Lintian Fixes - biojava-live

Ready changes

Merge these changes:

git pull https://janitor.debian.net/git/biojava-live lintian-fixes

Summary

Diff

=== modified file 'debian/changelog'
--- a/debian/changelog	2018-11-12 15:33:43 +0000
+++ b/debian/changelog	2020-04-15 17:24:37 +0000
@@ -1,3 +1,11 @@
+biojava-live (1:1.7.1-9) UNRELEASED; urgency=medium
+
+  * Bump debhelper from old 11 to 12.
+  * Set debhelper-compat version in Build-Depends.
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Wed, 15 Apr 2020 17:23:16 +0000
+
 biojava-live (1:1.7.1-8) unstable; urgency=medium
 
   * Point Vcs fields to salsa.debian.org

=== removed file 'debian/compat'
--- a/debian/compat	2018-01-23 13:18:39 +0000
+++ b/debian/compat	1970-01-01 00:00:00 +0000
@@ -1,1 +0,0 @@
-11

=== modified file 'debian/control'
--- a/debian/control	2018-11-01 06:10:52 +0000
+++ b/debian/control	2020-04-15 17:24:00 +0000
@@ -5,7 +5,7 @@
            Olivier Sallou <osallou@debian.org>
 Section: java
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                ant
 Build-Depends-Indep: libcommons-dbcp-java,
                      libhsqldb-java,

=== modified file 'debian/upstream/metadata'
--- a/debian/upstream/metadata	2019-09-15 10:47:28 +0000
+++ b/debian/upstream/metadata	2020-04-15 17:24:37 +0000
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/biojava/biojava-legacy/issues
+Bug-Submit: https://github.com/biojava/biojava-legacy/issues/new
 Reference:
  - Author: >
     R. C. G. Holland and T. Down and M. Pocock and A. Prlićand D. Huen and

Debdiff

[The following lists of changes regard files as different if they have different names, permissions or owners.]

Files in second set of .debs but not in first

-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/CircLocTest/TestFrame.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/biosql/SequenceTest.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/blastxml/input.xml
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dist/TestOrderNDistribution.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/Dice.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/PairwiseAlignment.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/SearchProfile.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/ViterbiAlign.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/fake.fasta
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/fakepromoter.xml
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/Blast2HTML.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/BlastLike2XML.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ACTN_HUMAN.uniprot
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AF438419.embl
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AL121903.embl
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AL121903.genbank
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ChrI.prom.fasta
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/GCG/blast.report
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/NP_001307.gp
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/clustal/keratin.aln
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fake.fasta
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fakepromoter.xml
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.db
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.m10
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/hmmer/plus_tot.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/Massive.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastp.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/shortBlastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/unsuppVersionBlastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/biosapiens.obo
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/evidence_code.obo
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/so.obo
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/out.gff
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/12E8.pdb
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/hgh_ori.pdb
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/hmga_1.pdb
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/tnf.pdb
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/test.hmm
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.dna
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.gff
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastp.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastp.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_tblastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastn.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastx.out
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/game/AE002734.game
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/AL121903.embl
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFCompare.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFFilter.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFMask.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/varC4-2.gff
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/nativeapps/BlastLike2XML.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/AlignProteins.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/ReverseComplement.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/SmithWatermanExample.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/prot/TestDigestIO.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.embl
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.genbank
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/BeadDemo.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/CircularEmblViewer.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer2.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/FastBeadDemo.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/ssbind/ProcessBlastReport.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/PatternDemo.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/TestAmbiguity.java
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/WindowCount.java

Files in first set of .debs but not in second

-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/CircLocTest/TestFrame.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/biosql/SequenceTest.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/blastxml/input.xml.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dist/TestOrderNDistribution.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/Dice.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/PairwiseAlignment.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/SearchProfile.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/ViterbiAlign.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/fake.fasta.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/dp/fakepromoter.xml.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/Blast2HTML.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/eventbasedparsing/BlastLike2XML.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ACTN_HUMAN.uniprot.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AF438419.embl.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AL121903.embl.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/AL121903.genbank.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ChrI.prom.fasta.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/GCG/blast.report.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/NP_001307.gp.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/clustal/keratin.aln.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fake.fasta.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fakepromoter.xml.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.db.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/fp_demo.m10.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/hmmer/plus_tot.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/Massive.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastp.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/blastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/shortBlastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/tblastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ncbiblast/unsuppVersionBlastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/biosapiens.obo.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/evidence_code.obo.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/ontology/so.obo.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/out.gff.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/12E8.pdb.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/hgh_ori.pdb.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/hmga_1.pdb.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/pdb/tnf.pdb.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/test.hmm.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.dna.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/varC4-2.gff.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastp.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/blastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastp.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_blastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/sh_tblastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastn.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/files/wublast/tblastx.out.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/game/AE002734.game.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/AL121903.embl.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFCompare.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFFilter.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/GFFMask.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/gff/varC4-2.gff.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/nativeapps/BlastLike2XML.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/AlignProteins.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/ReverseComplement.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/performance/SmithWatermanExample.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/prot/TestDigestIO.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.embl.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seq/AL121903.genbank.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/BeadDemo.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/CircularEmblViewer.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/EmblViewer2.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/seqviewer/FastBeadDemo.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/ssbind/ProcessBlastReport.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/PatternDemo.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/TestAmbiguity.java.gz
-rw-r--r--  root/root   /usr/share/doc/libbiojava-java-demos/examples/symbol/WindowCount.java.gz

No differences were encountered between the control files of package libbiojava-java

No differences were encountered between the control files of package libbiojava-java-demos

No differences were encountered between the control files of package libbiojava-java-doc

No differences were encountered between the control files of package libbiojava1.7-java

Run locally

Try this locally (using the lintian-brush package):

debcheckout biojava-live
cd biojava-live
lintian-brush

More details

Full run details