Source: fastdnaml
Version: 1.2.2-15
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas@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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Your message dated Sun, 07 Apr 2024 09:34:04 +0000
with message-id <E1rtOua-006q2O-LK@fasolo.debian.org>
and subject line Bug#1066709: fixed in fastdnaml 1.2.2-16
has caused the Debian Bug report #1066709,
regarding fastdnaml: FTBFS: fastDNAml.h:228:28: error: implicit declaration of function ‘free’ [-Werror=implicit-function-declaration]
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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1066709: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066709
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