[med-svn] [Git][med-team/rtax][master] 10 commits: fix lintian: file-contains-trailing-whitespace
肖盛文
gitlab at salsa.debian.org
Sat May 16 06:50:38 BST 2020
肖盛文 pushed to branch master at Debian Med / rtax
Commits:
f324dce5 by 肖盛文 at 2020-05-15T13:22:03+08:00
fix lintian: file-contains-trailing-whitespace
- - - - -
18d72704 by 肖盛文 at 2020-05-15T13:22:48+08:00
fix lintian: insecure-copyright-format-uri
- - - - -
f5d22e0d by 肖盛文 at 2020-05-15T13:24:40+08:00
Bump debhelper-compat (= 13)
Bump Standards-Version: 4.5.0
- - - - -
88d51cb7 by 肖盛文 at 2020-05-15T13:25:19+08:00
add Rules-Requires-Root: no
- - - - -
4124d7a7 by 肖盛文 at 2020-05-15T13:28:05+08:00
delete trailing-whitespace
- - - - -
3626c617 by 肖盛文 at 2020-05-15T13:30:47+08:00
New maintainer (Closes: #960138)
- - - - -
4d23101a by 肖盛文 at 2020-05-15T13:42:14+08:00
add fix.perl.path.patch
- - - - -
70e92bd8 by 肖盛文 at 2020-05-15T13:44:50+08:00
Update changelog for 0.984-7 release
- - - - -
7be1268b by 肖盛文 at 2020-05-15T13:51:23+08:00
d/watch: use @PACKAGE@ @ANY_VERSION@ @ARCHIVE_EXT@
- - - - -
e703b77a by 肖盛文 at 2020-05-15T13:52:43+08:00
Update changelog for 0.984-7
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/fix.perl.path.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,28 @@
+rtax (0.984-7) unstable; urgency=medium
+
+ [ Dylan Aïssi ]
+ * Fix Maintainer
+
+ [ Steffen Moeller ]
+ * d/u/metadata: yamllint
+
+ [ Steffen Möller ]
+ * Update metadata with ref to conda
+
+ [ 肖盛文 ]
+ * fix lintian: file-contains-trailing-whitespace
+ * fix lintian: insecure-copyright-format-uri
+ * New maintainer (Closes: #960138)
+ * add fix.perl.path.patch
+ * d/control:
+ - Bump debhelper-compat (= 13)
+ - Bump Standards-Version: 4.5.0
+ - add Rules-Requires-Root: no
+ * d/watch:
+ - use @PACKAGE@ @ANY_VERSION@ @ARCHIVE_EXT@
+
+ -- xiao sheng wen <atzlinux at sina.com> Fri, 15 May 2020 13:51:45 +0800
+
rtax (0.984-6) unstable; urgency=medium
* Team upload.
@@ -29,7 +54,7 @@ rtax (0.984-3) unstable; urgency=medium
* Team upload.
* Upstream author moved to github.com, updated all metadata URLs.
- * Move debian/upstream to debian/upstream/metadata (Thanks to
+ * Move debian/upstream to debian/upstream/metadata (Thanks to
James McCoy <jamessan at debian.org> ). Removes lintian warning.
-- Simon Kainz <simon at familiekainz.at> Thu, 27 Nov 2014 12:03:57 +0000
@@ -46,7 +71,7 @@ rtax (0.984-1) unstable; urgency=low
* Initial release. (Closes: #724280)
* Removed broken magic to find scripts-subdir,
because we know where rtax is installed (set_script_dir.path)
- * Change interpreter to bash to prevent syntax
+ * Change interpreter to bash to prevent syntax
error warnings (fix-bash-syntax-error.patch)
* Added minimal manpage.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,10 +1,11 @@
Source: rtax
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Simon Kainz <skainz at debian.org>
+Uploaders: xiao sheng wen <atzlinux at sina.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.5
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
+Rules-Requires-Root: no
Vcs-Browser: https://salsa.debian.org/med-team/rtax
Vcs-Git: https://salsa.debian.org/med-team/rtax.git
Homepage: https://github.com/davidsoergel/rtax/
@@ -14,7 +15,7 @@ Architecture: all
Depends: ${misc:Depends},
${perl:Depends}
Description: Classification of sequence reads of 16S ribosomal RNA gene
- Short-read technologies for microbial community profiling are increasingly
- popular, yet previous techniques for assigning taxonomy to paired-end reads
- perform poorly. RTAX provides rapid taxonomic assignments of paired-end
+ Short-read technologies for microbial community profiling are increasingly
+ popular, yet previous techniques for assigning taxonomy to paired-end reads
+ perform poorly. RTAX provides rapid taxonomic assignments of paired-end
reads using a consensus algorithm.
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: RTAX
Upstream-Contact: David A. W. Soergel <soergel at cs.umass.edu>
Source: https://github.com/davidsoergel/rtax
=====================================
debian/patches/fix.perl.path.patch
=====================================
@@ -0,0 +1,81 @@
+Description: update perl path
+ .
+Author: xiao sheng wen <atzlinux at sina.com>
+
+---
+
+Origin: xiao sheng wen <atzlinux at sina.com>
+Last-Update: 2020-05-15
+
+--- rtax-0.984.orig/scripts/classificationQualityFilter.pl
++++ rtax-0.984/scripts/classificationQualityFilter.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ my $countThreshold = $ARGV[0];
+ my $localMinProportionThreshold = $ARGV[1];
+--- rtax-0.984.orig/scripts/classificationQualityStripper.pl
++++ rtax-0.984/scripts/classificationQualityStripper.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ while (<STDIN>) {
+ my $line = $_;
+--- rtax-0.984.orig/scripts/fastaidx.pl
++++ rtax-0.984/scripts/fastaidx.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- rtax-0.984.orig/scripts/greengenesExtract.pl
++++ rtax-0.984/scripts/greengenesExtract.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- rtax-0.984.orig/scripts/joinDelimitedFasta.pl
++++ rtax-0.984/scripts/joinDelimitedFasta.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
+--- rtax-0.984.orig/scripts/parseUclustClusters.pl
++++ rtax-0.984/scripts/parseUclustClusters.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # read a uclust result file; for each query sequence, collect the prokMSAids of the hits.
+
+--- rtax-0.984.orig/scripts/rtaxSearch.pl
++++ rtax-0.984/scripts/rtaxSearch.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # RTAX: Rapid and accurate taxonomic classification of short paired-end
+ # sequence reads from the 16S ribosomal RNA gene.
+--- rtax-0.984.orig/scripts/rtaxVote.pl
++++ rtax-0.984/scripts/rtaxVote.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # read the prokMSAids of the hits, as produced by exactMatchIds.
+ # Then grab the taxonomy info for those prokMSAids and make some classification info from the set.
+--- rtax-0.984.orig/scripts/splitDelimitedFasta.pl
++++ rtax-0.984/scripts/splitDelimitedFasta.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ use strict;
+ use warnings;
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
fix-bash-syntax-error.patch
find_script_path.patch
+fix.perl.path.patch
=====================================
debian/rules
=====================================
@@ -1,5 +1,3 @@
#!/usr/bin/make -f
%:
dh $@
-
-
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-https://github.com/davidsoergel/rtax .*davidsoergel.com/rtax-(\d[.\d]+)\.tgz
+https://github.com/davidsoergel/@PACKAGE@ .*davidsoergel.com/@PACKAGE@@ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/rtax/-/compare/5fe6f704e5ccca010bf3641c6f6974acf5a6802e...e703b77a3b6c1f9d7b0997e4582e6103b6ca799b
--
View it on GitLab: https://salsa.debian.org/med-team/rtax/-/compare/5fe6f704e5ccca010bf3641c6f6974acf5a6802e...e703b77a3b6c1f9d7b0997e4582e6103b6ca799b
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