[Debian-med-packaging] Bug#938565: Bug#938565: Autopkgtest failing - any takers for Segmentation fault in bowtie (Was: Bug#938565: sspace: Python2 removal in sid/bullseye)

Fri Dec 20 13:40:40 GMT 2019

Hi,

I've had another look at:

> autopkgtest [15:40:05]: test example-tests: [-----------------------
> + which python
> /usr/bin/python
> + python
> + which bowtie-build
> /usr/bin/bowtie-build
> + bowtie-build --help
> Segmentation fault
> autopkgtest [15:40:06]: test example-tests: -----------------------]
> autopkgtest [15:40:06]: test example-tests:  - - - - - - - - - - results - - - - - - - - - -
> example-tests        FAIL non-zero exit status 139
> autopkgtest [15:40:06]: @@@@@@@@@@@@@@@@@@@@ summary
> example-tests        FAIL non-zero exit status 139
> autopkgtest [15:40:06]: Binaries: resetting testbed apt configuration
> 
> 
> I'm worried about
> 
> 
> $ bowtie-build --help
> Segmentation fault    
> 
> 
> which does NOT happen on a local machine where the test suite
> runs successfully.  Anybody volunteering to check that issue?

And I can confirm that this does no longer happen on my sid autopkgtest
 setup, see attached log. I will do a new upload with debugging code
removed soon.

Cheers
Sascha
-------------- next part --------------
$ sudo autopkgtest ../sspace_2.1.1+dfsg-5_amd64.changes -- lxc autopkgtest-sid
autopkgtest [14:35:13]: version 5.10
autopkgtest [14:35:13]: host XX; command line: /usr/bin/autopkgtest ../sspace_2.1.1+dfsg-5_amd64.changes -- lxc autopkgtest-sid
autopkgtest [14:35:19]: testbed dpkg architecture: amd64
autopkgtest [14:35:19]: testbed running kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11)
autopkgtest [14:35:19]: @@@@@@@@@@@@@@@@@@@@ source ../sspace_2.1.1+dfsg-5.dsc
dpkg-source: warning: extracting unsigned source package (/tmp/autopkgtest-lxc.37vrddgj/downtmp/sspace_2.1.1+dfsg-5.dsc)
dpkg-source: info: extracting sspace in src
dpkg-source: info: unpacking sspace_2.1.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking sspace_2.1.1+dfsg-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying shebangs.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying debug.patch
autopkgtest [14:35:20]: testing package sspace version 2.1.1+dfsg-5
autopkgtest [14:35:20]: build not needed
autopkgtest [14:35:20]: test example-tests: preparing testbed
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  libapt-inst2.0
The following NEW packages will be installed:
  apt-utils libapt-inst2.0
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 632 kB of archives.
After this operation, 1,683 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libapt-inst2.0 amd64 1.8.4 [204 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 apt-utils amd64 1.8.4 [428 kB]
Fetched 632 kB in 0s (2,141 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libapt-inst2.0:amd64.
(Reading database ... 12394 files and directories currently installed.)
Preparing to unpack .../libapt-inst2.0_1.8.4_amd64.deb ...
Unpacking libapt-inst2.0:amd64 (1.8.4) ...
Selecting previously unselected package apt-utils.
Preparing to unpack .../apt-utils_1.8.4_amd64.deb ...
Unpacking apt-utils (1.8.4) ...
Setting up libapt-inst2.0:amd64 (1.8.4) ...
Setting up apt-utils (1.8.4) ...
Processing triggers for libc-bin (2.29-6) ...
Get:1 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  InRelease
Ign:1 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  InRelease
Get:2 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  Release [816 B]
Get:2 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  Release [816 B]
Get:3 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  Release.gpg
Ign:3 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  Release.gpg
Get:4 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  Packages [1,174 B]
Reading package lists...
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies...Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
 Done
Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
The following additional packages will be installed:
  bowtie libmpdec2 libpython3-stdlib libpython3.7-stdlib libtbb2 mime-support python3 python3.7 sspace
Suggested packages:
  bowtie-examples python3-doc python3-tk python3-venv python3.7-venv python3.7-doc
Recommended packages:
  file
The following NEW packages will be installed:
  bowtie libmpdec2 libpython3-stdlib libpython3.7-stdlib libtbb2 mime-support python3 python3.7 sspace
0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
Need to get 4,283 kB/5,521 kB of archives.
After this operation, 22.8 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest-lxc.37vrddgj/downtmp/binaries  sspace 2.1.1+dfsg-5 [1,238 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 mime-support all 3.64 [37.8 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libpython3.7-stdlib amd64 3.7.6-1 [1,733 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 python3.7 amd64 3.7.6-1 [350 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libtbb2 amd64 2019~U9-2 [153 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 bowtie amd64 1.2.3+dfsg-2 [1,839 kB]
Fetched 4,283 kB in 3s (1,546 kB/s)
Selecting previously unselected package mime-support.
(Reading database ... 12524 files and directories currently installed.)
Preparing to unpack .../0-mime-support_3.64_all.deb ...
Unpacking mime-support (3.64) ...
Selecting previously unselected package libmpdec2:amd64.
Preparing to unpack .../1-libmpdec2_2.4.2-2_amd64.deb ...
Unpacking libmpdec2:amd64 (2.4.2-2) ...
Selecting previously unselected package libpython3.7-stdlib:amd64.
Preparing to unpack .../2-libpython3.7-stdlib_3.7.6-1_amd64.deb ...
Unpacking libpython3.7-stdlib:amd64 (3.7.6-1) ...
Selecting previously unselected package python3.7.
Preparing to unpack .../3-python3.7_3.7.6-1_amd64.deb ...
Unpacking python3.7 (3.7.6-1) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../4-libpython3-stdlib_3.7.5-3_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.7.5-3) ...
Selecting previously unselected package python3.
Preparing to unpack .../5-python3_3.7.5-3_amd64.deb ...
Unpacking python3 (3.7.5-3) ...
Selecting previously unselected package libtbb2:amd64.
Preparing to unpack .../6-libtbb2_2019~U9-2_amd64.deb ...
Unpacking libtbb2:amd64 (2019~U9-2) ...
Selecting previously unselected package bowtie.
Preparing to unpack .../7-bowtie_1.2.3+dfsg-2_amd64.deb ...
Unpacking bowtie (1.2.3+dfsg-2) ...
Selecting previously unselected package sspace.
Preparing to unpack .../8-sspace.deb ...
Unpacking sspace (2.1.1+dfsg-5) ...
Setting up mime-support (3.64) ...
Setting up libtbb2:amd64 (2019~U9-2) ...
Setting up libmpdec2:amd64 (2.4.2-2) ...
Setting up libpython3.7-stdlib:amd64 (3.7.6-1) ...
Setting up libpython3-stdlib:amd64 (3.7.5-3) ...
Setting up python3.7 (3.7.6-1) ...
Setting up python3 (3.7.5-3) ...
Setting up bowtie (1.2.3+dfsg-2) ...
Setting up sspace (2.1.1+dfsg-5) ...
Setting up autopkgtest-satdep (0) ...
Processing triggers for libc-bin (2.29-6) ...
(Reading database ... 13056 files and directories currently installed.)
Removing autopkgtest-satdep (0) ...
autopkgtest [14:35:29]: test example-tests: [-----------------------
+ which python3
/usr/bin/python3
+ python3
+ which bowtie-build
/usr/bin/bowtie-build
+ bowtie-build --help
Usage: bowtie-build [options]* <reference_in> <ebwt_outfile_base>
    reference_in            comma-separated list of files with ref sequences
    ebwt_outfile_base       write Ebwt data to files with this dir/basename
Options:
    -f                      reference files are Fasta (default)
    -c                      reference sequences given on cmd line (as <seq_in>)
    --large-index           force generated index to be 'large', even if ref
                            has fewer than 4 billion nucleotides
    -C/--color              build a colorspace index
    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting
    -p/--packed             use packed strings internally; slower, uses less mem
    --bmax <int>            max bucket sz for blockwise suffix-array builder
    --bmaxdivn <int>        max bucket sz as divisor of ref len (default: 4)
    --dcv <int>             diff-cover period for blockwise (default: 1024)
    --nodc                  disable diff-cover (algorithm becomes quadratic)
    -r/--noref              don't build .3/.4.ebwt (packed reference) portion
    -3/--justref            just build .3/.4.ebwt (packed reference) portion
    -o/--offrate <int>      SA is sampled every 2^offRate BWT chars (default: 5)
    -t/--ftabchars <int>    # of chars consumed in initial lookup (default: 10)
    --threads <int>         # of threads
    --ntoa                  convert Ns in reference to As
    --seed <int>            seed for random number generator
    -q/--quiet              verbose output (for debugging)
    -h/--help               print detailed description of tool and its options
    --usage                 print this usage message
    --version               print version information and quit
+ ls -l
total 6328
-rw-r--r-- 1 root root  949357 Dec 20 13:35 SRR001665_1.fastq
-rw-r--r-- 1 root root  949357 Dec 20 13:35 SRR001665_2.fastq
-rwxr-xr-x 1 root root 4571848 Dec 20 13:35 contigs_abyss.fasta
-rwxr-xr-x 1 root root      52 Dec 20 13:35 libraries.txt
+ sspace -l libraries.txt -s contigs_abyss.fasta
Your inserted inputs on [SSPACE_Basic v2.1] at Fri Dec 20 13:35:29 2019:
Required inputs: 
	-l = libraries.txt
	-s = contigs_abyss.fasta
	-b = standard_output

Optional inputs:
	-x = 0
	-z = 0
	-k = 5
	-a = 0.7
	-n = 15
	-T = 1
	-p = 0

=>Fri Dec 20 13:35:29 2019: Reading, filtering and converting input sequences of library file initiated
Reading read-pairs lib1.1 @ 0       

------------------------------------------------------------

=>Fri Dec 20 13:35:29 2019: Storing contigs to format for scaffolding

LIBRARY lib1
------------------------------------------------------------

=>Fri Dec 20 13:35:30 2019: Reading contig file

=>Fri Dec 20 13:35:30 2019: Building Bowtie index for contigs

=>Fri Dec 20 13:35:30 2019: Mapping reads to contigs. Reading bowtie output and pairing contigs
# reads processed: 19924
# reads with at least one reported alignment: 1879 (9.43%)
# reads that failed to align: 18045 (90.57%)
Reported 1879 alignments

=>Fri Dec 20 13:35:30 2019: Building scaffolds file

=>Fri Dec 20 13:35:30 2019: Merging contigs and creating FASTA file of scaffolds

------------------------------------------------------------

=>Fri Dec 20 13:35:30 2019: Creating summary file
**************************************************

Process run succesfully on Fri Dec 20 13:35:30 2019 in 0 minutes and 1 seconds

+ [ -s standard_output.final.evidence ]
+ [ -s standard_output.final.scaffolds.fasta ]
+ [ -s standard_output.logfile.txt ]
+ [ -s standard_output.summaryfile.txt ]
autopkgtest [14:35:30]: test example-tests: -----------------------]
autopkgtest [14:35:30]: test example-tests:  - - - - - - - - - - results - - - - - - - - - -
example-tests        PASS
autopkgtest [14:35:30]: @@@@@@@@@@@@@@@@@@@@ summary
example-tests        PASS
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