[Debian-med-packaging] Bug#875535: sambamba: FTBFS: Segmentation fault
Andreas Tille
andreas at an3as.eu
Tue Sep 12 05:59:35 UTC 2017
control: tags -1 help
Hello,
I admit I have no idea what to do and I'm hereby sending a desperate
call for help to the Debian D team.
Kind regards
Andreas.
On Tue, Sep 12, 2017 at 08:37:00AM +0900, Nobuhiro Iwamatsu wrote:
> Package: sambamba
> Version: 0.6.6-1
> Severity: serious
> Tags: buster sid
> Justification: FTBFS on amd64
>
> Dear Maintainer,
>
> sambamba FTBFS on sid.
>
> https://buildd.debian.org/status/fetch.php?pkg=sambamba&arch=amd64&ver=0.6.6-1%2Bb1&stamp=1504167027&raw=0
>
> ------
> Build targets in project: 2
> dh_auto_build -a -O--buildsystem=meson
> ninja -j4 -v
> [1/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/main.d.o' -c ../main.d
> ../sambamba/utils/common/readstorage.d(22): Deprecation: module
> std.c.stdlib is deprecated - Import core.stdc.stdlib or
> core.sys.posix.stdlib instead
> ../sambamba/utils/common/readstorage.d(23): Deprecation: module
> std.c.string is deprecated - Import core.stdc.string instead
> ../sambamba/sort.d(45): Deprecation: module std.c.stdlib is deprecated
> - Import core.stdc.stdlib or core.sys.posix.stdlib instead
> ../sambamba/sort.d(46): Deprecation: module std.c.string is deprecated
> - Import core.stdc.string instead
> ../sambamba/markdup.d(37): Deprecation: module std.c.stdlib is
> deprecated - Import core.stdc.stdlib or core.sys.posix.stdlib instead
> ../sambamba/depth.d(1154): Deprecation: Implicit string concatenation
> is deprecated, use "mapping_quality > 0 and " ~ "not duplicate and "
> instead
> ../sambamba/depth.d(1155): Deprecation: Implicit string concatenation
> is deprecated, use "not duplicate and " ~ "not failed_quality_control"
> instead
> [2/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
> [3/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/sambamba_depth.d.o' -c ../sambamba/depth.d
> FAILED: sambamba at exe/sambamba_depth.d.o
> ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
> -enable-color -O3 -g -release -of 'sambamba at exe/sambamba_depth.d.o'
> -c ../sambamba/depth.d
> ../sambamba/depth.d(1154): Deprecation: Implicit string concatenation
> is deprecated, use "mapping_quality > 0 and " ~ "not duplicate and "
> instead
> ../sambamba/depth.d(1155): Deprecation: Implicit string concatenation
> is deprecated, use "not duplicate and " ~ "not failed_quality_control"
> instead
> 0 libLLVM-4.0.so.1 0x00007fdf83fb4f45
> llvm::sys::PrintStackTrace(llvm::raw_ostream&) + 37
> 1 libLLVM-4.0.so.1 0x00007fdf83fb31a6 llvm::sys::RunSignalHandlers() + 86
> 2 libLLVM-4.0.so.1 0x00007fdf83fb32c3
> 3 libpthread.so.0 0x00007fdf8321b0c0
> 4 ldc2 0x0000562179492ee2
> 5 ldc2 0x0000562179518017
> 6 ldc2 0x00005621795185dc
> 7 ldc2 0x00005621794dc090
> 8 ldc2 0x00005621794d5be1
> 9 ldc2 0x00005621794e1696
> 10 ldc2 0x00005621794d7041
> 11 ldc2 0x00005621794c4dfd
> 12 ldc2 0x00005621794c3bc4
> 13 ldc2 0x00005621794c1dd4
> 14 ldc2 0x000056217948be81
> 15 ldc2 0x0000562179482b00
> 16 ldc2 0x0000562179482c9b
> 17 ldc2 0x0000562179483564
> 18 ldc2 0x000056217949e915
> 19 ldc2 0x0000562179534dc2
> 20 ldc2 0x000056217950ded9
> 21 ldc2 0x00005621793ffa0d
> 22 ldc2 0x000056217951072a
> 23 ldc2 0x000056217955b35f
> 24 ldc2 0x000056217955b324
> 25 ldc2 0x000056217955b250
> 26 libc.so.6 0x00007fdf825f32e1 __libc_start_main + 241
> 27 ldc2 0x00005621792b57ea
> Segmentation fault
> [4/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/sambamba_index.d.o' -c ../sambamba/index.d
> [5/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/sambamba_flagstat.d.o' -c ../sambamba/flagstat.d
> [6/74] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/
> -I/usr/include/htslib -enable-color -O3 -g -release -of
> 'sambamba at exe/sambamba_markdup.d.o' -c ../sambamba/markdup.d
> FAILED: sambamba at exe/sambamba_markdup.d.o
> ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d/ -I/usr/include/htslib
> -enable-color -O3 -g -release -of 'sambamba at exe/sambamba_markdup.d.o'
> -c ../sambamba/markdup.d
> ../sambamba/markdup.d(37): Deprecation: module std.c.stdlib is
> deprecated - Import core.stdc.stdlib or core.sys.posix.stdlib instead
> 0 libLLVM-4.0.so.1 0x00007f56575adf45
> llvm::sys::PrintStackTrace(llvm::raw_ostream&) + 37
> 1 libLLVM-4.0.so.1 0x00007f56575ac1a6 llvm::sys::RunSignalHandlers() + 86
> 2 libLLVM-4.0.so.1 0x00007f56575ac2c3
> 3 libpthread.so.0 0x00007f56568140c0
> 4 ldc2 0x000055c9d4f89ee2
> 5 ldc2 0x000055c9d500f017
> 6 ldc2 0x000055c9d500f5dc
> 7 ldc2 0x000055c9d4fd3090
> 8 ldc2 0x000055c9d4fccbe1
> 9 ldc2 0x000055c9d4fd8696
> 10 ldc2 0x000055c9d4fce041
> 11 ldc2 0x000055c9d4fbbdfd
> 12 ldc2 0x000055c9d4fbabc4
> 13 ldc2 0x000055c9d4fb8dd4
> 14 ldc2 0x000055c9d4f82e81
> 15 ldc2 0x000055c9d4f79b00
> 16 ldc2 0x000055c9d4f79c9b
> 17 ldc2 0x000055c9d4f7a564
> 18 ldc2 0x000055c9d4f95915
> 19 ldc2 0x000055c9d502bdc2
> 20 ldc2 0x000055c9d5004ed9
> 21 ldc2 0x000055c9d4ef6a0d
> 22 ldc2 0x000055c9d500772a
> 23 ldc2 0x000055c9d505235f
> 24 ldc2 0x000055c9d5052324
> 25 ldc2 0x000055c9d5052250
> 26 libc.so.6 0x00007f5655bec2e1 __libc_start_main + 241
> 27 ldc2 0x000055c9d4dac7ea
> Segmentation fault
> ninja: build stopped: subcommand failed.
> dh_auto_build: ninja -j4 -v returned exit code 1
> debian/rules:16: recipe for target 'build-arch' failed
> make: *** [build-arch] Error 1
> dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
> --------------------------------------------------------------------------------
> Build finished at 2017-08-31T08:10:18Z
> ------
>
> Coudl you check about this problem?
>
> -- System Information:
> Debian Release: buster/sid
> APT prefers unstable
> APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 4.11.0-2-amd64 (SMP w/8 CPU cores)
> Locale: LANG=ja_JP.UTF-8, LC_CTYPE=ja_JP.UTF-8 (charmap=UTF-8),
> LANGUAGE=ja_JP.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
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>
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