genometools (1.4.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #657923)
+ * the GFF3 parser now handles children which are defined before their parents
+ * many small improvements to the GFF3 parser
+
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 09 Jul 2012 14:10:23 +0100
Deleted: trunk/packages/genometools/tags/1.5.2-4/debian/patches/series
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/series 2014-05-22 12:04:26 UTC (rev 16999)
+++ trunk/packages/genometools/tags/1.5.2-4/debian/patches/series 2014-05-24 18:11:53 UTC (rev 17004)
@@ -1,12 +0,0 @@
-fix-unsigned-char
-add-libtre
-adding_soname
-libbam-fix
-remove-gitignores
-fix-exports
-missing-libs
-mips-64
-no-xmllint
-spelling
-split-manuals
-arm64-no-m64
Copied: trunk/packages/genometools/tags/1.5.2-4/debian/patches/series (from rev 17003, trunk/packages/genometools/trunk/debian/patches/series)
===================================================================
--- trunk/packages/genometools/tags/1.5.2-4/debian/patches/series (rev 0)
+++ trunk/packages/genometools/tags/1.5.2-4/debian/patches/series 2014-05-24 18:11:53 UTC (rev 17004)
@@ -0,0 +1,13 @@
+fix-unsigned-char
+add-libtre
+adding_soname
+libbam-fix
+remove-gitignores
+fix-exports
+missing-libs
+mips-64
+no-xmllint
+spelling
+split-manuals
+arm64-no-m64
+typecheck-fixes
Copied: trunk/packages/genometools/tags/1.5.2-4/debian/patches/typecheck-fixes (from rev 17003, trunk/packages/genometools/trunk/debian/patches/typecheck-fixes)
===================================================================
--- trunk/packages/genometools/tags/1.5.2-4/debian/patches/typecheck-fixes (rev 0)
+++ trunk/packages/genometools/tags/1.5.2-4/debian/patches/typecheck-fixes 2014-05-24 18:11:53 UTC (rev 17004)
@@ -0,0 +1,224 @@
+Description: Type conversion problem fixes.
+Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
+--- a/src/gtlua/encseq_lua.c
++++ b/src/gtlua/encseq_lua.c
+@@ -80,8 +80,10 @@
+ GtReadmode readmode;
+ reader = check_encseq_reader(L, 1);
+ encseq = check_encseq(L, 2);
+- readmode = luaL_checknumber(L, 3);
+- startpos = luaL_checknumber(L, 4);
++ readmode = luaL_checklong(L, 3);
++ startpos = luaL_checklong(L, 4);
++ luaL_argcheck(L, readmode <= 3, 3,
++ "invalid readmode value, must be <= 3");
+ luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 4,
+ "cannot exceed total length of encoded sequence");
+ gt_encseq_reader_reinit_with_readmode(*reader, *encseq, readmode, startpos);
+@@ -113,10 +115,12 @@
+ int readmode;
+ unsigned char cc;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
+- readmode = luaL_checknumber(L, 3);
++ pos = luaL_checklong(L, 2);
++ readmode = luaL_checklong(L, 3);
+ luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
+ "cannot exceed total length of encoded sequence");
++ luaL_argcheck(L, readmode <= 3, 3,
++ "invalid readmode value, must be <= 3");
+ cc = gt_encseq_get_encoded_char(*encseq, pos, readmode);
+ lua_pushnumber(L, cc);
+ return 1;
+@@ -129,10 +133,12 @@
+ int readmode;
+ char cc;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
+- readmode = luaL_checknumber(L, 3);
++ pos = luaL_checklong(L, 2);
++ readmode = luaL_checklong(L, 3);
+ luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
+ "cannot exceed total length of encoded sequence");
++ luaL_argcheck(L, readmode <= 3, 3,
++ "invalid readmode value, must be <= 3");
+ cc = gt_encseq_get_decoded_char(*encseq, pos, readmode);
+ lua_pushlstring(L, &cc, sizeof (char));
+ return 1;
+@@ -192,8 +198,8 @@
+ GtUword from, to;
+ unsigned char *string;
+ encseq = check_encseq(L, 1);
+- from = luaL_checknumber(L, 2);
+- to = luaL_checknumber(L, 3);
++ from = luaL_checklong(L, 2);
++ to = luaL_checklong(L, 3);
+ luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
+ luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
+ "cannot exceed total length of encoded sequence");
+@@ -209,8 +215,8 @@
+ GtUword from, to;
+ char *string;
+ encseq = check_encseq(L, 1);
+- from = luaL_checknumber(L, 2);
+- to = luaL_checknumber(L, 3);
++ from = luaL_checklong(L, 2);
++ to = luaL_checklong(L, 3);
+ luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
+ luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
+ "cannot exceed total length of encoded sequence");
+@@ -226,7 +232,7 @@
+ GtEncseq **encseq;
+ GtUword pos;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
++ pos = luaL_checklong(L, 2);
+ luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
+ "cannot exceed number of sequences");
+ lua_pushnumber(L, gt_encseq_seqlength(*encseq, pos));
+@@ -238,7 +244,7 @@
+ GtEncseq **encseq;
+ GtUword pos;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
++ pos = luaL_checklong(L, 2);
+ luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
+ "cannot exceed number of sequences");
+ lua_pushnumber(L, gt_encseq_seqstartpos(*encseq, pos));
+@@ -250,7 +256,7 @@
+ GtEncseq **encseq;
+ GtUword pos;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
++ pos = luaL_checklong(L, 2);
+ luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
+ "cannot exceed total length of encoded sequence");
+ lua_pushnumber(L, gt_encseq_seqnum(*encseq, pos));
+@@ -279,7 +285,7 @@
+ GtUword seqno, desclen;
+ const char *string;
+ encseq = check_encseq(L, 1);
+- seqno = luaL_checknumber(L, 2);
++ seqno = luaL_checklong(L, 2);
+ luaL_argcheck(L, seqno < gt_encseq_num_of_sequences(*encseq), 2,
+ "cannot exceed number of sequences");
+ string = gt_encseq_description(*encseq, &desclen, seqno);
+@@ -300,7 +306,7 @@
+ GtEncseq **encseq;
+ GtUword fileno;
+ encseq = check_encseq(L, 1);
+- fileno = luaL_checknumber(L, 2);
++ fileno = luaL_checklong(L, 2);
+ luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
+ "cannot exceed number of files");
+ lua_pushnumber(L, gt_encseq_effective_filelength(*encseq, fileno));
+@@ -312,7 +318,7 @@
+ GtEncseq **encseq;
+ GtUword fileno;
+ encseq = check_encseq(L, 1);
+- fileno = luaL_checknumber(L, 2);
++ fileno = luaL_checklong(L, 2);
+ luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
+ "cannot exceed number of files");
+ lua_pushnumber(L, gt_encseq_filestartpos(*encseq, fileno));
+@@ -324,7 +330,7 @@
+ GtEncseq **encseq;
+ GtUword pos;
+ encseq = check_encseq(L, 1);
+- pos = luaL_checknumber(L, 2);
++ pos = luaL_checklong(L, 2);
+ luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
+ "cannot exceed total length of encoded sequence");
+ lua_pushnumber(L, gt_encseq_filenum(*encseq, pos));
+@@ -397,8 +403,10 @@
+ GtUword startpos;
+ GtReadmode readmode;
+ encseq = check_encseq(L, 1);
+- readmode = luaL_checknumber(L, 2);
+- startpos = luaL_checknumber(L, 3);
++ readmode = luaL_checklong(L, 2);
++ startpos = luaL_checklong(L, 3);
++ luaL_argcheck(L, readmode <= 3, 2,
++ "invalid readmode value, must be <= 3");
+ luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 3,
+ "cannot exceed total length of encoded sequence");
+ reader = gt_encseq_create_reader_with_readmode(*encseq, readmode, startpos);
+--- a/src/gtlua/mathsupport_lua.c
++++ b/src/gtlua/mathsupport_lua.c
+@@ -21,7 +21,7 @@
+
+ static int gt_lua_mathsupport_rand_max(lua_State *L)
+ {
+- GtUword max = luaL_checknumber(L, 1);
++ GtUword max = luaL_checklong(L, 1);
+
+ lua_pushnumber(L, gt_rand_max(max));
+ return 1;
+--- a/src/match/eis-bwtseq.c
++++ b/src/match/eis-bwtseq.c
+@@ -473,7 +473,7 @@
+ CONTEXT_INTERVAL = 128,
+ };
+
+-int
++enum verifyBWTSeqErrCode
+ gt_BWTSeqVerifyIntegrity(BWTSeq *bwtSeq, const char *projectName,
+ int checkFlags,
+ GtUword tickPrint, FILE *fp,
+--- a/src/tools/gt_tir.c
++++ b/src/tools/gt_tir.c
+@@ -394,9 +394,9 @@
+ GtNodeVisitor *pdom_v;
+ ms = gt_pdom_model_set_new(arguments->hmm_files, err);
+ if (ms != NULL) {
+- pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->cutoff,
++ pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->evalue_cutoff,
+ arguments->chain_max_gap_length,
+- arguments->evalue_cutoff, rmap,
++ arguments->cutoff, rmap,
+ err);
+ if (pdom_v == NULL)
+ had_err = -1;
+--- a/testdata/gtscripts/encseq.lua
++++ b/testdata/gtscripts/encseq.lua
+@@ -60,6 +60,9 @@
+ rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 100, 0)
+ assert(not rval)
+ assert(string.find(err, "cannot exceed"))
++ rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
++ assert(not rval)
++ assert(string.find(err, "invalid readmode"))
+ end
+
+ function run_test_seq_startpos(es)
+@@ -99,6 +102,9 @@
+ rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
+ assert(not rval)
+ assert(string.find(err, "cannot exceed"))
++ rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
++ assert(not rval)
++ assert(string.find(err, "invalid readmode"))
+ end
+
+ function run_test_file_length_protein(es)
+@@ -128,7 +134,7 @@
+ rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 300, 500)
+ assert(not rval)
+ assert(string.find(err, "cannot exceed"))
+-
++
+ end
+
+ function run_test_seq_substr_decoded(es, seq1, seq2)
+@@ -168,7 +174,10 @@
+ rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 0, 300)
+ assert(not rval)
+ assert(string.find(err, "cannot exceed"))
+-end
++ rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 7, 3)
++ assert(not rval)
++ assert(string.find(err, "invalid readmode"))
++end
+
+ ee = gt.encseq_encoder_new()
+ ee:encode({dnaseqfile}, "dnaseqfile")
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