--- Begin Message ---
Source: lagan
Version: 2.0-9
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&[email protected]&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 ---
pgpUXiAzpcHUs.pgp
