0s autopkgtest [14:03:34]: starting date: 2024-03-05 0s autopkgtest [14:03:34]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [14:03:34]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.10n_mh_b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:zlib --apt-upgrade bedops --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=zlib/1:1.3.dfsg-3.1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-13.secgroup --name adt-noble-arm64-bedops-20240305-140334-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 82s autopkgtest [14:04:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 83s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [320 kB] 83s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1791 kB] 83s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [24.5 kB] 83s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 83s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [426 kB] 83s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 83s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 83s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 83s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2077 kB] 83s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 83s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [14.3 kB] 83s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 84s Fetched 4806 kB in 2s (3089 kB/s) 84s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 88s The following packages will be upgraded: 88s zlib1g 88s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 61.7 kB of archives. 88s After this operation, 0 B of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu1 [61.7 kB] 89s Fetched 61.7 kB in 0s (229 kB/s) 89s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74660 files and directories currently installed.) 89s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_arm64.deb ... 89s Unpacking zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 89s Setting up zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) ... 89s Processing triggers for libc-bin (2.39-0ubuntu2) ... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s sh: Attempting to set up Debian/Ubuntu apt sources automatically 92s sh: Distribution appears to be Ubuntu 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s eatmydata is already the newest version (131-1). 94s dbus is already the newest version (1.14.10-4ubuntu1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s rng-tools-debian is already the newest version (2.4). 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s haveged is already the newest version (1.9.14-1ubuntu1). 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s The following packages will be REMOVED: 98s cloud-init* python3-configobj* python3-debconf* 98s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 98s After this operation, 3248 kB disk space will be freed. 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74660 files and directories currently installed.) 98s Removing cloud-init (24.1-0ubuntu1) ... 99s Removing python3-configobj (5.0.8-3) ... 99s Removing python3-debconf (1.5.86) ... 99s Processing triggers for man-db (2.12.0-3) ... 100s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74271 files and directories currently installed.) 100s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 100s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 100s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s linux-generic is already the newest version (6.8.0-11.11+1). 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [14:05:22]: rebooting testbed after setup commands that affected boot 140s autopkgtest [14:05:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 140s autopkgtest [14:05:54]: testbed dpkg architecture: arm64 142s autopkgtest [14:05:56]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops 146s Get:1 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (dsc) [2178 B] 146s Get:2 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (tar) [13.5 MB] 146s Get:3 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (diff) [10.4 kB] 146s gpgv: Signature made Mon Jul 18 09:03:24 2022 UTC 146s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 146s gpgv: issuer "tille@debian.org" 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-1.dsc: no acceptable signature found 147s autopkgtest [14:06:01]: testing package bedops version 2.4.41+dfsg-1 147s autopkgtest [14:06:01]: build not needed 148s autopkgtest [14:06:02]: test run-unit-test: preparing testbed 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s Done 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 157s The following additional packages will be installed: 157s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 157s libjs-underscore tcsh 157s Suggested packages: 157s fonts-mathjax-extras fonts-stix libjs-mathjax-doc 157s Recommended packages: 157s javascript-common 157s The following NEW packages will be installed: 157s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 157s libjs-underscore tcsh 157s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 157s 1 not fully installed or removed. 157s Need to get 32.1 MB of archives. 157s After this operation, 87.1 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 tcsh arm64 6.24.10-3 [444 kB] 158s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 bedops arm64 2.4.41+dfsg-1 [1230 kB] 158s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 158s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 158s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 158s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 158s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 158s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 bedops-doc all 2.4.41+dfsg-1 [21.9 MB] 160s Fetched 32.1 MB in 2s (19.0 MB/s) 160s Selecting previously unselected package tcsh. 160s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74216 files and directories currently installed.) 160s Preparing to unpack .../0-tcsh_6.24.10-3_arm64.deb ... 160s Unpacking tcsh (6.24.10-3) ... 160s Selecting previously unselected package bedops. 160s Preparing to unpack .../1-bedops_2.4.41+dfsg-1_arm64.deb ... 160s Unpacking bedops (2.4.41+dfsg-1) ... 160s Selecting previously unselected package libjs-jquery. 160s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 160s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 160s Selecting previously unselected package libjs-underscore. 160s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 160s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 160s Selecting previously unselected package libjs-sphinxdoc. 160s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ... 160s Unpacking libjs-sphinxdoc (7.2.6-4) ... 160s Selecting previously unselected package fonts-mathjax. 160s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 160s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 160s Selecting previously unselected package libjs-mathjax. 160s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 160s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 161s Selecting previously unselected package bedops-doc. 161s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-1_all.deb ... 161s Unpacking bedops-doc (2.4.41+dfsg-1) ... 162s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 162s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 162s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 162s Setting up tcsh (6.24.10-3) ... 162s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode 162s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 162s Setting up libjs-sphinxdoc (7.2.6-4) ... 162s Setting up bedops (2.4.41+dfsg-1) ... 162s Setting up bedops-doc (2.4.41+dfsg-1) ... 162s Setting up autopkgtest-satdep (0) ... 162s Processing triggers for debianutils (5.16) ... 162s Processing triggers for man-db (2.12.0-3) ... 170s (Reading database ... 79334 files and directories currently installed.) 170s Removing autopkgtest-satdep (0) ... 171s autopkgtest [14:06:25]: test run-unit-test: [----------------------- 171s Testing bedops 171s Testing binary [bedops] and build type [] 171s make[1]: Entering directory '/tmp/autopkgtest.ohbTOg/autopkgtest_tmp/tests/bedops' 171s Missing binary [bedops] for build type [] 171s Writing to [/tmp/tmp.SJi2OaAXjV] 171s bedops --version 171s bedops 171s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 171s https://doi.org/10.1093/bioinformatics/bts277 171s version: 2.4.41 (typical) 171s authors: Shane Neph & Scott Kuehn 171s [bedops- --merge] - [Test 001] ...passed! 171s [bedops- --merge] - [Test 002] ...passed! 172s [bedops- --merge] - [Test 003] ...passed! 172s [bedops- --merge] - [Test 004] ...passed! 172s [bedops- --merge] - [Test 005] ...passed! 172s [bedops- --merge] - [Test 006] ...passed! 172s [bedops- --merge] - [Test 007] ...passed! 172s [bedops- --merge] - [Test 008] ...passed! 172s [bedops- --merge] - [Test 009] ...passed! 172s [bedops- --complement] - [Test 001] ...passed! 172s [bedops- --complement] - [Test 002] ...passed! 172s [bedops- --complement] - [Test 003] ...passed! 172s [bedops- --complement] - [Test 004] ...passed! 172s [bedops- --complement] - [Test 005] ...passed! 172s [bedops- --complement] - [Test 006] ...passed! 172s [bedops- --complement] - [Test 007] ...passed! 172s [bedops- --complement] - [Test 008] ...passed! 172s [bedops- --complement] - [Test 009] ...passed! 172s [bedops- --intersection] - [Test 001] ...passed! 172s [bedops- --intersection] - [Test 002] ...passed! 172s [bedops- --intersection] - [Test 003] ...passed! 172s [bedops- --intersection] - [Test 004] ...passed! 172s [bedops- --difference] - [Test 001] ...passed! 172s [bedops- --difference] - [Test 002] ...passed! 172s [bedops- --difference] - [Test 003] ...passed! 172s [bedops- --difference] - [Test 004] ...passed! 172s [bedops- --difference] - [Test 005] ...passed! 172s [bedops- --difference] - [Test 006] ...passed! 172s [bedops- --difference] - [Test 007] ...passed! 172s [bedops- --symdiff] - [Test 001] ...passed! 172s [bedops- --symdiff] - [Test 002] ...passed! 172s [bedops- --symdiff] - [Test 003] ...passed! 172s [bedops- --symdiff] - [Test 004] ...passed! 172s [bedops- --symdiff] - [Test 005] ...passed! 172s [bedops- --element-of] - [Test 001] ...passed! 172s [bedops- --element-of] - [Test 002] ...passed! 172s [bedops- --element-of] - [Test 003] ...passed! 172s [bedops- --element-of] - [Test 004] ...passed! 172s [bedops- --not-element-of] - [Test 001] ...passed! 172s [bedops- --not-element-of] - [Test 002] ...passed! 172s [bedops- --not-element-of] - [Test 003] ...passed! 172s [bedops- --union] - [Test 001] ...passed! 172s [bedops- --union] - [Test 002] ...passed! 172s [bedops- --union] - [Test 003] ...passed! 172s [bedops- --union] - [Test 004] ...passed! 172s [bedops- --union] - [Test 005] ...passed! 172s [bedops- --union] - [Test 006] ...passed! 172s [bedops- --union] - [Test 007] ...passed! 172s [bedops- --union] - [Test 008] ...passed! 172s [bedops- --union] - [Test 009] ...passed! 172s [bedops- --partition] - [Test 001] ...passed! 172s [bedops- --partition] - [Test 002] ...passed! 172s [bedops- --partition] - [Test 003] ...passed! 172s [bedops- --partition] - [Test 004] ...passed! 172s [bedops- --partition] - [Test 005] ...passed! 173s [bedops- --chrom] - [Test 001] ...passed! 173s [bedops- --chrom] - [Test 002] ...passed! 173s [bedops- --chrom] - [Test 003] ...passed! 173s [bedops- --chrom] - [Test 004] ...passed! 173s [bedops- --chop] - [Test 001] ...passed! 173s [bedops- --chop] - [Test 002] ...passed! 173s [bedops- --chop] - [Test 003] ...passed! 173s [bedops- --chop] - [Test 004] ...passed! 173s [bedops- --chop] - [Test 005] ...passed! 173s [bedops- --stdin] - [Test 001] ...passed! 173s [bedops- --named-pipe] - [Test 001] ...passed! 173s [bedops- --ec] - [Test 001] ...passed! (not expected to pass) 173s make[1]: Leaving directory '/tmp/autopkgtest.ohbTOg/autopkgtest_tmp/tests/bedops' 173s make[1]: *** [Makefile:380: ec] Error 1 173s make: *** [Makefile:10: all] Error 2 173s Testing starch 173s Testing binary group [starch] and build type [] 173s make[1]: Entering directory '/tmp/autopkgtest.ohbTOg/autopkgtest_tmp/tests/starch' 173s Missing binary [unstarch] for build type [] 173s Writing to [/tmp/tmp.fcR87h2ZDi] 173s unstarch --version 173s unstarch 173s binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older) 173s [starch-unstarch- --signature] - [Test 001] ...passed! 173s [starch-unstarch- --signature] - [Test 002] ...passed! 173s Missing binary [bedops-starch] for build type [] 173s bedops-starch --version 173s starch 173s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 173s Writing to [/tmp/tmp.fcR87h2ZDi] 173s Missing binary [bedmap] for build type [] 173s bedmap --help 173s bedmap 173s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 173s https://doi.org/10.1093/bioinformatics/bts277 173s version: 2.4.41 (typical) 173s authors: Shane Neph & Scott Kuehn 173s 173s USAGE: bedmap [process-flags] [overlap-option] [map-file] 173s Any input file must be sorted per the sort-bed utility. 173s The program accepts BED and Starch file formats. 173s You may use '-' for a BED file to indicate the input comes from stdin. 173s 173s Traverse , while applying on qualified, overlapping elements from 173s . Output is one line for each line in , sent to standard output. There 173s is no limit on the number of operations you can specify to compute in one bedmap call. 173s If is omitted, the given file is treated as both the and . 173s This usage is more efficient than specifying the same file twice. 173s Arguments may be given in any order before the input file(s). 173s 173s Process Flags: 173s -------- 173s --chrom Jump to and process data for given only. 173s --delim Change output delimiter from '|' to between columns (e.g. '\t'). 173s --ec Error check all input files (slower). 173s --faster (advanced) Strong input assumptions are made. Compatible with: 173s --bp-ovr, --range, --fraction-both, and --exact overlap options only. 173s --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. 173s --help Print this message and exit successfully. 173s --min-memory Minimize memory usage (slower). 173s --multidelim Change delimiter of multi-value output columns from ';' to . 173s --prec Change the post-decimal precision of scores to . 0 <= . 173s --sci Use scientific notation for score outputs. 173s --skip-unmapped Print no output for a row with no mapped elements. 173s --sweep-all Ensure is read completely (helps to prevent broken pipes). 173s --unmapped-val Print on unmapped --echo-map* and --min/max-element* operations. 173s The default is to print nothing. 173s --version Print program information. 173s 173s 173s Overlap Options (At most, one may be selected. By default, --bp-ovr 1 is used): 173s -------- 173s --bp-ovr Require bp overlap between elements of input files. 173s --exact First 3 fields from must be identical to 's. 173s --fraction-both Both --fraction-ref and --fraction-map must be true to 173s qualify as overlapping. Expect 0 < val <= 1. 173s --fraction-either Either --fraction-ref or --fraction-map must be true to 173s qualify as overlapping. Expect 0 < val <= 1. 173s --fraction-map The fraction of the element's size from that must overlap 173s the element in . Expect 0 < val <= 1. 173s --fraction-ref The fraction of the element's size from that must overlap 173s an element in . Expect 0 < val <= 1. 173s --range Grab elements within bp of 's element, 173s where 0 <= int. --range 0 is an alias for --bp-ovr 1. 173s 173s 173s Operations: (Any number of operations may be used any number of times.) 173s ---------- 173s SCORE: 173s must have at least 3 columns and 5 columns. 173s 173s --cv The result of --stdev divided by the result of --mean. 173s --kth Generalized median. Report the value, x, such that the fraction 173s of overlapping elements' scores from is less than x, 173s and the fraction 1- of scores is greater than x. 0 < val <= 1. 173s --mad The median absolute deviation of overlapping elements in . 173s Multiply mad score by . 0 < mult, and mult is 1 by default. 173s --max The highest score from overlapping elements in . 173s --max-element A (non-random) highest-scoring and overlapping element in . 173s --max-element-rand A random highest-scoring and overlapping element in . 173s --mean The average score from overlapping elements in . 173s --median The median score from overlapping elements in . 173s --min The lowest score from overlapping elements in . 173s --min-element A (non-random) lowest-scoring and overlapping element in . 173s --min-element-rand A random lowest-scoring and overlapping element in . 173s --stdev The square root of the result of --variance. 173s --sum Accumulated scores from overlapping elements in . 173s --tmean The mean score from overlapping elements in , after 173s ignoring the bottom and top fractions of those scores. 173s 0 <= low <= 1. 0 <= hi <= 1. low+hi <= 1. 173s --variance The variance of scores from overlapping elements in . 173s --wmean Weighted mean, scaled in proportion to the coverage of the 173s element by each overlapping element. 173s 173s ---------- 173s NON-SCORE: 173s must have at least 3 columns. 173s For --echo-map-id/echo-map-id-uniq, must have at least 4 columns. 173s For --echo-map-score, must have at least 5 columns. 173s For all others, requires at least 3 columns. 173s 173s --bases The total number of overlapping bases from . 173s --bases-uniq The number of distinct bases from 's element covered by 173s overlapping elements in . 173s --bases-uniq-f The fraction of distinct bases from 's element covered by 173s overlapping elements in . 173s --count The number of overlapping elements in . 173s --echo Print each line from . 173s --echo-map List all overlapping elements from . 173s --echo-map-id List IDs from all overlapping elements. 173s --echo-map-id-uniq List unique IDs from overlapping elements. 173s --echo-map-range Print genomic range of overlapping elements from . 173s --echo-map-score List scores from overlapping elements. 173s --echo-map-size List the full length of every overlapping element. 173s --echo-overlap-size List lengths of overlaps. 173s --echo-ref-name Print the first 3 fields of using chrom:start-end format. 173s --echo-ref-row-id Print 'id-' followed by the line number of . 173s --echo-ref-size Print the length of each line from . 173s --indicator Print 1 if there exists an overlapping element in , 0 otherwise. 173s 173s 173s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed! 173s Missing binary [bedops-starch] for build type [] 173s Writing to [/tmp/tmp.fcR87h2ZDi] 173s bedops-starch --version 173s starch 173s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 173s Generating random intervals... 173s ./generate_random_intervals.sh /tmp/autopkgtest.ohbTOg/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.fcR87h2ZDi/random_intervals.bed 177s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001] ...passed! 177s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed! 177s Removing [/tmp/tmp.fcR87h2ZDi] 177s make[1]: Leaving directory '/tmp/autopkgtest.ohbTOg/autopkgtest_tmp/tests/starch' 177s autopkgtest [14:06:31]: test run-unit-test: -----------------------] 178s autopkgtest [14:06:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 178s run-unit-test PASS 178s autopkgtest [14:06:32]: @@@@@@@@@@@@@@@@@@@@ summary 178s run-unit-test PASS 199s Creating nova instance adt-noble-arm64-bedops-20240305-140334-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240305.img (UUID 1a8a2f7d-2f12-433c-87a5-93dadd986985)...