[med-svn] [Git][med-team/acedb][master] 3 commits: Extend autopkgtest with acediff and acediffsorted checks

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Sep 22 15:08:02 BST 2026 


Andreas Tille pushed to branch master at Debian Med / acedb


Commits:
b125a52b by Andreas Tille at 2026-09-22T15:51:51+02:00
Extend autopkgtest with acediff and acediffsorted checks

- - - - -
24246386 by Andreas Tille at 2026-09-22T16:03:36+02:00
Fix DEP3 fields

- - - - -
483f0f46 by Andreas Tille at 2026-09-22T16:05:43+02:00
Upload to unstable

- - - - -


19 changed files:

- debian/changelog
- debian/patches/acedb-parser-fixes.patch
- debian/patches/acedb-signal-fix.patch
- debian/patches/belvu_help.patch
- debian/patches/blxview_gtk_namespace_conflict.patch
- debian/patches/dotter_help.patch
- debian/patches/efetch_help.patch
- debian/patches/fix_hardening_errors.patch
- debian/patches/gcc-14.patch
- debian/patches/glibc2.32.patch
- debian/patches/glibc2.38.patch
- debian/patches/hardening.patch
- debian/patches/just_build_efetch.patch
- debian/patches/libfl.patch
- debian/patches/mayhem.patch
- debian/patches/no-curses.patch
- debian/patches/no_dotter_and_belvu.patch
- debian/patches/spelling.patch
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-acedb (4.9.39+dfsg.02-10) UNRELEASED; urgency=medium
+acedb (4.9.39+dfsg.02-10) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Fix gcc-14 build issues
@@ -11,7 +11,7 @@ acedb (4.9.39+dfsg.02-10) UNRELEASED; urgency=medium
      - Add missing standard headers to efetch.c and dbidx.c
      - Include acelib.h in metadata.c and dna.h/peptide.h in dump.c
      - Fix old-style function pointer declarations that break gcc-15
-    Closes: #1066334
+    Closes: #1066334, #1147991 
   * Build-Depends: libtirpc-dev
   * Replace pkg-config with pkgconf in Build-Depends
   * Install acediff and acediffsorted (ACE format diff tools) with man pages
@@ -25,11 +25,12 @@ acedb (4.9.39+dfsg.02-10) UNRELEASED; urgency=medium
   * d/watch:
      - Version=5
      - Fix
+  * Fix DEP3 fields
 
   [ Jeremy Sowden ]
   * Fixes for missing declarations
 
- -- Andreas Tille <tille at debian.org>  Mon, 21 Sep 2026 19:24:51 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 22 Sep 2026 16:04:05 +0200
 
 acedb (4.9.39+dfsg.02-9) unstable; urgency=medium
 


=====================================
debian/patches/acedb-parser-fixes.patch
=====================================
@@ -4,6 +4,7 @@ Description: Fix missing declarations
              `yylex`   - this needs to be added to the yacc source
              `yyerror` - this is present but hidden by a CPP conditional
              `yywrap`  - this is not needed (grep for "YY_SKIP_YYWRAP") and can be disabled
+Forwarded: No (orphaned upstream)
 
 --- a/waql/aql_.h
 +++ b/waql/aql_.h


=====================================
debian/patches/acedb-signal-fix.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Jeremy Sowden <azazel at debian.org>
 Last-Update: 2024-04-13
 Description: Add undeclared identifier
+Forwarded: No (orphaned upstream)
 
 --- a/w4/sigsubs.c
 +++ b/w4/sigsubs.c


=====================================
debian/patches/belvu_help.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Steffen Moeller <moeller at debian.org>
 Last-Update: 2010-07-11
 Description: Add -h argument for help and -v for version info
+Forwarded: No (orphaned upstream)
 
 --- a/w9/belvu.c
 +++ b/w9/belvu.c


=====================================
debian/patches/blxview_gtk_namespace_conflict.patch
=====================================
@@ -1,4 +1,7 @@
 Description: Adapt to current version of gtk
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2016-12-03
+Forwarded: No (orphaned upstream)
 
 --- a/w9/blxview.c
 +++ b/w9/blxview.c


=====================================
debian/patches/dotter_help.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Steffen Moeller <moeller at debian.org>
 Last-Update: 2010-07-11
 Description: Add -h argument for help
+Forwarded: No (orphaned upstream)
 
 --- a/w9/dotterMain.c
 +++ b/w9/dotterMain.c


=====================================
debian/patches/efetch_help.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Steffen Moeller <moeller at debian.org>
 Last-Update: 2010-07-11
 Description: Add -h argument for help and -v for version info
+Forwarded: No (orphaned upstream)
 
 --- a/w9/efetch.c
 +++ b/w9/efetch.c


=====================================
debian/patches/fix_hardening_errors.patch
=====================================
@@ -2,6 +2,7 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: 2015-12-10
 Description: Fix code errors preventing compilation with
  hardening switched on
+Forwarded: No (orphaned upstream)
 
 --- a/wace/homonym.c
 +++ b/wace/homonym.c


=====================================
debian/patches/gcc-14.patch
=====================================
@@ -1,6 +1,8 @@
-Desription:
-            - Definition of AceType is broken since it redefines _Int with different meaning than in whooks/systags.h
-              -> its not used anyway so remove all instances
+Desription: Definition of AceType is broken since it redefines _Int with different meaning than in whooks/systags.h
+          -> its not used anyway so remove all instances
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-12-14
+Forwarded: No (orphaned upstream)
 
 --- a/w1/acein.c
 +++ b/w1/acein.c


=====================================
debian/patches/glibc2.32.patch
=====================================
@@ -4,7 +4,7 @@ Description: use strsignal for Debian builds
  available in Debian.
 Author: Étienne Mollier <emollier at debian.org>
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997105
-Forwarded: no
+Forwarded: No (orphaned upstream)
 Last-Update: 2021-10-24
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/


=====================================
debian/patches/glibc2.38.patch
=====================================
@@ -6,7 +6,7 @@ Description: Fix build against glibc 2.38
 Author: Olivier Gayot <olivier.gayot at canonical.com>
 Bug: https://bugs.debian.org/1056591
 Bug-Ubuntu: https://launchpad.net/bugs/2044385
-Forwarded: no
+Forwarded: No (orphaned upstream)
 Last-Update: 2023-11-23
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/


=====================================
debian/patches/hardening.patch
=====================================
@@ -2,6 +2,8 @@ Author: Andreas Tille <tille at debian.org>
 Description: Propagate hardening options
 Reviewed-By: Étienne Mollier <emollier at debian.org>
 Last-Update: 2021-10-25
+Forwarded: No (orphaned upstream)
+
 --- acedb.orig/wmake/LINUX_64_DEF
 +++ acedb/wmake/LINUX_64_DEF
 @@ -23,12 +23,12 @@


=====================================
debian/patches/just_build_efetch.patch
=====================================
@@ -2,6 +2,7 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: 2023-08-15
 Bug-Debian: https://bugs.debian.org/967243
 Description: Build only efetch which does not depend on GTK+2 which will be removed from Debian
+Forwarded: No (orphaned upstream)
 
 --- a/wmake/makefile
 +++ b/wmake/makefile


=====================================
debian/patches/libfl.patch
=====================================
@@ -3,6 +3,7 @@ Description: With shared libfl needless linking causes FTBFS
 Author: Adrian Bunk <bunk at debian.org>
 Last-Update: 2018-02-26
 Bug-Debian: https://bugs.debian.org/891529
+Forwarded: No (orphaned upstream)
 
 --- acedb-4.9.39+dfsg.02.orig/wmake/truemake
 +++ acedb-4.9.39+dfsg.02/wmake/truemake


=====================================
debian/patches/mayhem.patch
=====================================
@@ -3,6 +3,7 @@ Last-Update: 2015-12-13
 Bug-Debian: https://bugs.debian.org/715832
             https://bugs.debian.org/715860
 Description: Fix crashes reported by Mayhem
+Forwarded: No (orphaned upstream)
 
 --- a/w9/dotterMain.c
 +++ b/w9/dotterMain.c


=====================================
debian/patches/no-curses.patch
=====================================
@@ -2,6 +2,7 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: 2011-10-21
 Bug-Debian: http://bugs.debian.org/646133
 Description: Do not build against ncurses
+Forwarded: No (orphaned upstream)
 
 --- a/wmake/LINUX_64_DEF
 +++ b/wmake/LINUX_64_DEF


=====================================
debian/patches/no_dotter_and_belvu.patch
=====================================
@@ -5,6 +5,7 @@ Description: Package acedb-other-dotter and acedb-other-belvu are now
  So do not even build these binaries
 Author: Andreas Tille <tille at debian.org>
 Last-Update: 2017-12-19
+Forwarded: No (orphaned upstream)
 
 --- acedb.orig/wmake/makefile
 +++ acedb/wmake/makefile


=====================================
debian/patches/spelling.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: 2015-12-13
 Description: Silence lintians spelling nitpicking
+Forwarded: No (orphaned upstream)
 
 --- a/w1/helpsubs.c
 +++ b/w1/helpsubs.c


=====================================
debian/tests/run-unit-test
=====================================
@@ -90,3 +90,41 @@ check_fails efetch -D "$D" NOSUCH
 check_contains "EFETCH - retrieve entries from sequence databases" efetch -h
 
 echo "All efetch autopkgtests passed."
+
+# acediff / acediffsorted emit the ACE commands needed to transform one
+# ACE-format text file into another (the acedb equivalent of diff for ACE
+# data).  acediff sorts the input internally, acediffsorted expects the
+# input files to be pre-sorted.
+
+cat > old.ace <<'EOF'
+Object : "Gene_A"
+  Locus "A1";
+  Chromosome "I";
+  Notes "original";
+EOF
+
+cat > new.ace <<'EOF'
+Object : "Gene_A"
+  Locus "A1";
+  Chromosome "I";
+  Notes "updated";
+  Evidence "curated";
+EOF
+
+# acediff must emit the ACE commands that turn old.ace into new.ace.
+check_contains 'Object "Gene_A"' acediff old.ace new.ace
+check_contains 'Evidence "curated";' acediff old.ace new.ace
+check_contains 'Notes "updated";' acediff old.ace new.ace
+check_contains '-D Notes "original";' acediff old.ace new.ace
+
+# acediffsorted must emit the same commands.
+check_contains 'Object "Gene_A"' acediffsorted old.ace new.ace
+check_contains 'Evidence "curated";' acediffsorted old.ace new.ace
+check_contains 'Notes "updated";' acediffsorted old.ace new.ace
+check_contains '-D Notes "original";' acediffsorted old.ace new.ace
+
+# Identical files yield an empty diff, just the header/footer comments.
+check_contains '// end of file' acediff old.ace old.ace
+check_contains '// end of file' acediffsorted old.ace old.ace
+
+echo "All acediff/acediffsorted autopkgtests passed."



View it on GitLab: https://salsa.debian.org/med-team/acedb/-/compare/79b09c0f065b3f25edb46b392b3576ad5f4d56c0...483f0f46d1a1393af1b068e75c7842f5a89ed0bd

-- 
View it on GitLab: https://salsa.debian.org/med-team/acedb/-/compare/79b09c0f065b3f25edb46b392b3576ad5f4d56c0...483f0f46d1a1393af1b068e75c7842f5a89ed0bd
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