[med-svn] [Git][med-team/kallisto][master] 4 commits: Fix test

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
ae8cabfc by Andreas Tille at 2026-02-22T16:50:32+01:00
Fix test

- - - - -
5c86a3c1 by Andreas Tille at 2026-02-22T16:53:50+01:00
Standards-Version: 4.7.3

- - - - -
29816e22 by Andreas Tille at 2026-02-22T17:01:21+01:00
Do not build in parallel

- - - - -
2aac6e75 by Andreas Tille at 2026-02-22T17:04:32+01:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/more_verbose_output_in_testing.patch → debian/patches/fix_testing.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,8 @@
-kallisto (0.51.1+dfsg-1) UNRELEASED; urgency=medium
+kallisto (0.51.1+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
-  * Standards-Version: 4.7.2 (routine-update)
+  * Standards-Version: 4.7.3
   * Add support for loongarch64 in d/control
     Closes: #1057131
   * Remove patch Check_busOptions.seq_length_before_accessing.patch that is
@@ -16,6 +16,7 @@ kallisto (0.51.1+dfsg-1) UNRELEASED; urgency=medium
   * Try hard to get bifrost build with recent gcc
   * bifrost: Add default values for MAX_KMER_SIZE and MAX_GMER_SIZE
   * Fix typo in bifrost
+  * Do not build in parallel
 
   [ Michael R. Crusoe ]
   * d/control: simplify architecture specifications by using provisions
@@ -25,7 +26,7 @@ kallisto (0.51.1+dfsg-1) UNRELEASED; urgency=medium
   * Upstream has forked bifrost, use their copy instead.
   * d/rules: need cmake option needed: USE_BAM.
 
- -- Andreas Tille <tille at debian.org>  Sun, 13 Oct 2024 17:09:54 +0200
+ -- Andreas Tille <tille at debian.org>  Sun, 22 Feb 2026 17:01:24 +0100
 
 kallisto (0.48.0+dfsg-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,10 +1,9 @@
 Source: kallisto
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders:
  Andreas Tille <tille at debian.org>,
 Section: science
-Priority: optional
 Build-Depends:
  debhelper-compat (= 13),
  architecture-is-64-bit,


=====================================
debian/patches/more_verbose_output_in_testing.patch → debian/patches/fix_testing.patch
=====================================
@@ -1,15 +1,15 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: 2025-10-21
-Description: FIXME: Just for debugging test
+Description: Directly kall kallisto in test
 
 --- a/func_tests/runtests.sh
 +++ b/func_tests/runtests.sh
-@@ -231,6 +231,8 @@ cmdexec "$kallisto index --aa -i $test_d
+@@ -231,7 +231,7 @@ cmdexec "$kallisto index --aa -i $test_d
  
  # Test k=7
  
-+set -x
+-cmdexec "$kallisto index -i $test_dir/basic7.idx -k 7 $test_dir/simple.fasta"
 +$kallisto index -i $test_dir/basic7.idx -k 7 $test_dir/simple.fasta
- cmdexec "$kallisto index -i $test_dir/basic7.idx -k 7 $test_dir/simple.fasta"
  
  # Test k=9
+ 


=====================================
debian/patches/series
=====================================
@@ -7,4 +7,4 @@ fix_bifrost_defines.patch
 bifrost_typo.patch
 std_gnu17.patch
 cmake4.patch
-more_verbose_output_in_testing.patch
+fix_testing.patch


=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
@@ -9,7 +9,7 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
                      -DBUILD_FUNCTESTING=1 -DUSE_BAM=1
 
 %:
-	dh $@
+	dh $@ --no-parallel
 
 override_dh_auto_clean:
 	dh_auto_clean



View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/a756bc394a0ba520c40a27dc44d892afe5aaf118...2aac6e756307a19ae4c15f69d28d68a08c846dec

-- 
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/a756bc394a0ba520c40a27dc44d892afe5aaf118...2aac6e756307a19ae4c15f69d28d68a08c846dec
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