debian/changelog

+genometools (1.5.10+ds-3) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Do not parse d/changelog
+  * Remove unused patches
+
+ -- Andreas Tille <tille@debian.org>  Sun, 28 Oct 2018 14:54:51 +0100
+
 genometools (1.5.10+ds-2) unstable; urgency=medium
 
   * Ensure that src/external is not repopulated by patches.

debian/compat

-9
+11

debian/control

@@ -4,7 +4,7 @@ Uploaders: Sascha Steinbiss <satta@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                liblua5.1-0-dev,
                lua-md5-dev,
@@ -32,9 +32,9 @@ Build-Depends: debhelper (>= 9),
                docbook-xml,
                faketime,
                imagemagick
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/genometools.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/genometools.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/genometools
+Vcs-Git: https://salsa.debian.org/med-team/genometools.git
 Homepage: http://genometools.org
 
 Package: genometools

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: genometools
 Source: http://genometools.org
 Files-Excluded: src/external

debian/genometools-doc.doc-base

@@ -11,4 +11,4 @@ Abstract: User manuals for GenomeTools
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/genometools-doc/*.pdf.gz
+Files: /usr/share/doc/genometools/*.pdf.gz

debian/patches/add-libtre

-Description: add soname to linker call in Makefile
- Upstream Makefile does not build a shared object with soname or version
- number. This patch adds support for sonames, as well a symlink from
- the .so to the .so.X file.
-Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -191,7 +191,7 @@
- # add necessary shared lib dependencies then not building them ourselves
- ifeq ($(useshared),yes)
-   DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
--           -llua5.1-filesystem -llua5.1-des56 -lbam
-+           -llua5.1-filesystem -llua5.1-des56 -lbam -ltre
- else
-   DEPLIBS:=
- endif

debian/patches/arm64-no-m64

-Description: Do not use -m64 in arm64.
-Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -308,7 +308,7 @@
- endif
- 
- ifeq ($(m64),yes)
--  ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
-+  ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
-     GT_CFLAGS += -m64
-     GT_LDFLAGS += -m64
-     SQLITE_CFLAGS += -m64

debian/patches/fix-unsigned-char

-Description: Adapt code to work with char being unsigned by default.
-Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
---- a/src/core/safearith.c
-+++ b/src/core/safearith.c
-@@ -182,8 +182,10 @@
-   gt_error_check(err);
- 
-   {
-+    /* This is not always true, e.g. on PPC and ARM!
-+       cf. http://www.network-theory.co.uk/docs/gccintro/gccintro_71.html
-     gt_ensure(__MIN(char) == -128);
--    gt_ensure(__MAX(char) == 127);
-+    gt_ensure(__MAX(char) == 127); */
-     gt_ensure(__MIN(unsigned char) == 0);
-     gt_ensure(__MAX(unsigned char) == 255);
- 
---- a/src/core/tokenizer.c
-+++ b/src/core/tokenizer.c
-@@ -45,7 +45,9 @@
- 
- GtStr* gt_tokenizer_get_token(GtTokenizer *t)
- {
--  char c = EOF;
-+  char c;
-+  bool has_eof = true;
-+  int rval = 0;
-   gt_assert(t);
- 
-   /* if we have no current token, get it if possible */
-@@ -53,32 +55,44 @@
-     if (t->skip_comment_lines && gt_io_line_start(t->io)) {
-       for (;;) {
-         gt_assert(gt_io_line_start(t->io));
--        if ((gt_io_get_char(t->io, &c) != -1)) {
--          if (c == '#') {
-+        if ((gt_io_get_char(t->io, (char*) &c) != -1)) {
-+          if ((char) c == '#') {
-             /* skip line */
-             while ((gt_io_get_char(t->io, &c) != -1) && c != '\n');
--            c = EOF;
-+            has_eof = true;
-           }
-           else {
-             gt_io_unget_char(t->io, c);
-+            has_eof = false;
-             break;
-           }
-         }
--        else
-+        else {
-+          c = EOF;
-           break;
-+        }
-       }
--    }
--    while ((gt_io_get_char(t->io, &c) != -1) && c == ' '); /* skip blanks */
-+    } /* skip blanks */
-+    while (((rval = gt_io_get_char(t->io, &c)) != -1) && c == ' ');
-+    if (rval == -1)
-+      has_eof = true;
-+    else
-+      has_eof = false;
-     do {
--      if (c != EOF) {
-+      if (!has_eof) {
-         if (!t->token)
-           t->token = gt_str_new();
-         if (c == '\n')
-           break;
-         gt_str_append_char(t->token, c);
-       }
--    } while ((gt_io_get_char(t->io, &c) != -1) && c != ' ' && c != '\n');
--    if (c == '\n' && c != EOF) {
-+    } while (((rval = gt_io_get_char(t->io, &c)) != -1)
-+              && c != ' ' && c != '\n');
-+    if (rval == -1)
-+      has_eof = true;
-+    else
-+      has_eof = false;
-+    if (c == '\n' && !has_eof) {
-       gt_assert(t->token);
-       gt_str_append_char(t->token, c);
-     }
---- a/src/core/tokenizer.h
-+++ b/src/core/tokenizer.h
-@@ -33,7 +33,7 @@
- bool          gt_tokenizer_has_token(GtTokenizer*);
- bool          gt_tokenizer_line_start(const GtTokenizer*);
- void          gt_tokenizer_next_token(GtTokenizer*); /* go to the next token */
--GtUword gt_tokenizer_get_line_number(const GtTokenizer*);
-+GtUword       gt_tokenizer_get_line_number(const GtTokenizer*);
- const char*   gt_tokenizer_get_filename(const GtTokenizer*);
- int           gt_tokenizer_unit_test(GtError*);
- void          gt_tokenizer_delete(GtTokenizer*);
---- a/src/core/trans_table.c
-+++ b/src/core/trans_table.c
-@@ -21,7 +21,7 @@
- #include "core/ma.h"
- #include "core/trans_table.h"
- 
--#define GT_AMINOACIDFAIL            -1
-+#define GT_AMINOACIDFAIL ((char) 0)
- 
- /* The integer which a T is encoded to. */
- #define GT_T_CODE  0
---- a/src/extended/gff3_escaping.c
-+++ b/src/extended/gff3_escaping.c
-@@ -64,7 +64,8 @@
-   unsigned char d;
-   gt_assert(str && out);
-   if (!(GtIsHexChar[(int) *(str+1)] & 2)
--        || !(GtIsHexChar[(int) *(str+2)] & 1)) {
-+        || !(GtIsHexChar[(int) *(str+2)] & 1)
-+        || !strncmp(str, "%7F", 3 * (sizeof (char)))) {
-     return -1;
-   }
-   d = (GtHexToDec[(int) *(str+1)] << 4) | (GtHexToDec[(int) *(str+2)]);

debian/patches/fix_caption.patch

-Description: change test caption to be less problematic
-Author: Sascha Steinbiss <satta@debian.org>
-Origin: https://github.com/genometools/genometools/commit/d86b83dda1eb43a5adf27f831b103f817e1dc48f#commitcomment-20423074
---- a/testdata/gt_sketch_textwidth.gff3
-+++ b/testdata/gt_sketch_textwidth.gff3
-@@ -1,6 +1,6 @@
- ##gff-version 3
- ##sequence-region ctg123 1 1497228
- ctg123	.	gene	1000	2000	.	+	0	ID=g00001;Name=thisisalongname123
--ctg123	.	gene	2001	3000	.	+	0	ID=g00002;Name=anotherlongname123
-+ctg123	.	gene	2001	3000	.	+	0	ID=g00002;Name=anotherlongname
- ctg123	.	gene	3001	4000	.	+	0	ID=g00003;Name=stillanotherlonglonglonglonglonglonglongname
- ctg123	.	gene	4001	5000	.	+	0	ID=g00004;Name=shortname

debian/patches/manual_fixed_dates.patch

-From 3bf0e31b3a020c415d99d8661c5aca32647c7a6f Mon Sep 17 00:00:00 2001
-From: Sascha Steinbiss <ss34@sanger.ac.uk>
-Date: Thu, 7 Apr 2016 10:25:25 +0100
-Subject: [PATCH] introduce dates for manuals
-
-IMHO manuals should have a specific date, and the build date should not be
-relevant here. This commit initialises the date fields in the manuals by
-setting the date to the last modification date of the file in git, as
-given by:
-
-for f in doc/manuals/*.tex; do
-  export OUT=`TZ=UTC LC_ALL=C date -d "$(git log -1 --format='%aD' -- $f )" +'%d\/%m\/%Y'`;
-  sed -ri "s/.begin.document./\\\date{$OUT}\n\\\begin{document}/g" $f;
-  unset OUT;
-done
----
- doc/manuals/annotationsketch.tex | 1 +
- doc/manuals/genomediff.tex       | 1 +
- doc/manuals/hop.tex              | 1 +
- doc/manuals/ltrdigest.tex        | 1 +
- doc/manuals/ltrharvest.tex       | 1 +
- doc/manuals/mgth.tex             | 1 +
- doc/manuals/packedindex.tex      | 1 +
- doc/manuals/readjoiner.tex       | 1 +
- doc/manuals/repfind.tex          | 1 +
- doc/manuals/tagerator.tex        | 1 +
- doc/manuals/tallymer.tex         | 1 +
- doc/manuals/uniquesub.tex        | 1 +
- 12 files changed, 12 insertions(+)
-
---- a/doc/manuals/annotationsketch.tex
-+++ b/doc/manuals/annotationsketch.tex
-@@ -50,6 +50,7 @@
- \subject{Supplementary Information}
- \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
- 
-+\date{11/07/2012}
- \begin{document}
- 
- \maketitle
---- a/doc/manuals/genomediff.tex
-+++ b/doc/manuals/genomediff.tex
-@@ -59,6 +59,7 @@
-   \url{willrodt@zbh.uni-hamburg.de}\\
- \end{tabular}}
- 
-+\date{02/10/2012}
- \begin{document}
- %\tsuhhfamily
- \maketitle
---- a/doc/manuals/hop.tex
-+++ b/doc/manuals/hop.tex
-@@ -32,6 +32,7 @@
-          \url{kurtz@zbh.uni-hamburg.de}\\[1cm]
-         \end{tabular}}
- 
-+\date{15/05/2014}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/ltrdigest.tex
-+++ b/doc/manuals/ltrdigest.tex
-@@ -41,6 +41,7 @@
-         \end{tabular}
-         \end{tabular}}
- 
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/ltrharvest.tex
-+++ b/doc/manuals/ltrharvest.tex
-@@ -41,6 +41,7 @@
-         \url{http://www.biomedcentral.com/1471-2105/9/18}
-         \end{tabular}
-         \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/mgth.tex
-+++ b/doc/manuals/mgth.tex
-@@ -37,6 +37,7 @@
-          20146 Hamburg\\
-          Germany\\[1cm]
-         \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/packedindex.tex
-+++ b/doc/manuals/packedindex.tex
-@@ -38,6 +38,7 @@
- %        BMC Bioinformatics 2008, 9:18
-         \end{tabular}
-         \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/readjoiner.tex
-+++ b/doc/manuals/readjoiner.tex
-@@ -45,6 +45,7 @@
-          \url{kurtz@zbh.uni-hamburg.de}\\[1cm]
-         \end{tabular}}
- 
-+\date{18/02/2014}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/repfind.tex
-+++ b/doc/manuals/repfind.tex
-@@ -28,6 +28,7 @@
-          University of Hamburg
-         \end{tabular}}
- 
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- This manual describes the options of the program \Repfind. It also gives
---- a/doc/manuals/tagerator.tex
-+++ b/doc/manuals/tagerator.tex
-@@ -22,6 +22,7 @@
-          University of Hamburg
-         \end{tabular}}
- 
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/manuals/tallymer.tex
-+++ b/doc/manuals/tallymer.tex
-@@ -95,6 +95,7 @@
-          University of Hamburg
-         \end{tabular}}
- 
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- This manual describes the \textit{Tallymer}-software, a collection of programs
---- a/doc/manuals/uniquesub.tex
-+++ b/doc/manuals/uniquesub.tex
-@@ -24,6 +24,7 @@
-          University of Hamburg
-         \end{tabular}}
- 
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- 
---- a/doc/devguide/devguide.tex
-+++ b/doc/devguide/devguide.tex
-@@ -36,6 +36,7 @@
- \author{Sascha Steinbiss, Gordon Gremme and Stefan
-         Kurtz\thanks{please send comments to:
-         \texttt{steinbiss@zbh.uni-hamburg.de}}}
-+\date{18/02/2016}
- 
- 
- \begin{document}
---- a/doc/manuals/matstat.tex
-+++ b/doc/manuals/matstat.tex
-@@ -23,6 +23,7 @@
-          Center for Bioinformatics,\\
-          University of Hamburg
-         \end{tabular}}
-+\date{26/01/2008}
- 
- \begin{document}
- \maketitle

debian/patches/mips-64

-Description: Fix compilation on mips64.
-Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -308,12 +308,10 @@
- endif
- 
- ifeq ($(m64),yes)
--  ifneq ($(MACHINE),ia64)
--    ifneq ($(MACHINE),alpha)
--      GT_CFLAGS += -m64
--      GT_LDFLAGS += -m64
--      SQLITE_CFLAGS += -m64
--    endif
-+  ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
-+    GT_CFLAGS += -m64
-+    GT_LDFLAGS += -m64
-+    SQLITE_CFLAGS += -m64
-   endif
- endif
- 

debian/patches/sort-inputs

-Description: Sort inputs
---- a/Makefile
-+++ b/Makefile
-@@ -115,7 +115,7 @@
- EXAMPLES_SRC:=src/example.c
- EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d)
- 
--TOOLS_SRC:=$(wildcard src/tools/*.c)
-+TOOLS_SRC:=$(sort $(wildcard src/tools/*.c))
- TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o)
- TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d)
- 
-@@ -449,7 +449,7 @@
- endif
- 
- # the GenomeTools library
--LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*.c))
-+LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*.c)))
- # remove AnnotationSketch-only bindings
- LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\
-                          $(LIBGENOMETOOLS_PRESRC))
-@@ -664,7 +664,7 @@
- 	@test -d $(@D) || mkdir -p $(@D)
- 	@$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@
- 
--API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*_api.h))
-+API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*_api.h)))
- 
- obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
- 	@echo '[gathering public API symbols to $@]'
-@@ -999,8 +999,8 @@
- ABTOOLS=${shell grep -l Blaufelder src/tools/*.c}
- 
- ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\
--             ${filter-out ${EISFILES},${wildcard ${CURDIR}/src/match/*.c}}\
--             ${wildcard ${CURDIR}/src/ltr/*.c}\
-+             ${filter-out ${EISFILES},${sort ${wildcard ${CURDIR}/src/match/*.c}}}\
-+             ${sort ${wildcard ${CURDIR}/src/ltr/*.c}}\
-              ${SKTOOLS} ${SKCORE} ${SKEXT} \
- 						 ${DWTOOLS} ${DWCORE} ${DWEXT} \
-              ${GGTOOLS} ${GGCORE} ${GGEXT} \
---- a/gtscripts/gtdoc.lua
-+++ b/gtscripts/gtdoc.lua
-@@ -104,6 +104,25 @@
-   end
- end
- 
-+local function iter (a, i) -- taken from PiL, page 59
-+  i = i + 1
-+  local v = a[i]
-+  if v then
-+    return i, v
-+  end
-+end
-+
-+function sorted_dir(dir)
-+  local entries = {}
-+  local i = 0
-+  for name in lfs.dir(dir) do
-+    i = i + 1
-+    entries[i] = name
-+  end
-+  table.sort(entries)
-+  return iter, entries, 0
-+end
-+
- local export = nil
- local is_lua = nil
- 
-@@ -127,7 +146,7 @@
-   for _, v in ipairs(export) do
-     local filename = gt_home .. "/" .. v
-     if is_dir(filename) then
--      for f in lfs.dir(filename) do
-+      for _, f in sorted_dir(filename) do
-         local filename = filename .. "/" .. f
-         process_file(filename, be_verbose, is_lua)
-       end

debian/patches/spelling

-Description: fix spelling issues
-Author: Sascha Steinbiss <satta@debian.org>
-Forwarded: https://github.com/genometools/genometools/pull/727, https://github.com/genometools/genometools/pull/762, https://github.com/genometools/genometools/pull/767
-Applied-Upstream: 1.5.9, commit:f47cc4a6e13d037d6342b0213a5739031ada59c1
-Last-Update: 2016-03-15

debian/patches/spelling.patch

-Description: fix minor spelling issues
-Author: Sascha Steinbiss <satta@debian.org>
---- a/src/extended/condenseq_creator.c
-+++ b/src/extended/condenseq_creator.c
-@@ -1723,7 +1723,7 @@
-   if (!had_err) {
-     if (gt_showtime_enabled())
-       gt_timer_show_progress(timer, "write data, alphabet", stderr);
--    gt_log_log(GT_WU " kmer positons in final kmer_db",
-+    gt_log_log(GT_WU " kmer positions in final kmer_db",
-                gt_kmer_database_get_kmer_count(condenseq_creator->kmer_db));
-     gt_log_log(GT_WU " xdrop calls.", ces_c_xdrops);
-     gt_log_log(GT_WU " uniques", condenseq_creator->ces->udb_nelems);
---- a/src/extended/intset.h
-+++ b/src/extended/intset.h
-@@ -74,7 +74,7 @@
- size_t    gt_intset_best_memory_size(GtUword maxelement, GtUword num_of_elems);
- 
- /* Write <intset> to file <fp>. Fails with exit on IO-error. Returns NULL if
--   data error occures and writes it to <err>, <intset> will be deleted at that
-+   data error occurs and writes it to <err>, <intset> will be deleted at that
-    point. */
- GtIntset* gt_intset_write(GtIntset *intset, FILE *fp, GtError *err);
- 
---- a/src/extended/wtree_encseq.c
-+++ b/src/extended/wtree_encseq.c
-@@ -84,7 +84,7 @@
- 
-     if (bit == 0) {
-       pos = gt_compressed_bitsequence_rank_0(we->c_bits, node_start + pos) -
--        zero_rank_prefix - 1; /*convert count (rank) to positon */
-+        zero_rank_prefix - 1; /*convert count (rank) to position */
-       alpha_end = middle;
-       node_start += we->parent_instance.members->length;
-       node_size = left_child_size;
-@@ -96,7 +96,7 @@
-         one_rank_prefix =
-           gt_compressed_bitsequence_rank_1(we->c_bits, node_start - 1);
-       pos = gt_compressed_bitsequence_rank_1(we->c_bits, node_start + pos) -
--        one_rank_prefix - 1; /*convert count (rank) to positon */
-+        one_rank_prefix - 1; /*convert count (rank) to position */
-       alpha_start = middle + 1;
-       node_size =
-         gt_compressed_bitsequence_rank_1(we->c_bits,
---- a/src/match/seqabstract.h
-+++ b/src/match/seqabstract.h
-@@ -71,7 +71,7 @@
- /* return the length of <sa> */
- GtUword        gt_seqabstract_length(const GtSeqabstract *sa);
- 
--/* return character at positon <idx> (relative to <startpos>) of <sa> */
-+/* return character at position <idx> (relative to <startpos>) of <sa> */
- GtUchar        gt_seqabstract_encoded_char(const GtSeqabstract *sa,
-                                            GtUword idx);
- 
---- a/src/match/sfx-diffcov.c
-+++ b/src/match/sfx-diffcov.c
-@@ -491,7 +491,7 @@
-   return countderived;
- }
- 
--static int dc_compareCodeatpositon(const void *vala,const void *valb)
-+static int dc_compareCodeatposition(const void *vala,const void *valb)
- {
-   const Codeatposition *a = (const Codeatposition *) vala;
-   const Codeatposition *b = (const Codeatposition *) valb;
-@@ -516,7 +516,7 @@
-   return 0;
- }
- 
--static void dc_validate_samplepositons(const GtDifferencecover *dcov)
-+static void dc_validate_samplepositions(const GtDifferencecover *dcov)
- {
-   GtUword pos;
-   unsigned int modvalue;
-@@ -1268,7 +1268,7 @@
-     gt_assert(codelist.spaceCodeatposition != NULL);
-     qsort(codelist.spaceCodeatposition,
-           (size_t) codelist.nextfreeCodeatposition,
--          sizeof (*codelist.spaceCodeatposition),dc_compareCodeatpositon);
-+          sizeof (*codelist.spaceCodeatposition),dc_compareCodeatposition);
-   }
-   if (dcov->effectivesamplesize > 0)
-   {
-@@ -1690,7 +1690,7 @@
-     printf("v=%u (size=%u)\n",dcov->vparam,dcov->size);
-     if (withcheck)
-     {
--      dc_validate_samplepositons(dcov);
-+      dc_validate_samplepositions(dcov);
-     }
-     dc_differencecover_sortsample(dcov,NULL,NULL,NULL,withcheck);
-     gt_differencecover_delete(dcov);
---- a/src/tools/gt_kmer_database.c
-+++ b/src/tools/gt_kmer_database.c
-@@ -126,8 +126,8 @@
-   gt_option_exclude(option_mean_cutoff, option);
- 
-   /* -disable_prune */
--  option = gt_option_new_bool("disable_prune", "disables the removel of kmers, "
--                              "which occure more often than the cutoff.",
-+  option = gt_option_new_bool("disable_prune", "disables the removal of kmers "
-+                              "which occur more often than the cutoff.",
-                               &arguments->prune, false);
-   gt_option_parser_add_option(op, option);
-   gt_option_imply(option, option_use_cutoff);
---- a/src/tools/gt_show_seedext.c
-+++ b/src/tools/gt_show_seedext.c
-@@ -119,7 +119,7 @@
- 
-   /* -sort */
-   op_sortmatches = gt_option_new_bool("sort","sort matches in ascending order "
--                                             "of their end positon on the "
-+                                             "of their end position on the "
-                                              "query",
-                                       &arguments->sortmatches,false);
-   gt_option_parser_add_option(op, op_sortmatches);

debian/patches/strip-nonpublic

---- a/Makefile
-+++ b/Makefile
-@@ -894,8 +894,13 @@
- 	$(RANLIB) $(prefix)/lib/libgenometools.a
- endif
- ifneq ($(sharedlib),no)
--	cp lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib
-+	find src -name '*_api.h' | xargs egrep -ho '(gt_[0-9a-zA-Z_]+)(\[|\()' \
-+	  | sort | uniq | sed s'/.$$//' > apisyms
-+	objcopy --strip-all --keep-symbols apisyms \
-+	  lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) \
-+	  $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION)
- 	ln -fs $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)
-+	rm apisyms
- endif
- 	@echo '[build config script $(@F)]'
- 	sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \

debian/patches/typecheck-fixes

-Description: Type conversion problem fixes.
-Author: Sascha Steinbiss <steinbiss@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")

debian/patches/use-pkgconfig

-From afaed82084071e9d11663b7ce593fa83e6eabbe5 Mon Sep 17 00:00:00 2001
-From: Justus Winter <justus@gnupg.org>
-Date: Fri, 19 Feb 2016 14:06:41 +0100
-Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)'
-
-* Makefile: Drop spurious '$(3)', likely a left-over from copying
-'COMPILE_template'.
----
- Makefile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
---- /dev/null
-+++ b/src/external/lpeg-0.10.2/lua-lpeg.h
-@@ -0,0 +1,39 @@
-+/*
-+** $Id: lpeg.h,v 1.1 2009/12/23 16:15:36 roberto Exp $
-+** LPeg - PEG pattern matching for Lua
-+** Copyright 2009, Lua.org & PUC-Rio  (see 'lpeg.html' for license)
-+** written by Roberto Ierusalimschy
-+*/
-+
-+#ifndef lpeg_h
-+#define lpeg_h
-+
-+#include "lua.h"
-+
-+int luaopen_lpeg (lua_State *L);
-+
-+#define KEYNEWPATT	"lpeg.newpf"
-+
-+
-+/*
-+** type of extension functions that define new "patterns" for LPEG
-+** It should return the new current position or NULL if match fails
-+*/
-+typedef const char *(*PattFunc) (const char *s,  /* current position */
-+                                 const char *e,  /* string end */
-+                                 const char *o,  /* string start */
-+                                 const void *ud);  /* user data */
-+
-+/*
-+** function to create new patterns based on 'PattFunc' functions.
-+** This function is available at *registry[KEYNEWPATT]. (Notice
-+** the extra indirection; the userdata at the registry points to
-+** a variable that points to the function. In ANSI C a void* cannot
-+** point to a function.)
-+*/
-+typedef void (*Newpf) (lua_State *L,
-+                       PattFunc f,  /* pattern */
-+                       const void *ud,  /* (user) data to be passed to 'f' */
-+                       size_t l);  /* size of data to be passed to 'f' */
-+
-+#endif

debian/rules

@@ -5,13 +5,14 @@
 export DESTDIR=$(CURDIR)/debian/tmp
 export DH_ALWAYS_EXCLUDE=.gitignore
 export PATH := $(CURDIR)/debian/strip-nondeterminism:$(PATH)
-export SOURCE_DATE_EPOCH = $(shell date -d "$$(dpkg-parsechangelog -SDate)" +%s)
+
+include /usr/share/dpkg/default.mk
+
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=')
 BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=')
 
-
 ifeq ($(DARCH),x32)
   X32:=yes
 else
@@ -57,8 +58,10 @@ override_dh_auto_build:
 	$(FAKETIME) dh_auto_build -- verbose=yes useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	bin/gt -test
 	cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby'
+endif
 
 override_dh_auto_install:
 	dh_auto_install -- installmanpages useshared=yes \