Hi, On 2026-08-20 14:40, Paul Gevers wrote: > Source: sra-sdk > Version: 3.2.1+dfsg-6 > Severity: serious > X-Debbugs-CC: [email protected] [email protected] > Control: affects -1 src:glibc > > Hi, > > While checking the glibc transition (bug 1141940), I noticed that your > autopkgtest fails with the new glibc and it failing with a Segmentation > fault. To be open about it, we'll not be holding back the glibc transition > for this package, please have a look at it. > > Paul > > https://ci.debian.net/packages/s/sra-sdk/unstable/amd64/74480346/ > > 60s autopkgtest [12:02:15]: test run-unit-test: [----------------------- > 60s >>>>>Decompressing test-data archive... > 60s dbGaP-0/ > 60s dbGaP-0/SRR2042184.fasta > 60s meta/ > 60s meta/prj_phs710EA_test.ngc > 60s meta/SRR6650398_experiment.xml > 60s meta/SRR6650398.bam > 60s meta/SRR2042184_run.xml > 60s meta/SRR2042184_experiment.xml > 60s meta/SRR6650398_illumina_run.xml > 60s meta/SRR7032226_run.xml > 60s meta/SRR7032226_experiment.xml > 60s meta/reference.fna > 60s meta/SRR6650398_fastq_run.xml > 60s public/ > 60s public/nannot/ > 60s public/wgs/ > 60s public/refseq/ > 60s public/refseq/NC_000962.3 > 60s public/sra/ > 60s public/sra/SRR7032226.sra > 60s public/sra/SRR6650398.sra > 60s public/sra/SRR2042184.sra > 60s public/files/ > 60s >>>>>Running test-sra... > 63s 2026-08-20T12:02:18 test-sra.3.2.1 fatal: SIGNAL - Segmentation fault > 64s autopkgtest [12:02:19]: test run-unit-test: -----------------------]
This is the corresponding backtrace of the crash:
(gdb) bt
#0 __strlen_avx2 () at ../sysdeps/x86_64/multiarch/strlen-avx2.S:76
#1 0x00007ffff7ce4ed3 in KOutMsgNulTermStringFmt (arg=<optimized out>) at
./libs/klib/out.c:50
#2 KOutVMsg (fmt=<optimized out>, args=args@entry=0x7fffffffd3c0) at
./libs/klib/out.c:154
#3 0x00007ffff7ce518d in KOutMsg (fmt=fmt@entry=0x55555556c0b4 "%s") at
./libs/klib/out.c:177
#4 0x000055555555ac02 in MainRanges (self=self@entry=0x7fffffffd7e0,
arg=arg@entry=0x55555556bc0a "SRR000001", bol=bol@entry=0x55555556b54d " ",
get=get@entry=true, aHost=aHost@entry=0x7fffffffd610,
aPath=aPath@entry=0x7fffffffd630, https=true) at
./tools/external/test-sra/test-sra.c:2703
#5 0x000055555555be39 in MainNetwotk (self=self@entry=0x7fffffffd7e0,
arg=arg@entry=0x55555556bc0a "SRR000001", bol=0x55555556b54d " ",
eol=eol@entry=0x55555556b78b "\n")
at ./tools/external/test-sra/test-sra.c:2910
#6 0x00005555555617d0 in KMain (argc=<optimized out>, argv=<optimized out>) at
./tools/external/test-sra/test-sra.c:4121
#7 0x0000555555566c51 in KMane ()
#8 0x000055555555a123 in main ()
(gdb)
#0 __strlen_avx2 () at ../sysdeps/x86_64/multiarch/strlen-avx2.S:76
#1 0x00007ffff7ce4ed3 in KOutMsgNulTermStringFmt (arg=<optimized out>) at
./libs/klib/out.c:50
#2 KOutVMsg (fmt=<optimized out>, args=args@entry=0x7fffffffd3c0) at
./libs/klib/out.c:154
#3 0x00007ffff7ce518d in KOutMsg (fmt=fmt@entry=0x55555556c0b4 "%s") at
./libs/klib/out.c:177
#4 0x000055555555ac02 in MainRanges (self=self@entry=0x7fffffffd7e0,
arg=arg@entry=0x55555556bc0a "SRR000001", bol=bol@entry=0x55555556b54d " ",
get=get@entry=true, aHost=aHost@entry=0x7fffffffd610,
aPath=aPath@entry=0x7fffffffd630, https=true) at
./tools/external/test-sra/test-sra.c:2703
#5 0x000055555555be39 in MainNetwotk (self=self@entry=0x7fffffffd7e0,
arg=arg@entry=0x55555556bc0a "SRR000001", bol=0x55555556b54d " ",
eol=eol@entry=0x55555556b78b "\n")
at ./tools/external/test-sra/test-sra.c:2910
#6 0x00005555555617d0 in KMain (argc=<optimized out>, argv=<optimized out>) at
./tools/external/test-sra/test-sra.c:4121
#7 0x0000555555566c51 in KMane ()
#8 0x000055555555a123 in main ()
And valgrind already sopt that location, with glibc 2.42 or 2.43:
==3640786== Invalid read of size 1
==3640786== at 0x48700A6: strlen (vg_replace_strmem.c:506)
==3640786== by 0x49BFED2: KOutMsgNulTermStringFmt (out.c:50)
==3640786== by 0x49BFED2: KOutVMsg (out.c:154)
==3640786== by 0x49C018C: KOutMsg (out.c:177)
==3640786== by 0x4006C01: MainRanges.constprop.0.isra.0 (test-sra.c:2703)
==3640786== by 0x4007E38: MainNetwotk.isra.0 (test-sra.c:2910)
==3640786== by 0x400D7CF: KMain (test-sra.c:4121)
==3640786== by 0x4012C50: KMane (in /usr/bin/test-sra)
==3640786== by 0x4006122: main (in /usr/bin/test-sra)
==3640786== Address 0xffffffff is not stack'd, malloc'd or (recently) free'd
==3640786==
2026-08-20T18:09:49 test-sra.3.2.1 fatal: SIGNAL - Segmentation fault
==3640786==
==3640786== HEAP SUMMARY:
==3640786== in use at exit: 1,497,081 bytes in 5,970 blocks
==3640786== total heap usage: 47,871 allocs, 41,901 frees, 5,726,644 bytes
allocated
==3640786==
==3640786== LEAK SUMMARY:
==3640786== definitely lost: 4,112 bytes in 1 blocks
==3640786== indirectly lost: 0 bytes in 0 blocks
==3640786== possibly lost: 0 bytes in 0 blocks
==3640786== still reachable: 1,492,969 bytes in 5,969 blocks
==3640786== suppressed: 0 bytes in 0 blocks
==3640786== Rerun with --leak-check=full to see details of leaked memory
==3640786==
==3640786== For lists of detected and suppressed errors, rerun with: -s
==3640786== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
So this is not a glibc bug. glibc 2.43 got changes to the memory
allocator, the memory is not allocated or reused the same way. This just
reveal an existing bug.
Regards
Aurelien
--
Aurelien Jarno GPG: 4096R/1DDD8C9B
[email protected] http://aurel32.net
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