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
$ 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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