Source: lagan Version: 2.0-9 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 > -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=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.
