Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration

Relevant part (hopefully):
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/acedb_4.9.39+dfsg.02-9_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

Hi,

while I was able to fix the origininal cause of the failure I'm now blocked by
some issue that cython seems to miss adding some
   #include <lex.h>
but I have no idea how to accomplish this.  The Salsa CI build log[1] says:

...
y.tab.c: In function 'yyparse':
y.tab.c:1409:16: error: implicit declaration of function 'yylex' [-Werror=implicit-function-declaration]
y.tab.c:2185:7: error: implicit declaration of function 'yyerror'; did you mean 'YYerror'? [-Werror=implicit-function-declaration]
In file included from aqlparse.y:335:
aqlparse.l: In function 'yylex':
...

Any help would be welcome
    Andreas.


[1] https://salsa.debian.org/med-team/acedb/-/jobs/5580840

You are 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

Patch attached.

You can find more info about all three in the flex and bison manuals.

J.

I attach a fix for the next error:

  gcc -g -Wall  -DACEDB4 `../w3rdparty/include-config glib-2.0 gtk+-2.0`  -I.. -I../wh -I../wstaden -DACEDB_GTK -DLINUX -c -o sigsubs.o sigsubs.c
  sigsubs.c: In function 'getSignalText':
  sigsubs.c:486:30: error: '_sys_siglist' undeclared (first use in this function)
    486 |   char **signal_textlist = &(_sys_siglist[0]) ;
        |                              ^~~~~~~~~~~~
  sigsubs.c:486:30: note: each undeclared identifier is reported only once for each function it appears in

The one after this looks like a GTK problem, and that's the point at
which I bow out.

J.

Hi Jeremy,

Am Sat, Apr 13, 2024 at 10:46:17PM +0100 schrieb Jeremy Sowden:

Thanks a lot for your help so far.  Your patches are pushed to Git.

Kind regards
   Andreas.

H again,

Am Sun, Apr 14, 2024 at 07:17:41AM +0200 schrieb Andreas Tille:
not were connected to GTK) but I'm now stumbling upon:

...
In file included from disknew.c:85:
../whooks/systags.h:57:15: error: expected identifier before numeric constant
   57 | #define _Int  24
      |               ^~
../wh/acetypes.h:36:16: note: in expansion of macro '_Int'
   36 | typedef enum { _Int, _Text, _Float, _DateType, _Key, _Tag } AceType;
      |                ^~~~
...


which is caused by whooks/systags.h[2]

...
#define _Int  24
#define _Unsigned  25
#define _Long  26               /* not supported */
#define _Long_Unsigned  27      /* not supported */
#define _Float  28
...

Is there any trick I could use here instead of replacing these
definitions by something else like _Int_acedb or so globally to get this
build by modern compilers?

Kind regards
    Andreas.

[1] https://salsa.debian.org/med-team/acedb/-/jobs/5586407#L1893
[2] https://salsa.debian.org/med-team/acedb/-/blob/master/whooks/systags.h?ref_type=heads#L57-61

Hi

I noticed the enum and the functions associated with the enum are
unused. You could just simply patch them out.
There are more errors after that though.

did
not were connected to GTK) but I'm now stumbling upon:

...
In file included from disknew.c:85:
../whooks/systags.h:57:15: error: expected identifier before numeric
constant
   57 | #define _Int  24
      |               ^~
../wh/acetypes.h:36:16: note: in expansion of macro '_Int'
   36 | typedef enum { _Int, _Text, _Float, _DateType, _Key, _Tag }
AceType;
      |                ^~~~
...


which is caused by whooks/systags.h[2]

...
#define _Int  24
#define _Unsigned  25
#define _Long  26               /* not supported */
#define _Long_Unsigned  27      /* not supported */
#define _Float  28
...

Is there any trick I could use here instead of replacing these
definitions by something else like _Int_acedb or so globally to get this
build by modern compilers?

Kind regards
    Andreas.

[1] https://salsa.debian.org/med-team/acedb/-/jobs/5586407#L1893
[2]
https://salsa.debian.org/med-team/acedb/-/blob/master/whooks/systags.h?ref_type=heads#L57-61

I had a look at what happened to AceDB and it seems like it is now hosted on
https://github.com/ncbi/AceView/blob/master/w9/dotter.c
at least the dotter application that is. I find that tool of high (and underrated)
educational and practical value and would not want to miss that.

I will not get around comparing the source trees for an unforseeable future, though.

Best,
Steffen

We believe that the bug you reported is fixed in the latest version of
acedb, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1066334@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated acedb package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Tue, 22 Sep 2026 16:04:05 +0200
Source: acedb
Architecture: source
Version: 4.9.39+dfsg.02-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1066334 1134595 1147991
Changes:
 acedb (4.9.39+dfsg.02-10) unstable; urgency=medium
 .
   [ Andreas Tille ]
   * Fix gcc-14 build issues
      - Add missing readline/history.h header
      - Definition of AceType is broken since it redefines _Int with different
        meaning than in whooks/systags.h
      - Do not include wh/acelib_.h in wh/lex.h to avoid conflicting type
        definitions; regular.h and keyset.h provide the needed types
      - Add missing declarations for dnaDumpKeyCstyle/peptideDumpKeyCstyle
      - 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, #1147991
   * Build-Depends: libtirpc-dev
   * Replace pkg-config with pkgconf in Build-Depends
   * Install acediff and acediffsorted (ACE format diff tools) with man pages
   * Fix Homepage
     Closes: #1134595
   * Reformat the Last-Update date as ISO YYYY-MM-DD.
   * Remove redundant Priority: optional from source stanza.
   * Update standards version to 4.7.4, no changes needed.
   * cme fix dpkg-control
   * Add autopkgtest
   * d/watch:
      - Version=5
      - Fix
   * Fix DEP3 fields
 .
   [ Jeremy Sowden ]
   * Fixes for missing declarations
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