This is an automated email from the git hooks/post-receive script. tille pushed a commit to tag debian/1.0.2-1 in repository freebayes.
commit a06c13fadadb4c48eec0795deb4d33c776a9d151 Author: Andreas Tille <[email protected]> Date: Sat Sep 2 07:44:44 2017 +0200 Commit as freebayes was uploaded --- debian/README.source | 11 --- debian/changelog | 6 -- debian/control | 9 +- .../patches/use_debian_packaged_libjsoncpp.patch | 17 ---- debian/patches/use_debian_packaged_seqlib.patch | 87 ---------------- debian/patches/vcffirstheader.patch | 29 ------ debian/rules | 6 +- debian/test-simple-bash/lib/test-simple.bash | 110 --------------------- debian/test-simple-bash/test/basics.t | 26 ----- debian/test-simple-bash/test/doc.t | 15 --- debian/test-simple-bash/test/no-label.t | 25 ----- 11 files changed, 3 insertions(+), 338 deletions(-) diff --git a/debian/README.source b/debian/README.source deleted file mode 100644 index 26e4dc4..0000000 --- a/debian/README.source +++ /dev/null @@ -1,11 +0,0 @@ -To run the test suite some bash testing framework was used -bu upstream as Git submodules. For the Git packaging these -were downloaded separately - -Files: debian/bash-tap/* - Obtained from - https://github.com/illusori/bash-tap - -Files: debian/test-simple-bash/* - Obtained from - https://github.com/ingydotnet/test-simple-bash/tree/master/lib diff --git a/debian/changelog b/debian/changelog index 4fec7a2..eaeaad5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,3 @@ -freebayes (1.1.0-1) UNRELEASED; urgency=medium - - * New upstream version - - -- Andreas Tille <[email protected]> Sun, 18 Jun 2017 14:47:55 +0200 - freebayes (1.0.2-1) unstable; urgency=low * Initial packaging (Closes: #851306) diff --git a/debian/control b/debian/control index 99d8397..301577b 100644 --- a/debian/control +++ b/debian/control @@ -7,16 +7,12 @@ Priority: optional Build-Depends: debhelper (>= 9), cmake, pkg-config, - python, zlib1g-dev, libbamtools-dev, - libvcflib-dev (>= 1.0.0~rc1+dfsg1-4), + libvcflib-dev, libtabixpp-dev, - libseqlib-dev, bc, - samtools, - parallel, - libvcflib-tools + samtools Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/freebayes.git Vcs-Git: https://anonscm.debian.org/git/debian-med/freebayes.git @@ -26,7 +22,6 @@ Package: freebayes Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} -Recommends: parallel Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide diff --git a/debian/patches/use_debian_packaged_libjsoncpp.patch b/debian/patches/use_debian_packaged_libjsoncpp.patch deleted file mode 100644 index 5ded25a..0000000 --- a/debian/patches/use_debian_packaged_libjsoncpp.patch +++ /dev/null @@ -1,17 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 28 May 2014 21:23:38 +0200 -Description: Use Debian packaged libjsoncpp - ---- a/src/Makefile -+++ b/src/Makefile -@@ -12,8 +12,8 @@ C=gcc - CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g - #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 - --LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` --INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` -+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp` -+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` - - all: autoversion ../bin/freebayes ../bin/bamleftalign - diff --git a/debian/patches/use_debian_packaged_seqlib.patch b/debian/patches/use_debian_packaged_seqlib.patch deleted file mode 100644 index 9e7a35b..0000000 --- a/debian/patches/use_debian_packaged_seqlib.patch +++ /dev/null @@ -1,87 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 28 May 2014 21:23:38 +0200 -Description: Use Debian packaged htslib and seqlib - seqlib carries another copy of htslib - we replace both - ---- a/src/Makefile -+++ b/src/Makefile -@@ -12,10 +12,8 @@ C=gcc - CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g - #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 - --SEQLIB_ROOT=../SeqLib -- --LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` --INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib -+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` -+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` - - all: autoversion ../bin/freebayes ../bin/bamleftalign - -@@ -33,12 +31,6 @@ gprof: - - .PHONY: all static debug profiling gprof - --$(HTSLIB_ROOT)/libhts.a: -- cd $(HTSLIB_ROOT) && make -- --$(SEQLIB_ROOT)/src/libseqlib.a: -- cd $(SEQLIB_ROOT) && ./configure && make -- - OBJECTS=BedReader.o \ - CNV.o \ - fastlz.o \ -@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \ - Bias.o \ - Contamination.o \ - NonCall.o \ -- SegfaultHandler.o \ -- $(SEQLIB_ROOT)/src/libseqlib.a \ -- $(SEQLIB_ROOT)/bwa/libbwa.a \ -- $(SEQLIB_ROOT)/fermi-lite/libfml.a \ -- $(SEQLIB_ROOT)/htslib/libhts.a -+ SegfaultHandler.o - - HEADERS=multichoose.h version_git.h - -@@ -81,10 +69,10 @@ alleles ../bin/alleles: alleles.o $(OBJE - dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) - $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS) - --bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS) -+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS) - --bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS) -+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS) - $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS) - - -@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al - dummy.o: dummy.cpp AlleleParser.o Allele.o - $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp - --freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a -+freebayes.o: freebayes.cpp TryCatch.h - $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp - - fastlz.o: fastlz.c fastlz.h -@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle - Ewens.o: Ewens.cpp Ewens.h - $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp - --AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a -+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h - $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp - - Utility.o: Utility.cpp Utility.h Sum.h Product.h -@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli - bamfiltertech.o: bamfiltertech.cpp - $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp - --LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a -+LeftAlign.o: LeftAlign.h LeftAlign.cpp - $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp - - IndelAllele.o: IndelAllele.cpp IndelAllele.h diff --git a/debian/patches/vcffirstheader.patch b/debian/patches/vcffirstheader.patch deleted file mode 100644 index 070fcd0..0000000 --- a/debian/patches/vcffirstheader.patch +++ /dev/null @@ -1,29 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Fri, 10 Feb 2017 09:09:35 +0100 -Description: This script was not part of the vcflib release - tarball but is available in Git - https://github.com/vcflib/vcflib/blob/master/scripts/vcffirstheader - Since it is used in the test suite of freebayes 1.1 it is installed - here as quilt patch. Once vcflib might be release including the - scripts directory the patch can be dropped and replaced by an according - symlink inside rules or by setting PATH accordingly - ---- /dev/null -+++ b/vcflib/scripts/vcffirstheader -@@ -0,0 +1,16 @@ -+#!/usr/bin/env python -+ -+import sys -+ -+header=True -+for line in sys.stdin: -+ if line.startswith('##'): -+ if header: -+ print line.strip() -+ continue -+ elif line.startswith('#'): -+ if header: -+ print line.strip() -+ header=False -+ continue -+ print line.strip() diff --git a/debian/rules b/debian/rules index 666b949..8045fdf 100755 --- a/debian/rules +++ b/debian/rules @@ -9,9 +9,5 @@ override_dh_auto_install: override_dh_auto_test: mkdir -p $(CURDIR)/test/bash-tap/ for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done - ln -s $(CURDIR)/debian/test-simple-bash/lib test/test-simple-bash - chmod +x vcflib/scripts/vcffirstheader - # export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test - echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully" + export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully" rm -rf $(CURDIR)/test/bash-tap - rm test/test-simple-bash/lib diff --git a/debian/test-simple-bash/lib/test-simple.bash b/debian/test-simple-bash/lib/test-simple.bash deleted file mode 100644 index dab44e7..0000000 --- a/debian/test-simple-bash/lib/test-simple.bash +++ /dev/null @@ -1,110 +0,0 @@ -# test-simple.bash - Simple TAP test framework for Bash -# -# Copyright (c) 2013 Ingy döt Net - -TestSimple_VERSION='0.0.1' - -TestSimple.init() { - TestSimple_plan=0 - TestSimple_run=0 - TestSimple_failed=0 - TestSimple_usage='Usage: source test-simple.bash tests <number>' - - if [ $# -gt 0 ]; then - [[ $# -eq 2 ]] && [[ "$1" == 'tests' ]] || - TestSimple.die "$TestSimple_usage" - [[ "$2" =~ ^-?[0-9]+$ ]] || - TestSimple.die 'Plan must be a number' - [[ $2 -gt 0 ]] || - TestSimple.die 'Plan must greater then 0' - TestSimple_plan=$2 - printf "1..%d\n" $TestSimple_plan - fi - - trap TestSimple.END EXIT -} - -ok() { - local args=("$@") - local last=$((${#args[@]} - 1)) - local label='' - local ending_re='^]]?$' - let TestSimple_run=TestSimple_run+1 - ( - set +e - local rc= - if [[ $last -gt 0 ]] && [[ ! "${args[$last]}" =~ $ending_re ]]; then - label="${args[$last]}" - unset args[$last] - fi - if [[ ${#args[@]} -eq 1 ]] && [[ "${args[0]}" =~ ^[0-9]+$ ]]; then - rc=${args[0]} - elif [ ${args[0]} == '[[' ]; then - # XXX Currently need eval to support [[. Is there another way? - # Is [[ overkill? So many questons! - eval "${args[@]}" &> /dev/null - rc=$? - else - "${args[@]}" &> /dev/null - rc=$? - fi - if [ $rc -eq 0 ]; then - if [ -n "$label" ]; then - echo "ok $TestSimple_run - $label" - else - echo "ok $TestSimple_run" - fi - else - let TestSimple_failed=TestSimple_failed+1 - if [ -n "$label" ]; then - echo "not ok $TestSimple_run - $label" - TestSimple.failure "$label" - else - echo "not ok $TestSimple_run" - TestSimple.failure "$label" - fi - fi - return $rc - ) -} - -TestSimple_CALL_STACK_LEVEL=1 -TestSimple.failure() { - local c=( $(caller $TestSimple_CALL_STACK_LEVEL) ) - local file=${c[2]} - local line=${c[0]} - local label="$1" - label=${label:+"'$label'\n# at $file line $line."} - label=${label:-"at $file line $line."} - echo -e "# Failed test $label" >&2 -} - -TestSimple.END() { - for v in plan run failed; do eval local $v=\$TestSimple_$v; done - if [ $plan -eq 0 ]; then - if [ $run -gt 0 ]; then - echo "# Tests were run but no plan was declared." >&2 - fi - else - if [ $run -eq 0 ]; then - echo "# No tests run!" >&2 - elif [ $run -ne $plan ]; then - local msg="# Looks like you planned $plan tests but ran $run." - [ $plan -eq 1 ] && msg=${msg/tests/test} - echo "$msg" >&2 - fi - fi - local exit_code=0 - if [ $TestSimple_failed -gt 0 ]; then - exit_code=$TestSimple_failed - [ $exit_code -gt 254 ] && exit_code=254 - local msg="# Looks like you failed $failed tests of $run run." - [ $TestSimple_failed -eq 1 ] && msg=${msg/tests/test} - echo "$msg" >&2 - fi - exit $exit_code -} - -TestSimple.die() { echo "$@" >&2; trap EXIT; exit 255; } - -[[ "${BASH_SOURCE[0]}" != "${0}" ]] && TestSimple.init "$@" diff --git a/debian/test-simple-bash/test/basics.t b/debian/test-simple-bash/test/basics.t deleted file mode 100644 index 61949ea..0000000 --- a/debian/test-simple-bash/test/basics.t +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -PATH=lib:$PATH -source test-simple.bash tests 14 - -ok 0 '0 is true' -ok $((6 * 7 -42)) 'Math result is 0' -ok true 'true is ok' -ok $(false || true; echo $?) 'Expression expansion' - -ls &> /dev/null -ok $? '$? is success' -ls --qqq &> /dev/null -ok $((! $?)) 'Negate $? failure' - -fruit=apple - -ok [ $fruit = apple ] '[ … ] testing works' -ok [ "0" == "0" -a 1 -eq 1 ] '[ … -a … ] (AND) testing works' -ok [ ${fruit/a/A} = Apple ] 'Substitution expansion works' -ok [ "${fruit}s" = 'app''les' ] 'Quote removal works' -ok [[ $fruit = apple ]] '[[ … ]] works' -ok [[ $fruit == apple ]] '== works' -ok [[ $((6 * 7)) -eq 42 ]] '-eq works with math expression' -ok $(ls | grep lib &> /dev/null; echo $?) \ - 'Testing a grep command works' diff --git a/debian/test-simple-bash/test/doc.t b/debian/test-simple-bash/test/doc.t deleted file mode 100644 index 7d77db7..0000000 --- a/debian/test-simple-bash/test/doc.t +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -question() { echo yes; } - -PATH=lib:$PATH -source test-simple.bash tests 5 - -ok 0 '0 is true (other numbers are false)' - -answer=$(question "...?") -ok [ $answer == yes ] 'The answer is yes!' -ok [[ $answer =~ ^y ]] 'The answer begins with y' - -ok true 'true is ok' -ok '! false' '! false is true' diff --git a/debian/test-simple-bash/test/no-label.t b/debian/test-simple-bash/test/no-label.t deleted file mode 100644 index 9b58eb4..0000000 --- a/debian/test-simple-bash/test/no-label.t +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -PATH=lib:$PATH -source test-simple.bash tests 14 - -ok 0 -ok $((6 * 7 -42)) -ok true -ok $(false || true; echo $?) - -ls &> /dev/null -ok $? -ls --qqq &> /dev/null -ok $((! $?)) - -fruit=apple - -ok [ $fruit = apple ] -ok [ "0" == "0" -a 1 -eq 1 ] -ok [ ${fruit/a/A} = Apple ] -ok [ "${fruit}s" = 'app''les' ] -ok [[ $fruit = apple ]] -ok [[ $fruit == apple ]] -ok [[ $((6 * 7)) -eq 42 ]] -ok $(ls | grep lib &> /dev/null; echo $?) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
