Your message dated Mon, 29 Dec 2025 03:50:13 +0000
with message-id <[email protected]>
and subject line Bug#1123553: fixed in ncbi-tools6 6.1.20170106+dfsg2-7
has caused the Debian Bug report #1123553,
regarding ncbi-tools6: autopktest failure on amd64 with libc6 2.42-6 due to
unspecified return value
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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1123553: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1123553
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-tools6
Version: 6.1.20170106+dfsg2-6
Severity: serious
X-Debbugs-Cc: [email protected]
User: [email protected]
Usertags: amd64
Dear maintainer,
ncbi-tools6 autopkgtest fails on amd64 with a non 0 return code in the
debruijn test:
| 40s autopkgtest [11:03:16]: test run-unit-test: [-----------------------
| 40s ---asn2asn test---
| 41s ---asn2all test---
| 41s ---asn2fsa test---
| 42s ---asn2gb test---
| 42s ---asn2idx test---
| 43s ---asn2xml test---
| 43s ---cleanasn test---
| 43s ---gene2xml test---
| 44s ---vecscreen test---
| 47s ---asndisc test---
| 50s ---asnval test---
| 51s ---asnmacro test---
| 53s ---asntool test---
| 53s ---indexpub test---
| 53s ---getpub test---
| 53s ---getmesh test---
| 53s ---debruijn test---
| 54s autopkgtest [11:03:30]: test run-unit-test: -----------------------]
| 54s autopkgtest [11:03:30]: test run-unit-test: - - - - - - - - - - results
- - - - - - - - - -
| 54s run-unit-test FAIL non-zero exit status 160
| 54s autopkgtest [11:03:30]: @@@@@@@@@@@@@@@@@@@@ summary
| 54s run-unit-test FAIL non-zero exit status 160
The full autopkgtest log is available here:
https://ci.debian.net/data/autopkgtest/testing/amd64/n/ncbi-tools6/67219817/log.gz
It appears that the return value is actually undefined, and depends on
how the rax register is used before. This is actually reported as a warning
at build time:
|x86_64-linux-gnu-gcc -o debruijn -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/ncbi-tools6-6.1.20170106+dfsg2=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wall -Wdate-time -D_FORTIFY_SOURCE=2
-Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,-rpath-link,../shlib -I../include
-L../shlib debruijn.c -lblast -lblastcompadj -lncbi -lm
|In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
| from ../include/ncbilcl.h:150,
| from ../include/ncbi.h:57,
| from debruijn.c:38:
|/usr/include/features.h:199:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
| 199 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| | ^~~~~~~
|debruijn.c: In function ‘Nlm_Main’:
|debruijn.c:72:12: warning: pointer targets in assignment from ‘Nlm_CharPtr’
{aka ‘char *’} to ‘Nlm_Uint1 *’ {aka ‘unsigned char *’} differ in signedness
[-Wpointer-sign]
| 72 | alphabet = myargs[1].strvalue;
| | ^
|debruijn.c:80:14: warning: pointer targets in passing argument 1 of ‘strlen’
differ in signedness [-Wpointer-sign]
| 80 | k = strlen(alphabet);
| | ^~~~~~~~
| | |
| | Nlm_Uint1 * {aka unsigned char *}
|In file included from ../include/ncbilcl.h:156:
|/usr/include/string.h:407:35: note: expected ‘const char *’ but argument is of
type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’}
| 407 | extern size_t strlen (const char *__s)
| | ~~~~~~~~~~~~^~~
|debruijn.c:89:10: warning: pointer targets in assignment from ‘char *’ to
‘Nlm_Uint1 *’ {aka ‘unsigned char *’} differ in signedness [-Wpointer-sign]
| 89 | output = (char *) malloc(outputsize + 1);
| | ^
|debruijn.c:106:8: warning: pointer targets in passing argument 1 of ‘puts’
differ in signedness [-Wpointer-sign]
| 106 | puts(output);
| | ^~~~~~
| | |
| | Nlm_Uint1 * {aka unsigned char *}
|In file included from ../include/ncbilcl.h:154:
|/usr/include/stdio.h:714:30: note: expected ‘const char *’ but argument is of
type ‘Nlm_Uint1 *’ {aka ‘unsigned char *’}
| 714 | extern int puts (const char *__s);
| | ~~~~~~~~~~~~^~~
|debruijn.c:109:1: warning: control reaches end of non-void function
[-Wreturn-type]
| 109 | }
| | ^
This means that the return value is undefined. Luckily it was 0 with
glibc compiled with GCC 14, but unfortunately it gets another value
when glibc is compiled with GCC 15.
|debruijn.c: At top level:
|debruijn.c:29:19: warning: ‘rcsid’ defined but not used
[-Wunused-const-variable=]
| 29 | static char const rcsid[] = "$Id: debruijn.c,v 1.4 2004/02/09 21:24:59
ucko Exp $";
| | ^~~~~
The following patch fixes the issue:
--- ncbi-tools6-6.1.20170106+dfsg2.orig/demo/debruijn.c
+++ ncbi-tools6-6.1.20170106+dfsg2/demo/debruijn.c
@@ -106,4 +106,6 @@ Int2 Main(void)
puts(output);
free(output);
+
+ return 0;
}
Note however there are many other similar warning in the build log, you
probably want to fix all of them.
Regards
Aurelien
--- End Message ---
--- Begin Message ---
Source: ncbi-tools6
Source-Version: 6.1.20170106+dfsg2-7
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ncbi-tools6, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-tools6 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 28 Dec 2025 22:30:14 -0500
Source: ncbi-tools6
Architecture: source
Version: 6.1.20170106+dfsg2-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1123553
Changes:
ncbi-tools6 (6.1.20170106+dfsg2-7) unstable; urgency=medium
.
* debian/.ncbirc: Belatedly set [BLAST]BLASTDB to /usr/share/ncbi/data.
(See #1117994.)
* Always return a value from non-void functions. (Closes: #1123553.)
- biostruc/cdd/thrd*.[ch] (bwfi, cp[alr]l, cxei, salu, sgoi, slou,
spe[al], spni, ttb0, zsc): Correct return type to void to match
implementation and usage.
- demo/debruijn.c ([Nlm_]Main): Return 0 when not bailing.
- tools/taxblast.c (RDTaxLookupReset): Return tax_looxup, modified
in place.
* Standards-Version: 4.7.3 (routine-update)
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