Your message dated Sat, 16 Mar 2024 15:37:18 +0000
with message-id <e1rlw62-005uc7...@fasolo.debian.org>
and subject line Bug#1066559: fixed in dialign-t 1.0.2-15
has caused the Debian Bug report #1066559,
regarding dialign-t: FTBFS: museq.c:168:9: error: implicit declaration of
function ‘free_diag’; did you mean ‘free_diag_col’?
[-Werror=implicit-function-declaration]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1066559: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066559
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: dialign-t
Version: 1.0.2-14
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
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):
> gcc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx
> -c -o orf.o orf.c
> alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never
> defined
> 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col
> *dcol, struct scr_matrix* smatrix,
> | ^~~~~~~~~~~~~~
> alig.c:13:20: warning: inline function ‘calc_weight’ declared but never
> defined
> 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix*
> smatrix,
> | ^~~~~~~~~~~
> assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never
> defined
> 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int
> seqnum, int pos);
> | ^~~~~~~~
> museq.c: In function ‘main’:
> assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but
> never defined
> 25 | extern inline struct simple_diag_col* find_diags_guided(struct
> scr_matrix *smatrix,
> | ^~~~~~~~~~~~~~~~~
> assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but
> never defined
> 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col
> *dcol, struct scr_matrix* smatrix,
> | ^~~~~~~~~~~~~~
> museq.c:168:9: error: implicit declaration of function ‘free_diag’; did you
> mean ‘free_diag_col’? [-Werror=implicit-function-declaration]
> 168 | free_diag(adcol.diags[i]);
> | ^~~~~~~~~
> | free_diag_col
> io.c: In function ‘read_anchors’:
> museq.c:278:27: error: implicit declaration of function ‘free_alignment’
> [-Werror=implicit-function-declaration]
> 278 | if(! para->FAST_MODE) free_alignment(algn);
> | ^~~~~~~~~~~~~~
> io.c:535:23: warning: format ‘%li’ expects argument of type ‘long int *’, but
> argument 3 has type ‘int *’ [-Wformat=]
> 535 | while( fscanf(fp,"%li %li %li %li %li
> %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
> | ~~^ ~~~
> | | |
> | long int * int *
> | %i
> io.c:535:27: warning: format ‘%li’ expects argument of type ‘long int *’, but
> argument 4 has type ‘int *’ [-Wformat=]
> 535 | while( fscanf(fp,"%li %li %li %li %li
> %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
> | ~~^ ~~~
> | | |
> | long int * int *
> | %i
> io.c:535:31: warning: format ‘%li’ expects argument of type ‘long int *’, but
> argument 5 has type ‘int *’ [-Wformat=]
> 535 | while( fscanf(fp,"%li %li %li %li %li
> %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
> | ~~^ ~~~~
> | | |
> | long int * int *
> | %i
> io.c:535:35: warning: format ‘%li’ expects argument of type ‘long int *’, but
> argument 6 has type ‘int *’ [-Wformat=]
> 535 | while( fscanf(fp,"%li %li %li %li %li
> %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
> | ~~^ ~~~~
> | | |
> | long int * int *
> | %i
> io.c:535:39: warning: format ‘%li’ expects argument of type ‘long int *’, but
> argument 7 has type ‘int *’ [-Wformat=]
> 535 | while( fscanf(fp,"%li %li %li %li %li
> %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
> | ~~^ ~~~~
> | | |
> | long int * int *
> | %i
> diag.c:1456:17: warning: ‘real_calc_weight’ is static but used in inline
> function ‘find_diags_dyn’ which is not static
> 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
> | ^~~~~~~~~~~~~~~~
> io.c: In function ‘read_scr_matrix’:
> io.c:270:17: warning: ignoring return value of ‘fscanf’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 270 | fscanf( fp, "%i", &is);
> | ^~~~~~~~~~~~~~~~~~~~~~
> io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 282 | fscanf(fp, "%s\n", rline);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~
> io.c: In function ‘read_diag_prob_dist’:
> io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> gcc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops -mfpmath=sse -msse -mmmx
> -c -o translate.o translate.c
> cc1: some warnings being treated as errors
> make[1]: *** [<builtin>: museq.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/dialign-t_1.0.2-14_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lu...@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.
--- End Message ---
--- Begin Message ---
Source: dialign-t
Source-Version: 1.0.2-15
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
dialign-t, 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 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated dialign-t 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 16 Mar 2024 16:11:18 +0100
Source: dialign-t
Architecture: source
Version: 1.0.2-15
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1066559
Changes:
dialign-t (1.0.2-15) unstable; urgency=medium
.
* Team upload.
* fix-declarations.patch: new: fix build failures. (Closes: #1066559)
* Update standards version to 4.6.2, no changes needed.
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Files:
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