đ ĐĄŃ, 17 ĐŽĐ”Đș. 2025âŻĐł. ĐČ 20:44, Aurelien Jarno <[email protected]>:
> 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 âNlm_Mainâ: > |debruijn.c:72:12: warning: pointer targets in assignment from > âNlm_CharPtrâ {aka âchar *â} to âNlm_Uint1 *â {aka âunsigned char *â} > differ in signedness [-Wpointer-sign] > | 72 | alphabet = myargs[1].strvalue; > | | ^ > |debruijn.c:80:14: warning: pointer targets in passing argument 1 of > âstrlenâ 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 âconst char *â but argument > is of type âNlm_Uint1 *â {aka âunsigned char *â} > | 407 | extern size_t strlen (const char *__s) > | | ~~~~~~~~~~~~^~~ > |debruijn.c:89:10: warning: pointer targets in assignment from âchar *â to > âNlm_Uint1 *â {aka âunsigned char *â} differ in signedness [-Wpointer-sign] > | 89 | output = (char *) malloc(outputsize + 1); > | | ^ > |debruijn.c:106:8: warning: pointer targets in passing argument 1 of > âputsâ 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 âconst char *â but argument > is of type âNlm_Uint1 *â {aka âunsigned char *â} > | 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: ârcsidâ 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 >
