[med-svn] [Git][med-team/genometester][master] 10 commits: New upstream version 4.0+git20200511.91cecb5+dfsg

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / genometester


Commits:
cffef4cc by Steffen Moeller at 2020-05-17T20:06:48+02:00
New upstream version 4.0+git20200511.91cecb5+dfsg
- - - - -
016ace6e by Steffen Moeller at 2020-05-17T20:06:48+02:00
routine-update: New upstream version

- - - - -
58e80171 by Steffen Moeller at 2020-05-17T20:06:48+02:00
Update upstream source from tag 'upstream/4.0+git20200511.91cecb5+dfsg'

Update to upstream version '4.0+git20200511.91cecb5+dfsg'
with Debian dir 5efe3c9d5388655e1eed16c8c02f11d023cf1b54
- - - - -
c8568ad9 by Steffen Moeller at 2020-05-17T20:06:48+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
fd619d64 by Steffen Moeller at 2020-05-17T20:06:49+02:00
routine-update: debhelper-compat 12

- - - - -
eb3d6a87 by Steffen Moeller at 2020-05-17T20:06:51+02:00
routine-update: Add salsa-ci file

- - - - -
7cdc1e15 by Steffen Moeller at 2020-05-17T20:06:51+02:00
routine-update: Rules-Requires-Root: no

- - - - -
e1c46a6f by Steffen Moeller at 2020-05-17T20:06:54+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
e86fee6c by Steffen Moeller at 2020-05-17T20:07:11+02:00
routine-update: Ready to upload to unstable

- - - - -
830f259f by Steffen Moeller at 2020-05-17T20:10:56+02:00
Clean-up.

- - - - -


8 changed files:

- + debian/TODO
- debian/changelog
- − debian/compat
- debian/control
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
- src/database.c


Changes:

=====================================
debian/TODO
=====================================
@@ -0,0 +1 @@
+Add manpage: W: genometester: binary-without-manpage usr/bin/gdistribution


=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+genometester (4.0+git20200511.91cecb5+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 12 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse. (routine-update)
+  * Added d/TODO to indicate missing man page (also a lintian warning)
+  * Improved clean.
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 17 May 2020 20:06:55 +0200
+
 genometester (4.0+git20180508.a9c14a6+dfsg-1) unstable; urgency=medium
 
   * Remove binaries from upstream source


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,11 +4,12 @@ Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/genometester
 Vcs-Git: https://salsa.debian.org/med-team/genometester.git
 Homepage: https://github.com/bioinfo-ut/GenomeTester4
+Rules-Requires-Root: no
 
 Package: genometester
 Architecture: any


=====================================
debian/rules
=====================================
@@ -16,3 +16,7 @@ override_dh_auto_build:
 	dh_auto_build -- gmer_counter
 	dh_auto_build -- gmer_caller
 	dh_auto_build -- gdistribution
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f src/gdistribution src/gmer_caller src/gmer_counter


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/bioinfo-ut/GenomeTester4/issues
+Bug-Submit: https://github.com/bioinfo-ut/GenomeTester4/issues/new
 Reference:
  - Author: Lauris Kaplinski and Maarja Lepamets and Maido Remm
    Title: >
@@ -45,3 +47,5 @@ Registry:
    Entry: genometester
  - Name: conda:bioconda
    Entry: genometester4
+Repository: https://github.com/bioinfo-ut/GenomeTester4.git
+Repository-Browse: https://github.com/bioinfo-ut/GenomeTester4


=====================================
src/database.c
=====================================
@@ -380,14 +380,17 @@ read_database_from_binary (KMerDB *db, const unsigned char *cdata, unsigned long
   unsigned int version;
   unsigned int has_index = 0;
 
-  if (memcmp (cdata + cpos, DBKEY, 4)) return 0;
+  if (memcmp (cdata + cpos, DBKEY, 4)) {
+    fprintf (stderr, "read_database_from_binary: Invalid DB key\n");
+    return 0;
+  }
   cpos += 4;
   memcpy (&major, cdata + cpos, 2);
   cpos += 2;
   memcpy (&minor, cdata + cpos, 2);
   cpos += 2;
   version = (major << 16) | minor;
-  if (version < 1) return 0;
+  /* if (version < 1) return 0; */
   if (version >= 3) has_index = 1;
 
   memcpy (&db->wordsize, cdata + cpos, 4);



View it on GitLab: https://salsa.debian.org/med-team/genometester/-/compare/7e1b1f81bd8d3cf3d579421ac15833e5c208378f...830f259f40cad725e41caf8bc0208b8d96dc784b

-- 
View it on GitLab: https://salsa.debian.org/med-team/genometester/-/compare/7e1b1f81bd8d3cf3d579421ac15833e5c208378f...830f259f40cad725e41caf8bc0208b8d96dc784b
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