[Debian-med-packaging] Bug#875535: sambamba: FTBFS: Segmentation fault
Nobuhiro Iwamatsu
iwamatsu at nigauri.org
Mon Sep 11 23:37:00 UTC 2017
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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