This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.1.0+dfsg-1 in repository transdecoder.
commit 9f60ceb17b22a3232e1cddbdf90ec8dfa8b66db4 Author: Michael R. Crusoe <[email protected]> Date: Tue May 17 03:01:49 2016 -0700 new upstream release --- debian/changelog | 7 ++++++ debian/patches/cd-hit-est-rename | 2 +- debian/patches/fix-test | 14 ++++++++++++ debian/patches/reproducible-build | 33 --------------------------- debian/patches/reproducible-sample_data.patch | 14 ++++++------ debian/patches/series | 2 +- debian/rules | 2 +- debian/transdecoder-doc.docs | 1 - debian/transdecoder-doc.lintian-overrides | 25 ++++++++++++++++---- 9 files changed, 51 insertions(+), 49 deletions(-) diff --git a/debian/changelog b/debian/changelog index 61f9a4a..168f57e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +transdecoder (2.1.0+dfsg-1) unstable; urgency=medium + + * New upstream release + * Drop 'reproducible-build' patch, incorprorated upstream + + -- Michael R. Crusoe <[email protected]> Wed, 18 May 2016 02:28:29 -0700 + transdecoder (2.0.1+dfsg-3) unstable; urgency=medium [ Eduard Sanou ] diff --git a/debian/patches/cd-hit-est-rename b/debian/patches/cd-hit-est-rename index e1a02e6..118ca55 100644 --- a/debian/patches/cd-hit-est-rename +++ b/debian/patches/cd-hit-est-rename @@ -4,7 +4,7 @@ Description: Fix path to Debian location of cd-hit-est --- transdecoder.orig/TransDecoder.Predict +++ transdecoder/TransDecoder.Predict -@@ -56,7 +56,7 @@ +@@ -58,7 +58,7 @@ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}"; diff --git a/debian/patches/fix-test b/debian/patches/fix-test new file mode 100644 index 0000000..e76572c --- /dev/null +++ b/debian/patches/fix-test @@ -0,0 +1,14 @@ +Author: Michael R. Crusoe <[email protected]> +Description: Fix tests +--- transdecoder.orig/Makefile ++++ transdecoder/Makefile +@@ -8,6 +8,7 @@ + cd ./sample_data && ./cleanme.pl + + test: +- cd ./sample_data/ && ./runMe.sh +- ++ cd sample_data/cufflinks_example && ./runMe.sh ++ cd sample_data/pasa_example && ./runMe.sh ++ cd sample_data/simple_transcriptome_target && ./runMe.sh + diff --git a/debian/patches/reproducible-build b/debian/patches/reproducible-build deleted file mode 100644 index f5af92c..0000000 --- a/debian/patches/reproducible-build +++ /dev/null @@ -1,33 +0,0 @@ -From b0525d572b8e8528ad19e919f6943d234d3281d1 Mon Sep 17 00:00:00 2001 -From: Charles Plessy <[email protected]> -Date: Mon, 28 Dec 2015 11:37:23 +0900 -Subject: [PATCH] Make output reproducible. - -Author: Chris Lamb <[email protected]> -Bug-Debian: #809187 -Forwarded: https://github.com/TransDecoder/TransDecoder/pull/10 ---- - util/cufflinks_gtf_to_bed.pl | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/util/cufflinks_gtf_to_bed.pl b/util/cufflinks_gtf_to_bed.pl -index 28547ba..8bbb4ed 100755 ---- a/util/cufflinks_gtf_to_bed.pl -+++ b/util/cufflinks_gtf_to_bed.pl -@@ -68,11 +68,11 @@ main: { - - my $genes_href = $genome_trans_to_coords{$scaff}; - -- foreach my $gene_id (keys %$genes_href) { -+ foreach my $gene_id (sort keys %$genes_href) { - - my $trans_href = $genes_href->{$gene_id}; - -- foreach my $trans_id (keys %$trans_href) { -+ foreach my $trans_id (sort keys %$trans_href) { - - my $coords_href = $trans_href->{$trans_id}; - --- -2.1.4 - diff --git a/debian/patches/reproducible-sample_data.patch b/debian/patches/reproducible-sample_data.patch index 773faec..4fc44ea 100644 --- a/debian/patches/reproducible-sample_data.patch +++ b/debian/patches/reproducible-sample_data.patch @@ -3,14 +3,14 @@ Description: Make the sample data reproducible to get reproducible results Author: Eduard Sanou <[email protected]> Forwarded: https://github.com/TransDecoder/TransDecoder/pull/20 ---- transdecoder-2.0.1+dfsg.orig/sample_data/runMe.sh -+++ transdecoder-2.0.1+dfsg/sample_data/runMe.sh -@@ -26,7 +26,7 @@ fi - ../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 +--- transdecoder.orig/sample_data/cufflinks_example/runMe.sh ++++ transdecoder/sample_data/cufflinks_example/runMe.sh +@@ -25,7 +25,7 @@ + ../../util/cufflinks_gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3 ## generate transcripts fasta file --../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta -+PERL_HASH_SEED=0 ../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta +-../../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta ++PERL_HASH_SEED=0 ../../util/cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta ## Extract the long ORFs - ../TransDecoder.LongOrfs -t transcripts.fasta + ../../TransDecoder.LongOrfs -t transcripts.fasta diff --git a/debian/patches/series b/debian/patches/series index 8488ccc..1d2ac85 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,4 @@ +fix-test cd-hit-est-rename fix-whatis -reproducible-build reproducible-sample_data.patch diff --git a/debian/rules b/debian/rules index a00cfcb..e9af788 100755 --- a/debian/rules +++ b/debian/rules @@ -8,7 +8,7 @@ VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//' dh $@ --parallel override_dh_auto_clean: - cd ./sample_data && ./cleanme.pl + cd ./sample_data && ./*/cleanme.pl override_dh_auto_build: diff --git a/debian/transdecoder-doc.docs b/debian/transdecoder-doc.docs index 600b156..0fb2340 100644 --- a/debian/transdecoder-doc.docs +++ b/debian/transdecoder-doc.docs @@ -1,3 +1,2 @@ README debian/tests/run-tests -Release.Notes diff --git a/debian/transdecoder-doc.lintian-overrides b/debian/transdecoder-doc.lintian-overrides index c0d0003..1c50223 100644 --- a/debian/transdecoder-doc.lintian-overrides +++ b/debian/transdecoder-doc.lintian-overrides @@ -1,7 +1,22 @@ # Verbose copies from upstream tarball -transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/blastp.results.outfmt6.gz -transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pfam.domtblout.gz -transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/test.genome.fasta.gz -transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/test.tophat.sam.gz -transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/transcripts.gtf.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/blastp.results.outfmt6.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/blastp.results.outfmt6.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/pfam.domtblout.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/test.genome.fasta.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/test.genome.fasta.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/test.tophat.sam.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/test.tophat.sam.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/cufflinks_example/transcripts.gtf.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/cufflinks_example/transcripts.gtf.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/genome.fasta.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/genome.fasta.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.fasta.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.fasta.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.gff3.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/pasa_example/pasa_assemblies.gff3.gz +transdecoder-doc: package-contains-timestamped-gzip usr/lib/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.gz +transdecoder-doc: duplicated-compressed-file usr/lib/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/transdecoder.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
