[Debian-med-packaging] Bug#1066709: fastdnaml: FTBFS: fastDNAml.h:228:28: error: implicit declaration of function ‘free’ [-Werror=implicit-function-declaration]
Lucas Nussbaum
lucas at debian.org
Wed Mar 13 11:50:02 GMT 2024
Source: fastdnaml
Version: 1.2.2-15
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):
> cd source && cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection fastDNAml.c -o fastDNAml -lm -Wl,-z,relro -Wl,-z,now
> In file included from fastDNAml.c:207:
> fastDNAml.h:222:10: warning: conflicting types for built-in function ‘malloc’; expected ‘void *(long unsigned int)’ [-Wbuiltin-declaration-mismatch]
> 222 | char *malloc();
> | ^~~~~~
> fastDNAml.h:1:1: note: ‘malloc’ is declared in header ‘<stdlib.h>’
> +++ |+#include <stdlib.h>
> 1 | /* fastDNAml.h */
> fastDNAml.c: In function ‘freeTopol’:
> fastDNAml.h:228:28: error: implicit declaration of function ‘free’ [-Werror=implicit-function-declaration]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.c:208:1: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 207 | #include "fastDNAml.h" /* Requires version 1.2 */
> +++ |+#include <stdlib.h>
> 208 |
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:342:5: note: in expansion of macro ‘Free’
> 342 | Free(tpl->links);
> | ^~~~
> fastDNAml.c: In function ‘freeTreeNode’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1533:23: note: in expansion of macro ‘Free’
> 1533 | if (p->x->lv) Free(p->x->lv);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1533:23: note: in expansion of macro ‘Free’
> 1533 | if (p->x->lv) Free(p->x->lv);
> | ^~~~
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1534:9: note: in expansion of macro ‘Free’
> 1534 | Free(p->x);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1534:9: note: in expansion of macro ‘Free’
> 1534 | Free(p->x);
> | ^~~~
> fastDNAml.c: In function ‘freeTree’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1560:5: note: in expansion of macro ‘Free’
> 1560 | Free(tr->nodep[1]); /* Free the actual nodes */
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:1560:5: note: in expansion of macro ‘Free’
> 1560 | Free(tr->nodep[1]); /* Free the actual nodes */
> | ^~~~
> fastDNAml.c: In function ‘setupxarray’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2028:9: note: in expansion of macro ‘Free’
> 2028 | Free(x);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2028:9: note: in expansion of macro ‘Free’
> 2028 | Free(x);
> | ^~~~
> fastDNAml.c: In function ‘makenewz’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2604:5: note: in expansion of macro ‘Free’
> 2604 | Free(abi);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:2604:5: note: in expansion of macro ‘Free’
> 2604 | Free(abi);
> | ^~~~
> fastDNAml.c: In function ‘readKeyValue’:
> fastDNAml.c:2886:15: error: implicit declaration of function ‘strlen’ [-Werror=implicit-function-declaration]
> 2886 | string += strlen(key);
> | ^~~~~~
> fastDNAml.c:208:1: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> 207 | #include "fastDNAml.h" /* Requires version 1.2 */
> +++ |+#include <string.h>
> 208 |
> fastDNAml.c:2886:15: warning: incompatible implicit declaration of built-in function ‘strlen’ [-Wbuiltin-declaration-mismatch]
> 2886 | string += strlen(key);
> | ^~~~~~
> fastDNAml.c:2886:15: note: include ‘<string.h>’ or provide a declaration of ‘strlen’
> fastDNAml.c: In function ‘fopen_pid’:
> fastDNAml.c:3231:47: error: implicit declaration of function ‘getpid’ [-Werror=implicit-function-declaration]
> 3231 | (void) sprintf(name_pid, "%s.%d", filenm, getpid());
> | ^~~~~~
> fastDNAml.c: In function ‘treeOut’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:3683:5: note: in expansion of macro ‘Free’
> 3683 | Free(treestr);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:3683:5: note: in expansion of macro ‘Free’
> 3683 | Free(treestr);
> | ^~~~
> fastDNAml.c: In function ‘cmpBestTrees’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4535:5: note: in expansion of macro ‘Free’
> 4535 | Free(log_f0);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4535:5: note: in expansion of macro ‘Free’
> 4535 | Free(log_f0);
> | ^~~~
> fastDNAml.c: In function ‘makeDenovoTree’:
> fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4765:5: note: in expansion of macro ‘Free’
> 4765 | Free(enterorder);
> | ^~~~
> fastDNAml.h:228:28: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
> 228 | #define Free(x) (void) free((char *) (x)) /* BSD */
> | ^~~~
> fastDNAml.c:4765:5: note: in expansion of macro ‘Free’
> 4765 | Free(enterorder);
> | ^~~~
> fastDNAml.c: At top level:
> fastDNAml.c:4775:3: warning: return type defaults to ‘int’ [-Wimplicit-int]
> 4775 | main ()
> | ^~~~
> cc1: some warnings being treated as errors
> make[1]: *** [Makefile:4: fastDNAml] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/fastdnaml_1.2.2-15_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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