Source: codonw Version: 1.4.4-7 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): > cc -c -g -O2 -Werror=implicit-function-declaration > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection > -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c > In file included from menu.c:31: > menu.c: In function ‘main_menu’: > codonW.h:38:74: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> > ");gets(pm->junk);} > | > ^~~~ > menu.c:69:9: note: in expansion of macro ‘pause’ > 69 | pause; > | ^~~~~ > codons.c: In function ‘main’: > codons.c:190:55: warning: format ‘%i’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", > | ~^ > | | > | int > | %li > 191 | num_sequence); > | ~~~~~~~~~~~~ > | | > | long int > codons.c:196:32: warning: format ‘%i’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in > your" > | > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 197 | " input file has\ninternal stop codons (found %i" > 198 | " internal stops) \tWARNING\n",num_seq_int_stop); > | ~~~~~~~~~~~~~~~~ > | | > | long int > codons.c:197:68: note: format string is defined here > 197 | " input file has\ninternal stop codons (found %i" > | ~^ > | | > | int > | %li > codons.c:200:46: warning: format ‘%i’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal > " > | ~^ > | | > | int > | %li > 201 | "stop codons > \tWARNING\n",num_seq_int_stop); > | ~~~~~~~~~~~~~~~~ > | | > | long int > In file included from codons.c:90: > codonW.h:38:74: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> > ");gets(pm->junk);} > | > ^~~~ > codons.c:204:35: note: in expansion of macro ‘pause’ > 204 | if ( pm->codonW && pm->menu ) pause; > | ^~~~~ > codons.c: In function ‘toutput’: > codons.c:640:25: warning: unknown conversion type character ‘=’ in format > [-Wformat=] > 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codons.c:641:11: note: format string is defined here > 641 | " =%5.3f\n" /* with G+C content and length of > gene */ > | ^ > In file included from commline.c:28: > commline.c: In function ‘proc_comm_line’: > codonW.h:38:74: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> > ");gets(pm->junk);} > | > ^~~~ > commline.c:103:9: note: in expansion of macro ‘pause’ > 103 | pause; > | ^~~~~ > codons.c:647:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard > characters " > | ~^ > | | > | int > | %ld > 648 | "in sequence %i\n" > 649 | ,non_std_char - IUBC_TOT > | ~~~~~~~~~~~~~~~~~~~~~~~ > | | > | long int > codons.c:647:27: warning: format ‘%i’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard > characters " > | > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ...... > 650 | ,num_sequence); > | ~~~~~~~~~~~~ > | | > | long int > codons.c:648:25: note: format string is defined here > 648 | "in sequence %i\n" > | ~^ > | | > | int > | %li > codons.c:652:30: warning: format ‘%i’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" > | ~~^ > | | > | int > | %3li > 653 | ,num_sequence > | ~~~~~~~~~~~~ > | | > | long int > open_fil.c: In function ‘open_file’: > open_fil.c:88:13: error: implicit declaration of function ‘gets’; did you > mean ‘fgets’? [-Werror=implicit-function-declaration] > 88 | gets(infile_name); /* get > filename */ > | ^~~~ > | fgets > open_fil.c:128:28: warning: field precision specifier ‘.*’ expects argument > of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} > [-Wformat=] > 128 | fprintf(stderr,"\nThese are the files in the current > directory " > | > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 129 | "I cannot find %.*s > \n\n",strlen(infile_name),infile_name); > | ~~~~~~~~~~~~~~~~~~~ > | | > | size_t {aka long unsigned > int} > open_fil.c:129:34: note: format string is defined here > 129 | "I cannot find %.*s > \n\n",strlen(infile_name),infile_name); > | ~~^~ > | | > | int > codons.c:657:42: warning: format ‘%d’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 657 | fprintf(pm->my_err, "\t\t WARNING %d non " > | ~^ > | | > | int > | %ld > ...... > 660 | ,non_std_char > | ~~~~~~~~~~~~ > | | > | long int > open_fil.c:162:52: warning: field precision specifier ‘.*’ expects argument > of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} > [-Wformat=] > 162 | fprintf(stderr, "\nWarning :File %.*s " > | ~~^~ > | | > | int > ...... > 165 | strlen(infile_name), infile_name); > | ~~~~~~~~~~~~~~~~~~~ > | | > | size_t {aka long unsigned int} > codons.c:657:27: warning: format ‘%i’ expects argument of type ‘int’, but > argument 4 has type ‘long int’ [-Wformat=] > 657 | fprintf(pm->my_err, "\t\t WARNING %d non " > | ^~~~~~~~~~~~~~~~~~~~~~ > ...... > 661 | ,num_sequence); > | ~~~~~~~~~~~~ > | | > | long int > codons.c:659:25: note: format string is defined here > 659 | "in sequence %i\n" > | ~^ > | | > | int > | %li > menu.c: In function ‘printinfo’: > open_fil.c:166:17: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 166 | fgets(temp, 3, stdin); > | ^~~~~~~~~~~~~~~~~~~~~ > codons.c: In function ‘output’: > menu.c:1285:26: warning: field precision specifier ‘.*’ expects argument of > type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} > [-Wformat=] > 1285 | printf("\tVersion : %.*s\n", strlen(Revision) , Revision ); > | ~~^~ ~~~~~~~~~~~~~~~~ > | | | > | int size_t {aka long unsigned int} > codons.c:800:34: warning: format ‘%s’ expects argument of type ‘char *’, but > argument 3 has type ‘int’ [-Wformat=] > 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); > | ~^ ~~~~~~~~ > | | | > | char * int > | %d > codons.c:805:32: warning: format ‘%s’ expects argument of type ‘char *’, but > argument 3 has type ‘int’ [-Wformat=] > 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); > | ~^ ~~~~~~~~ > | | | > | char * int > | %d > tester.c: In function ‘tester’: > tester.c:88:17: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 88 | gets( pm->junk ) ; > | ^~~~ > | fgets > In file included from codon_us.c:77: > codon_us.c: In function ‘codon_error’: > codonW.h:38:74: error: implicit declaration of function ‘gets’; did you mean > ‘fgets’? [-Werror=implicit-function-declaration] > 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> > ");gets(pm->junk);} > | > ^~~~ > codon_us.c:347:6: note: in expansion of macro ‘pause’ > 347 | pause; > | ^~~~~ > codon_us.c: In function ‘codon_usage_out’: > codon_us.c:373:24: warning: format ‘%i’ expects argument of type ‘int’, but > argument 3 has type ‘long int’ [-Wformat=] > 373 | fprintf(fblkout, "%i%c",nncod[x],sp); > | ~^ ~~~~~~~~ > | | | > | int long int > | %li > codon_us.c: In function ‘raau_usage_out’: > codon_us.c:479:21: warning: too many arguments for format > [-Wformat-extra-args] > 479 | fprintf(fblkout, "\n",sp); > | ^~~~ > codon_us.c: In function ‘cbi_out’: > codon_us.c:831:32: warning: format ‘%f’ expects argument of type ‘double’, > but argument 3 has type ‘int’ [-Wformat=] > 831 | sprintf(pm->messages, " Serious error in CBI information > found" > | > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ...... > 836 | pcbi->fop_cod[x], x); > | ~~~~~~~~~~~~~~~~ > | | > | int > codon_us.c:832:38: note: format string is defined here > 832 | " an illegal CBI value of %f for codon %i" > | ~^ > | | > | double > | %d > codon_us.c: In function ‘fop_out’: > codon_us.c:988:28: warning: format ‘%f’ expects argument of type ‘double’, > but argument 3 has type ‘int’ [-Wformat=] > 988 | sprintf(pm->messages, " Serious error in fop information found" > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ...... > 993 | pfop->fop_cod[x], x); > | ~~~~~~~~~~~~~~~~ > | | > | int > codon_us.c:989:37: note: format string is defined here > 989 | " an illegal fop value of %f for codon %l" > | ~^ > | | > | double > | %d > codon_us.c:988:28: warning: unknown conversion type character ‘ ’ in format > [-Wformat=] > 988 | sprintf(pm->messages, " Serious error in fop information found" > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:990:11: note: format string is defined here > 990 | " permissible values are \n 1 for non-optimal" > | ^ > codon_us.c:988:28: warning: too many arguments for format > [-Wformat-extra-args] > 988 | sprintf(pm->messages, " Serious error in fop information found" > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:994:25: warning: unknown conversion type character ‘,’ in format > [-Wformat=] > 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); > | ^ > codon_us.c:994:33: warning: unknown conversion type character ‘,’ in format > [-Wformat=] > 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); > | ^ > codon_us.c:994:44: warning: unknown conversion type character ‘\x0a’ in > format [-Wformat=] > 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); > | ^~ > codon_us.c:994:18: warning: too many arguments for format > [-Wformat-extra-args] > 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c: In function ‘gc_out’: > codon_us.c:1181:10: warning: too many arguments for format > [-Wformat-extra-args] > 1181 | > "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" > | > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c: In function ‘textbin’: > coresp.c:98:5: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 98 | fscanf(pm->fcoa_in,"%s",pm->junk); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:104:9: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 104 | fscanf(pm->fcoa_in,"%i",&v2); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:108:9: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 108 | fscanf(pm->fcoa_in,"%i\n",&v2); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:115:10: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 115 | fscanf(pm->fcoa_in,"%i",&v2); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:119:9: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 119 | fscanf(pm->fcoa_in,"%i\n",&v2); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:127:9: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 127 | fscanf(pm->fcoa_in,"%i",&v2); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:131:7: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last > codon */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c: In function ‘dinuc_out’: > codon_us.c:1476:39: warning: precision used with ‘%c’ gnu_printf format > [-Wformat=] > 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); > | ^ > coresp.c: In function ‘rowout’: > coresp.c:277:5: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 277 | fgets(pm->junk,BUFSIZ,fnam); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c: In function ‘hydro_out’: > codon_us.c:2115:27: warning: too many arguments for format > [-Wformat-extra-args] > 2115 | fprintf(pm->my_err, "No output was written to file \n", > title); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c: In function ‘aromo_out’: > codon_us.c:2148:27: warning: too many arguments for format > [-Wformat-extra-args] > 2148 | fprintf(pm->my_err, "No output was written to file \n", > title); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c: In function ‘gen_cusort_fop’: > coresp.c: In function ‘inertialig’: > coresp.c:1271:7: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1271 | fgets(pm->junk,BUFSIZ,fnam); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ > coresp.c:1315:7: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1315 | fgets(pm->junk,BUFSIZ,fnam); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:1699:8: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in > */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:1700:7: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i > */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:1703:8: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 > */ > | ^~~~~~~~~~~~~~~~~~~~~~~ > coresp.c: In function ‘suprow’: > coresp.c:1619:7: warning: ignoring return value of ‘fgets’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1619 | fgets(pm->junk,BUFSIZ,fnam); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ > codon_us.c:1711:7: warning: ignoring return value of ‘fscanf’ declared with > attribute ‘warn_unused_result’ [-Wunused-result] > 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in > */ > | ^~~~~~~~~~~~~~~~~~~~~~~~~ > cc1: some warnings being treated as errors > make[1]: *** [Makefile:33: open_fil.o] Error 1 The full build log is available from: http://qa-logs.debian.net/2024/03/13/codonw_1.4.4-7_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.