[Debian-med-packaging] Bug#1066559: dialign-t: FTBFS: museq.c:168:9: error: implicit declaration of function ‘free_diag’; did you mean ‘free_diag_col’? [-Werror=implicit-function-declaration]
Lucas Nussbaum
lucas at debian.org
Wed Mar 13 11:49:20 GMT 2024
Source: dialign-t
Version: 1.0.2-14
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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=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.
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