[Debian-med-packaging] Bug#1066326: codonw: FTBFS: codonW.h:38:74: error: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Werror=implicit-function-declaration]
Lucas Nussbaum
lucas at debian.org
Wed Mar 13 11:48:36 GMT 2024
Source: codonw
Version: 1.4.4-7
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):
> 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=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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