[Debian-med-packaging] Bug#1066580: lagan: FTBFS: order.c:409:5: error: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Werror=implicit-function-declaration]

Lucas Nussbaum lucas at debian.org
Wed Mar 13 11:52:09 GMT 2024


Source: lagan
Version: 2.0-9
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 -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-z,relro
> anchors.c: In function ‘anchors_getline’:
> anchors.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   232 |   fgets(temp, 1024, infile);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~
> order.c: In function ‘doAlign’:
> order.c:409:5: error: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Werror=implicit-function-declaration]
>   409 |     printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
>       |     ^~~~~~~~~~~~~
>       |     printBinAlign
> order.c:411:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printTextAlign’? [-Werror=implicit-function-declaration]
>   411 |     printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name);
>       |     ^~~~~~~~~~~~~~
>       |     printTextAlign
> order.c: In function ‘readfile’:
> order.c:61:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    61 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> order.c: In function ‘readSubstMatrix’:
> order.c:145:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   145 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
>       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> order.c:149:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   149 |   fscanf (file, "%d", &gapstart);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> order.c:150:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   150 |   fscanf (file, "%d", &gapcont);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/cextract.c: In function ‘getLength’:
> utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    16 |   fgets (buffer, 1024, file);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/cextract.c: In function ‘readfile’:
> utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    41 |     fgets (buffer, 1024, file);
>       |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
> mlagan.c: In function ‘readfile’:
> mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
>    93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
>       |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> prolagan.c: In function ‘readfile’:
> prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args]
>    93 |         fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha);
>       |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> fchaos.c: In function ‘readfile’:
> fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args]
>   357 |         fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha);
>       |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> mlagan.c: In function ‘main’:
> mlagan.c:1071:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Werror=implicit-function-declaration]
>  1071 |     printXMFAAlign(outfile, final);
>       |     ^~~~~~~~~~~~~~
>       |     printFASTAAlign
> mlagan.c: In function ‘readfile’:
> mlagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    79 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> prolagan.c: In function ‘main’:
> prolagan.c:1091:5: error: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Werror=implicit-function-declaration]
>  1091 |     printXMFAAlign(outfile, final);
>       |     ^~~~~~~~~~~~~~
>       |     printFASTAAlign
> prolagan.c: In function ‘readfile’:
> prolagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    79 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> fchaos.c:344:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   344 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> fchaos.c: In function ‘readSubstMatrix’:
> fchaos.c:622:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   622 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
>       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> fchaos.c:627:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   627 |   fscanf (file, "%d", &gappenstart);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> fchaos.c:628:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>   628 |   fscanf (file, "%d", &gappenext);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-z,relro
> utils/cstat.c: In function ‘cntlets’:
> utils/cstat.c:51:10: error: implicit declaration of function ‘isspace’ [-Werror=implicit-function-declaration]
>    51 |     if (!isspace(currchar)) {
>       |          ^~~~~~~
> utils/cstat.c:6:1: note: include ‘<ctype.h>’ or provide a declaration of ‘isspace’
>     5 | #include <assert.h>
>   +++ |+#include <ctype.h>
>     6 | 
> utils/cstat.c:52:18: error: implicit declaration of function ‘toupper’ [-Werror=implicit-function-declaration]
>    52 |       currchar = toupper(currchar);
>       |                  ^~~~~~~
> utils/cstat.c:52:18: note: include ‘<ctype.h>’ or provide a declaration of ‘toupper’
> utils/cstat.c:44:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    44 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> utils/cstat.c: In function ‘readseq’:
> utils/cstat.c:67:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    67 |   fgets(temp, 255, input);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~
> gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-z,relro
> utils/contigorder.c: In function ‘getFileInfo’:
> utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
>    15 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
>       |                                                        ~^
>       |                                                         |
>       |                                                         char *
> utils/contigorder.c:26:25: warning: unknown conversion type character ‘&’ in format [-Wformat=]
>    26 |         fscanf (file, "%&d", &dummy);
>       |                         ^
> utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args]
>    26 |         fscanf (file, "%&d", &dummy);
>       |                       ^~~~~
> utils/contigorder.c: In function ‘getScores’:
> utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=]
>    52 |     fprintf (stderr, "contigorder: Error opening file: %s\n");
>       |                                                        ~^
>       |                                                         |
>       |                                                         char *
> skiplist.c: In function ‘printSLE’:
> skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
>    12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
>       |                  ~^                 ~~~~~~~~~~~
>       |                   |                    |
>       |                   unsigned int         void *
>       |                  %p
> gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-z,relro
> utils/contigorder.c: In function ‘getFileInfo’:
> utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    19 |   fscanf (file, "numContigs = %d\n", numContigs);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    20 |   fscanf (file, "seqLen = %d\n", seqLen);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    26 |         fscanf (file, "%&d", &dummy);
>       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/contigorder.c: In function ‘getScores’:
> utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    56 |   fscanf (file, "numContigs = %*d\n");
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    57 |   fscanf (file, "seqLen = %*d\n");
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    63 |         fscanf (file, "%d", &((*score)[i][j]));
>       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> utils/getbounds.c: In function ‘getLength’:
> utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    18 |   fgets (buffer, 1024, file);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
> gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-z,relro
> gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3  -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-z,relro
> utils/getlength.c: In function ‘main’:
> utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
>    20 |   fgets (buffer, BUF_SIZE, file);
>       |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> cc1: some warnings being treated as errors
> make[2]: *** [Makefile:28: ../utils/cstat] Error 1


The full build log is available from:
http://qa-logs.debian.net/2024/03/13/lagan_2.0-9_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.



More information about the Debian-med-packaging mailing list