This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository bowtie2.
commit a0c840aa278516c1d4c9024c0aa1619ee6089ff4 Author: Andreas Tille <[email protected]> Date: Mon Jan 9 13:29:35 2017 +0100 try to get building including runtime testing but failed --- debian/changelog | 3 + debian/control | 3 +- debian/patches/series | 1 + ...st_requiring_non-free_libmath-random-perl.patch | 193 +++++++++++++++++++++ 4 files changed, 199 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index a489af1..263b07e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,9 @@ bowtie2 (2.3.0-1) UNRELEASED; urgency=medium * Code available on Github * debhelper 10 * Remove Carlos Borroto from Uploaders + * Remove code from test suite that is requiring non-free package + libmath-random-perl + * New Build-Depends to run build time test: liblocal-lib-perl -- Andreas Tille <[email protected]> Mon, 09 Jan 2017 12:43:48 +0100 diff --git a/debian/control b/debian/control index 23b9667..bb8c43f 100644 --- a/debian/control +++ b/debian/control @@ -8,7 +8,8 @@ Priority: optional Build-Depends: debhelper (>= 10), help2man, libtbb-dev, - python + python, + liblocal-lib-perl Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bowtie2.git Vcs-Git: https://anonscm.debian.org/git/debian-med/bowtie2.git diff --git a/debian/patches/series b/debian/patches/series index 518af05..aacdb8b 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ hardening.patch reproducible.patch +skip_test_requiring_non-free_libmath-random-perl.patch diff --git a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch new file mode 100644 index 0000000..1500440 --- /dev/null +++ b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch @@ -0,0 +1,193 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Mon, 09 Jan 2017 11:13:13 +0100 +Description: Math::Random is in package libmath-random-perl which is + unfortunately in non-free thus we can not use it for testing while building + this package. Thus the occurences of references and the surrounding code + is removed here. + +--- a/example/reads/simulate.pl ++++ b/example/reads/simulate.pl +@@ -33,7 +33,6 @@ + use strict; + use warnings; + use Carp; +-use Math::Random qw(random_normal random_exponential); + use Getopt::Long; + use List::Util qw(max min); + +@@ -105,7 +104,6 @@ $rdlen_min = $rdlen_min || 40; # min + $frag_av = $frag_av || 250; # mean fragment len + $frag_sd = $frag_sd || 45; # s.d. when drawing frag len from normal dist + my @fraglens = (); # fragment lengths (for paired) +-my @readlens = (); # read/end lengths + + if($long) { + $nreads = 6000; +@@ -134,77 +132,15 @@ for(0..length($rf)-1) { + } + + print STDERR "Adding microindels...\n"; +-my $microgap = 0; +-{ +- my $newrf = ""; +- my $nins = int(length($rf) * 0.0005 + 0.5); +- my $ndel = int(length($rf) * 0.0005 + 0.5); +- $microgap = $nins + $ndel; +- my %indel = (); +- for(1..$nins) { +- my $off = int(rand(length($rf))); +- $indel{$off}{ty} = "ins"; +- $indel{$off}{len} = int(random_exponential(1, 3))+1; +- } +- for(1..$ndel) { +- my $off = int(rand(length($rf))); +- $indel{$off}{ty} = "del"; +- $indel{$off}{len} = int(random_exponential(1, 3))+1; +- } +- my $lasti = 0; +- for my $rfi (sort {$a <=> $b} keys %indel) { +- if($rfi > $lasti) { +- $newrf .= substr($rf, $lasti, $rfi - $lasti); +- $lasti = $rfi; +- } +- if($indel{$rfi}{ty} eq "ins") { +- $newrf .= rand_dna($indel{$rfi}{len}); +- } else { +- $lasti += $indel{$rfi}{len}; +- } +- } +- if($lasti < length($rf)-1) { +- $newrf .= substr($rf, $lasti, length($rf) - $lasti - 1); +- } +- $rf = $newrf; +-} + + print STDERR "Adding larger rearrangements...\n"; +-my $nrearr = int(random_exponential(1, 3)+1); +-for(0..$nrearr) { +- my $break = int(rand(length($rf))); +- my $before = substr($rf, 0, $break); +- my $after = substr($rf, $break); +- $after = revcomp($after) if int(rand()) == 0; +- $rf = $after.$before; +-} + + print STDERR "Added $nsnp SNPs\n"; +-print STDERR "Added $microgap Microindels\n"; +-print STDERR "Added $nrearr Rearrangements\n"; + + # + # Simulate reads + # + +-print STDERR "Picking read and fragment lengths...\n"; +-# Pick random read lengths +-if(defined($rdlen_exact)) { +- @readlens = ($rdlen_exact) x ($nreads * ($paired ? 2 : 1)); +-} else { +- @readlens = random_exponential($nreads * ($paired ? 2 : 1), $rdlen_av); +- @readlens = map int, @readlens; +- @readlens = map { int($_ + $rdlen_min) } @readlens; +-} +-if($paired) { +- # Pick random fragment and read lengths +- @fraglens = random_normal($nreads, $frag_av, $frag_sd); +- @fraglens = map int, @fraglens; +- for(my $i = 0; $i < scalar(@readlens); $i += 2) { +- $fraglens[$i/2] = max($fraglens[$i/2], $readlens[$i] + $readlens[$i+1]); +- } +-} +- + sub rand_quals($) { + my $ret = ""; + my $upper = (rand() < 0.2 ? 11 : 40); +@@ -259,61 +195,10 @@ if($paired) { + } + # Possibly reverse complement + $fstr = revcomp($fstr) if (int(rand(2)) == 0); +- # Get reads 1 and 2 +- my $rdlen1 = min($readlens[2*$i], $flen); +- my $rdlen2 = min($readlens[2*$i+1], $flen); +- my $rd1 = substr($fstr, 0, $rdlen1); +- my $rd2 = substr($fstr, length($fstr)-$rdlen2); +- length($rd2) == $rdlen2 || die "Got ".length($rd2)." expected $rdlen2"; +- # Reverse complement 2 to simulate --fr orientation +- $rd2 = revcomp($rd2); +- # Generate random quality values +- my $qu1 = rand_quals($rdlen1); +- $rd1 = add_seq_errs($rd1, $qu1); +- length($rd1) == length($qu1) || die; +- my $qu2 = rand_quals($rdlen2); +- $rd2 = add_seq_errs($rd2, $qu2); +- length($rd2) == length($qu2) || die; +- # Print +- print RD1 "\@r".($i+1)."\n$rd1\n+\n$qu1\n"; +- print RD2 "\@r".($i+1)."\n$rd2\n+\n$qu2\n"; + } + close(RD1); + close(RD2); + print STDERR "Made pairs: reads_1.fq/reads_2.fq\n"; +-} else { +- open(RD1, ">${prefix}.fq") || die; +- for(my $i = 0; $i < scalar(@readlens); $i++) { +- # Extract fragment +- my $rdlen = $readlens[$i]; +- my $off = int(rand($rflen - ($rdlen-1))); +- my $rd = substr($rf, $off, $rdlen); +- # Check if it has too many Ns +- my %ccnt = (); +- for my $j (1..$rdlen) { +- my $c = uc substr($rd, $j, 1); +- $ccnt{tot}++; +- $ccnt{non_acgt}++ if ($c ne "A" && $c ne "C" && $c ne "G" && $c ne "T"); +- $ccnt{$c}++; +- } +- # Skip if it has >10% Ns +- if(1.0 * $ccnt{non_acgt} / $ccnt{tot} > 0.10) { +- $i--; +- next; +- } +- length($rd) == $rdlen || die; +- # Possibly reverse complement +- $rd = revcomp($rd) if int(rand(2)) == 0; +- # Generate random quality values +- my $qu = rand_quals($rdlen); +- length($rd) == length($qu) || die "length(seq) = ".length($rd).", length(qual) = ".length($qu); +- $rd = add_seq_errs($rd, $qu); +- length($rd) == length($qu) || die "length(seq) = ".length($rd).", length(qual) = ".length($qu); +- # Print +- print RD1 "\@r".($i+1)."\n$rd\n+\n$qu\n"; +- } +- close(RD1); +- print STDERR "Made unpaired reads: $prefix.fq\n"; + } + + print STDERR "DONE\n"; +--- a/Makefile ++++ b/Makefile +@@ -483,13 +483,13 @@ install: all + cp -f $$file $(DESTDIR)$(bindir) ; \ + done + +-.PHONY: simple-test +-simple-test: all perl-deps ++.PHONY: simple-test perl-deps ++simple-test: all + eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ + sh ./scripts/test/simple_tests.sh + +-.PHONY: random-test +-random-test: all perl-deps ++.PHONY: random-test perl-deps ++random-test: all + eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ + sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2) + +@@ -500,7 +500,6 @@ perl-deps: + mkdir .perllib.tmp ; \ + $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \ + eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ +- cpanm Math::Random Clone Test::Deep Sys::Info ; \ + fi + + .PHONY: test -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bowtie2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
