[med-svn] [Git][med-team/kmc][master] 9 commits: Drop unneeded get-orig-source target
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 11 21:07:07 BST 2018
Andreas Tille pushed to branch master at Debian Med / kmc
Commits:
237c8f32 by Andreas Tille at 2018-07-11T21:11:28+02:00
Drop unneeded get-orig-source target
- - - - -
e70738dd by Andreas Tille at 2018-07-11T21:12:12+02:00
debhelper 11
- - - - -
2b38a8a0 by Andreas Tille at 2018-07-11T21:12:14+02:00
Point Vcs fields to salsa.debian.org
- - - - -
67020f59 by Andreas Tille at 2018-07-11T21:15:04+02:00
Standards-Version: 4.1.5
- - - - -
5209bd70 by Andreas Tille at 2018-07-11T21:16:41+02:00
Drop unnecessary Testsuite: autopkgtest
- - - - -
8fca372d by Andreas Tille at 2018-07-11T21:17:55+02:00
Delete unused patch files
- - - - -
74b16d5f by Andreas Tille at 2018-07-11T21:34:38+02:00
Do not parse d/changelog
- - - - -
7011d0ec by Andreas Tille at 2018-07-11T21:34:51+02:00
Fix spelling
- - - - -
1cf350ab by Andreas Tille at 2018-07-11T21:36:31+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/compat
- debian/control
- − debian/patches/0006-Fix-wildcard-to-define-libkmc-objects.patch
- − debian/patches/allow-dry-clean
- debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+kmc (2.3+dfsg-6) unstable; urgency=medium
+
+ * Drop unneeded get-orig-source target
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.5
+ * Drop unnecessary Testsuite: autopkgtest
+ * Do not parse d/changelog
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Wed, 11 Jul 2018 21:35:03 +0200
+
kmc (2.3+dfsg-5) unstable; urgency=medium
* Add missing include to header, fixes FTBFS.
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -6,17 +6,16 @@ Uploaders: Andreas Tille <tille at debian.org>,
Kevin Murray <spam at kdmurray.id.au>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
dh-exec,
zlib1g-dev,
libbz2-dev,
help2man,
asciidoctor,
d-shlibs
-Standards-Version: 3.9.7
-Testsuite: autopkgtest
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmc.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/kmc.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/kmc
+Vcs-Git: https://salsa.debian.org/med-team/kmc.git
Homepage: http://sun.aei.polsl.pl/kmc
Package: kmc
@@ -47,8 +46,8 @@ Description: count kmers in genomic sequences
order of the size of input data (usually it is smaller).
Package: libkmc-dev
-Section: libdevel
Architecture: any
+Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
Description: library to access KMC k-mer count files
=====================================
debian/patches/0006-Fix-wildcard-to-define-libkmc-objects.patch deleted
=====================================
--- a/debian/patches/0006-Fix-wildcard-to-define-libkmc-objects.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Fri, 2 Oct 2015 09:58:41 +1000
-Subject: Fix wildcard to define libkmc objects
-
----
- makefile | 9 +++++----
- 1 file changed, 5 insertions(+), 4 deletions(-)
-
-diff --git a/makefile b/makefile
-index bc2ed0f..ff7357d 100644
---- a/makefile
-+++ b/makefile
-@@ -23,14 +23,15 @@ $(KMC_MAIN_DIR)/kb_completer.o \
- $(KMC_MAIN_DIR)/kb_storer.o \
- $(KMC_MAIN_DIR)/kmer.o
-
--KMC_DUMP_OBJS = \
--$(KMC_DUMP_DIR)/nc_utils.o \
-+KMC_LIB_OBJS = \
- $(KMC_API_DIR)/mmer.o \
--$(KMC_DUMP_DIR)/kmc_dump.o \
- $(KMC_API_DIR)/kmc_file.o \
- $(KMC_API_DIR)/kmer_api.o
-
--KMC_LIB_OBJS = $(wildcard $(KMC_API_DIR)/*.o)
-+KMC_DUMP_OBJS = \
-+$(KMC_DUMP_DIR)/nc_utils.o \
-+$(KMC_DUMP_DIR)/kmc_dump.o \
-+$(KMC_LIB_OBJS)
-
- ifeq ($(DISABLE_ASMLIB),true)
- CFLAGS += -DDISABLE_ASMLIB
=====================================
debian/patches/allow-dry-clean deleted
=====================================
--- a/debian/patches/allow-dry-clean
+++ /dev/null
@@ -1,25 +0,0 @@
-From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Date: Thu, 1 Oct 2015 16:13:54 +1000
-Subject: allow-dry-clean
-
----
- makefile | 9 +++------
- 1 file changed, 3 insertions(+), 6 deletions(-)
-
-diff --git a/makefile b/makefile
-index 0706eb3..71dd3b2 100644
---- a/makefile
-+++ b/makefile
-@@ -52,9 +49,9 @@ kmc_dump: $(KMC_DUMP_OBJS)
- -mkdir -p $(KMC_BIN_DIR)
- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
- clean:
-- -rm $(KMC_MAIN_DIR)/*.o
-- -rm $(KMC_API_DIR)/*.o
-- -rm $(KMC_DUMP_DIR)/*.o
-+ -rm -f $(KMC_MAIN_DIR)/*.o
-+ -rm -f $(KMC_API_DIR)/*.o
-+ -rm -f $(KMC_DUMP_DIR)/*.o
- -rm -rf bin
-
- all: kmc kmc_dump
=====================================
debian/patches/spelling
=====================================
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -3,7 +3,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
--- a/kmc_tools/config.h
+++ b/kmc_tools/config.h
-@@ -243,7 +243,7 @@
+@@ -243,11 +243,11 @@ public:
std::cout << " sort - sorts k-mers from database generated by KMC2.x\n";
std::cout << " reduce - exclude too rare and too frequent k-mers\n";
std::cout << " compact - remove counters (store only k-mers)\n";
@@ -12,7 +12,21 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << " dump - dump k-mers and counters to text file\n";
std::cout << " more complex operations:\n";
std::cout << " complex - complex operations with a number of input databases\n";
-@@ -332,7 +332,7 @@
+- std::cout << " other operatations:\n";
++ std::cout << " other operations:\n";
+ std::cout << " filter - filter out reads with too small number of k-mers\n";
+ std::cout << " global parameters:\n";
+ std::cout << " -t<value> - total number of threads (default: no. of CPU cores)\n";
+@@ -301,7 +301,7 @@ public:
+ void Display() const override
+ {
+ Display2ArgGeneral();
+- std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than apropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
++ std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than appropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
+ std::cout << "Example:\n";
+ std::cout << "kmc -k28 file1.fastq kmers1 tmp\n";
+ std::cout << "kmc -k28 file2.fastq kmers2 tmp\n";
+@@ -332,7 +332,7 @@ public:
{}
void Display() const override
{
@@ -21,7 +35,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << "kmc_tools complex <operations_definition_file>\n";
std::cout << " operations_definition_file - path to file which define input sets and operations. It is text file with following syntax:\n";
std::cout << " __________________________________________________________________ \n";
-@@ -355,7 +355,7 @@
+@@ -355,7 +355,7 @@ public:
std::cout << "out_db_path - path to output database\n";
std::cout << "ref_input - one of input1, input2, ..., inputN\n";
std::cout << "oper - one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}\n";
@@ -30,7 +44,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << "output_params are:\n";
std::cout << " -ci<value> - exclude k-mers occurring less than <value> times \n";
std::cout << " -cx<value> - exclude k-mers occurring more of than <value> times\n";
-@@ -547,4 +547,4 @@
+@@ -547,4 +547,4 @@ public:
#endif
@@ -39,7 +53,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmer_counter/bkb_sorter.h
+++ b/kmer_counter/bkb_sorter.h
-@@ -367,7 +367,7 @@
+@@ -367,7 +367,7 @@ template<unsigned SIZE> void CBigKmerBin
}
//----------------------------------------------------------------------------------
@@ -50,7 +64,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/kb_sorter.h
+++ b/kmer_counter/kb_sorter.h
-@@ -830,7 +830,7 @@
+@@ -830,7 +830,7 @@ template <typename KMER_T, unsigned SIZE
}
//----------------------------------------------------------------------------------
@@ -61,7 +75,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/s_mapper.h
+++ b/kmer_counter/s_mapper.h
-@@ -30,12 +30,12 @@
+@@ -30,12 +30,12 @@ class CSignatureMapper
class Comp
{
@@ -79,7 +93,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
--- a/kmc_tools/kmc1_db_writer.h
+++ b/kmc_tools/kmc1_db_writer.h
-@@ -37,7 +37,7 @@
+@@ -37,7 +37,7 @@ public:
{
if (fwrite(buf, 1, size, kmc_suf) != size)
{
@@ -88,7 +102,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
delete[] buf;
-@@ -78,9 +78,9 @@
+@@ -78,9 +78,9 @@ private:
void store_pre_buf();
void send_suf_buf_to_queue();
@@ -100,7 +114,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
template<typename T> void write_header_part(T data);
void calc_lut_prefix_len();
-@@ -159,7 +159,7 @@
+@@ -159,7 +159,7 @@ template <unsigned SIZE> CKMC1DbWriter<S
template<unsigned SIZE> bool CKMC1DbWriter<SIZE>::Process()
{
@@ -109,7 +123,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
//Converts bundles to output buffers, sufix buffer is placed to another queue and write in separate thread (sufix_writer)
std::thread preparing_thread([this]{
-@@ -201,7 +201,7 @@
+@@ -201,7 +201,7 @@ template<unsigned SIZE> bool CKMC1DbWrit
preparing_thread.join();
suf_buf_writing_thread.join();
@@ -118,7 +132,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
return true;
}
-@@ -232,22 +232,22 @@
+@@ -232,22 +232,22 @@ template <unsigned SIZE> template <typen
}
/*****************************************************************************************************************************/
@@ -145,7 +159,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
{
uint32 max_prefix = (1 << 2 * lut_prefix_len);
while (current_prefix < max_prefix - 1)
-@@ -284,12 +284,12 @@
+@@ -284,12 +284,12 @@ template<unsigned SIZE> void CKMC1DbWrit
if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
{
@@ -160,7 +174,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
fclose(kmc_pre);
-@@ -327,7 +327,7 @@
+@@ -327,7 +327,7 @@ template<unsigned SIZE> void CKMC1DbWrit
{
if (fwrite(pre_buff, sizeof(uint64), pre_pos, kmc_pre) != pre_pos)
{
@@ -171,7 +185,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
pre_pos = 0;
--- a/kmer_counter/radix.cpp
+++ b/kmer_counter/radix.cpp
-@@ -143,7 +143,7 @@
+@@ -143,7 +143,7 @@ void RadixSort_uint8(uint32 *&data_ptr,
Satish, N., Kim, C., Chhugani, J., Nguyen, A.D., Lee, V.W., Kim, D., Dubey, P. (2010).
Fast Sort on CPUs and GPUs. A Case for Bandwidth Oblivious SIMD Sort.
Proc. of the 2010 Int. Conf. on Management of data, pp. 351362.
@@ -182,7 +196,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
template<typename COUNTER_TYPE, typename INT_TYPE>
--- a/kmc_tools/kmc2_db_reader.h
+++ b/kmc_tools/kmc2_db_reader.h
-@@ -869,7 +869,7 @@
+@@ -869,7 +869,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
my_fseek(kmc_pre, 4, SEEK_SET);
if (fread(LUTS, sizeof(uint64), lut_recs, kmc_pre) != lut_recs)
{
@@ -191,7 +205,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
fclose(kmc_pre);
-@@ -1005,7 +1005,7 @@
+@@ -1005,7 +1005,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
// my_fseek(kmc_suf, start, SEEK_SET);
// if (fread(buf, 1, size, kmc_suf) != size)
// {
@@ -200,7 +214,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
// exit(1);
// }
//#ifdef ENABLE_LOGGER
-@@ -1336,7 +1336,7 @@
+@@ -1336,7 +1336,7 @@ template<unsigned SIZE> CKMC2DbReader<SI
db_reader_counters_only = std::make_unique<CKMC2DbReaderCountersOnly<SIZE>>(header, desc);
break;
default: //should never be here
@@ -209,7 +223,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
-@@ -1395,4 +1395,4 @@
+@@ -1395,4 +1395,4 @@ template<unsigned SIZE> bool CKMC2DbRead
@@ -218,7 +232,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+#endif
--- a/kmc_tools/parameters_parser.cpp
+++ b/kmc_tools/parameters_parser.cpp
-@@ -140,7 +140,7 @@
+@@ -140,7 +140,7 @@ void CParametersParser::read_input_fastq
config.filtering_params.input_file_type = CFilteringParams::file_type::fastq;
break;
default:
@@ -227,7 +241,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
break;
}
-@@ -207,7 +207,7 @@
+@@ -207,7 +207,7 @@ void CParametersParser::read_dump_params
}
else
{
@@ -236,7 +250,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
}
++pos;
}
-@@ -242,7 +242,7 @@
+@@ -242,7 +242,7 @@ void CParametersParser::read_input_desc(
}
else
{
@@ -245,7 +259,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
-@@ -279,7 +279,7 @@
+@@ -279,7 +279,7 @@ void CParametersParser::read_output_desc
}
else
{
@@ -254,7 +268,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
-@@ -355,7 +355,7 @@
+@@ -355,7 +355,7 @@ void CParametersParser::Parse()
}
else
{
@@ -263,7 +277,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
Usage();
exit(1);
}
-@@ -533,4 +533,4 @@
+@@ -533,4 +533,4 @@ void CParametersParser::SetThreads()
@@ -272,7 +286,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmc_tools/parameters_parser.h
+++ b/kmc_tools/parameters_parser.h
-@@ -67,7 +67,7 @@
+@@ -67,7 +67,7 @@ CExpressionNode<SIZE>* CParametersParser
expression_root = new CCountersSubtractionNode<SIZE>;
break;
default:
@@ -281,7 +295,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
expression_root->AddLeftChild(left);
-@@ -98,7 +98,7 @@
+@@ -98,7 +98,7 @@ CExpressionNode<SIZE>* CParametersParser
}
else //should never be here
{
@@ -290,7 +304,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
#ifdef ENABLE_DEBUG
std::cout << __FUNCTION__ << " line: " << __LINE__ << "\n";
#endif
-@@ -108,4 +108,4 @@
+@@ -108,4 +108,4 @@ CExpressionNode<SIZE>* CParametersParser
#endif
@@ -299,7 +313,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmc_tools/parser.cpp
+++ b/kmc_tools/parser.cpp
-@@ -115,7 +115,7 @@
+@@ -115,7 +115,7 @@ void CParser::parseInputLine(const std::
desc.cutoff_max = atoi(tmp.c_str() + 3);
continue;
}
@@ -308,7 +322,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
-@@ -160,7 +160,7 @@
+@@ -160,7 +160,7 @@ void CParser::parseOtuputParamsLine()
config.output_desc.counter_max = atoi(tmp.c_str() + 3);
continue;
}
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -2,13 +2,15 @@
export DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-DATE := $(shell dpkg-parsechangelog -S Date)
+
+include /usr/share/dpkg/default.mk
+DATE := $(SOURCE_DATE_EPOCH)
mandir := $(CURDIR)/debian/man
debfolder := $(CURDIR)/debian
%:
- dh $@ --parallel
+ dh $@
override_dh_install:
dh_install
@@ -24,6 +26,3 @@ override_dh_installman:
asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression gz --destdir=..
View it on GitLab: https://salsa.debian.org/med-team/kmc/compare/55b0e1727d003208049764f0a1e9ff7443ac4fc0...1cf350ab58aac7e49624f54643d08688784f7687
--
View it on GitLab: https://salsa.debian.org/med-team/kmc/compare/55b0e1727d003208049764f0a1e9ff7443ac4fc0...1cf350ab58aac7e49624f54643d08688784f7687
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