0s autopkgtest [10:31:49]: starting date and time: 2024-03-22 10:31:49+0000 0s autopkgtest [10:31:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [10:31:49]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c2_4gh17/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:sphinx --apt-upgrade bedops --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-16.secgroup --name adt-noble-ppc64el-bedops-20240322-103149-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-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/ 197s autopkgtest [10:35:06]: testbed dpkg architecture: ppc64el 197s autopkgtest [10:35:06]: testbed apt version: 2.7.12 197s autopkgtest [10:35:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 198s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 198s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3806 kB] 201s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [54.0 kB] 201s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 201s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 201s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [669 kB] 201s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 201s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 201s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 201s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4090 kB] 201s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 201s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 201s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 204s Fetched 9310 kB in 4s (2635 kB/s) 204s Reading package lists... 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 208s Calculating upgrade... 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s sh: Attempting to set up Debian/Ubuntu apt sources automatically 209s sh: Distribution appears to be Ubuntu 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s eatmydata is already the newest version (131-1). 210s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 211s dbus is already the newest version (1.14.10-4ubuntu1). 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 211s rng-tools-debian is already the newest version (2.4). 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s The following packages will be REMOVED: 212s cloud-init* python3-configobj* python3-debconf* 212s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 212s After this operation, 3256 kB disk space will be freed. 212s (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 ... 70156 files and directories currently installed.) 212s Removing cloud-init (24.1.2-0ubuntu1) ... 213s Removing python3-configobj (5.0.8-3) ... 213s Removing python3-debconf (1.5.86) ... 213s Processing triggers for man-db (2.12.0-3) ... 213s (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 ... 69767 files and directories currently installed.) 213s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 214s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 214s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 214s invoke-rc.d: policy-rc.d denied execution of try-restart. 214s Reading package lists... 215s Building dependency tree... 215s Reading state information... 215s linux-generic is already the newest version (6.8.0-11.11+1). 215s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 215s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 215s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 215s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 218s Reading package lists... 218s Reading package lists... 218s Building dependency tree... 218s Reading state information... 219s Calculating upgrade... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s autopkgtest [10:35:28]: rebooting testbed after setup commands that affected boot 401s autopkgtest [10:38:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 404s autopkgtest [10:38:33]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops 412s Get:1 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-2 (dsc) [2321 B] 412s Get:2 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-2 (tar) [13.5 MB] 412s Get:3 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-2 (diff) [10.6 kB] 413s gpgv: Signature made Sun Mar 10 14:56:15 2024 UTC 413s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 413s gpgv: issuer "emollier@debian.org" 413s gpgv: Can't check signature: No public key 413s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-2.dsc: no acceptable signature found 413s autopkgtest [10:38:42]: testing package bedops version 2.4.41+dfsg-2 413s autopkgtest [10:38:42]: build not needed 418s autopkgtest [10:38:47]: test run-unit-test: preparing testbed 419s Reading package lists... 419s Building dependency tree... 419s Reading state information... 419s Starting pkgProblemResolver with broken count: 0 419s Starting 2 pkgProblemResolver with broken count: 0 419s Done 419s The following additional packages will be installed: 419s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 419s libjs-underscore tcsh 419s Suggested packages: 419s fonts-mathjax-extras fonts-stix libjs-mathjax-doc 419s Recommended packages: 419s javascript-common 419s The following NEW packages will be installed: 419s autopkgtest-satdep bedops bedops-doc fonts-mathjax libjs-jquery 419s libjs-mathjax libjs-sphinxdoc libjs-underscore tcsh 420s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 420s Need to get 32.2 MB/32.2 MB of archives. 420s After this operation, 89.0 MB of additional disk space will be used. 420s Get:1 /tmp/autopkgtest.p57FWy/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 420s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el tcsh ppc64el 6.24.10-3 [524 kB] 420s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el bedops ppc64el 2.4.41+dfsg-2 [1327 kB] 420s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 421s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 421s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 421s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 421s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 422s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el bedops-doc all 2.4.41+dfsg-2 [21.8 MB] 424s Fetched 32.2 MB in 4s (7854 kB/s) 424s Selecting previously unselected package tcsh. 424s (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 ... 69712 files and directories currently installed.) 424s Preparing to unpack .../0-tcsh_6.24.10-3_ppc64el.deb ... 424s Unpacking tcsh (6.24.10-3) ... 424s Selecting previously unselected package bedops. 424s Preparing to unpack .../1-bedops_2.4.41+dfsg-2_ppc64el.deb ... 424s Unpacking bedops (2.4.41+dfsg-2) ... 424s Selecting previously unselected package libjs-jquery. 424s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 424s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 424s Selecting previously unselected package libjs-underscore. 424s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 424s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 424s Selecting previously unselected package libjs-sphinxdoc. 424s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ... 424s Unpacking libjs-sphinxdoc (7.2.6-4) ... 424s Selecting previously unselected package fonts-mathjax. 424s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 424s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 425s Selecting previously unselected package libjs-mathjax. 425s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 425s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 426s Selecting previously unselected package bedops-doc. 426s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-2_all.deb ... 426s Unpacking bedops-doc (2.4.41+dfsg-2) ... 426s Selecting previously unselected package autopkgtest-satdep. 426s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 426s Unpacking autopkgtest-satdep (0) ... 426s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 426s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 426s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 426s Setting up tcsh (6.24.10-3) ... 426s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode 426s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 426s Setting up libjs-sphinxdoc (7.2.6-4) ... 426s Setting up bedops (2.4.41+dfsg-2) ... 426s Setting up bedops-doc (2.4.41+dfsg-2) ... 426s Setting up autopkgtest-satdep (0) ... 426s Processing triggers for debianutils (5.17) ... 426s Processing triggers for man-db (2.12.0-3) ... 429s (Reading database ... 74825 files and directories currently installed.) 429s Removing autopkgtest-satdep (0) ... 430s autopkgtest [10:38:59]: test run-unit-test: [----------------------- 430s Testing bedops 430s Testing binary [bedops] and build type [] 430s make[1]: Entering directory '/tmp/autopkgtest.p57FWy/autopkgtest_tmp/tests/bedops' 430s Missing binary [bedops] for build type [] 430s Writing to [/tmp/tmp.1uymjfxz2U] 430s bedops --version 430s bedops 430s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 430s https://doi.org/10.1093/bioinformatics/bts277 430s version: 2.4.41 (typical) 430s authors: Shane Neph & Scott Kuehn 430s [bedops- --merge] - [Test 001] ...passed! 430s [bedops- --merge] - [Test 002] ...passed! 430s [bedops- --merge] - [Test 003] ...passed! 430s [bedops- --merge] - [Test 004] ...passed! 430s [bedops- --merge] - [Test 005] ...passed! 430s [bedops- --merge] - [Test 006] ...passed! 430s [bedops- --merge] - [Test 007] ...passed! 430s [bedops- --merge] - [Test 008] ...passed! 430s [bedops- --merge] - [Test 009] ...passed! 430s [bedops- --complement] - [Test 001] ...passed! 430s [bedops- --complement] - [Test 002] ...passed! 430s [bedops- --complement] - [Test 003] ...passed! 430s [bedops- --complement] - [Test 004] ...passed! 430s [bedops- --complement] - [Test 005] ...passed! 430s [bedops- --complement] - [Test 006] ...passed! 430s [bedops- --complement] - [Test 007] ...passed! 430s [bedops- --complement] - [Test 008] ...passed! 430s [bedops- --complement] - [Test 009] ...passed! 430s [bedops- --intersection] - [Test 001] ...passed! 430s [bedops- --intersection] - [Test 002] ...passed! 430s [bedops- --intersection] - [Test 003] ...passed! 430s [bedops- --intersection] - [Test 004] ...passed! 430s [bedops- --difference] - [Test 001] ...passed! 430s [bedops- --difference] - [Test 002] ...passed! 430s [bedops- --difference] - [Test 003] ...passed! 430s [bedops- --difference] - [Test 004] ...passed! 430s [bedops- --difference] - [Test 005] ...passed! 430s [bedops- --difference] - [Test 006] ...passed! 430s [bedops- --difference] - [Test 007] ...passed! 430s [bedops- --symdiff] - [Test 001] ...passed! 430s [bedops- --symdiff] - [Test 002] ...passed! 430s [bedops- --symdiff] - [Test 003] ...passed! 430s [bedops- --symdiff] - [Test 004] ...passed! 430s [bedops- --symdiff] - [Test 005] ...passed! 430s [bedops- --element-of] - [Test 001] ...passed! 430s [bedops- --element-of] - [Test 002] ...passed! 430s [bedops- --element-of] - [Test 003] ...passed! 430s [bedops- --element-of] - [Test 004] ...passed! 430s [bedops- --not-element-of] - [Test 001] ...passed! 430s [bedops- --not-element-of] - [Test 002] ...passed! 430s [bedops- --not-element-of] - [Test 003] ...passed! 430s [bedops- --union] - [Test 001] ...passed! 430s [bedops- --union] - [Test 002] ...passed! 430s [bedops- --union] - [Test 003] ...passed! 430s [bedops- --union] - [Test 004] ...passed! 430s [bedops- --union] - [Test 005] ...passed! 430s [bedops- --union] - [Test 006] ...passed! 430s [bedops- --union] - [Test 007] ...passed! 430s [bedops- --union] - [Test 008] ...passed! 430s [bedops- --union] - [Test 009] ...passed! 430s [bedops- --partition] - [Test 001] ...passed! 430s [bedops- --partition] - [Test 002] ...passed! 430s [bedops- --partition] - [Test 003] ...passed! 430s [bedops- --partition] - [Test 004] ...passed! 430s [bedops- --partition] - [Test 005] ...passed! 430s [bedops- --chrom] - [Test 001] ...passed! 430s [bedops- --chrom] - [Test 002] ...passed! 430s [bedops- --chrom] - [Test 003] ...passed! 430s [bedops- --chrom] - [Test 004] ...passed! 430s [bedops- --chop] - [Test 001] ...passed! 430s [bedops- --chop] - [Test 002] ...passed! 430s [bedops- --chop] - [Test 003] ...passed! 430s [bedops- --chop] - [Test 004] ...passed! 431s [bedops- --chop] - [Test 005] ...passed! 431s [bedops- --stdin] - [Test 001] ...passed! 431s [bedops- --named-pipe] - [Test 001] ...passed! 431s [bedops- --ec] - [Test 001] ...passed! (not expected to pass) 431s make[1]: Leaving directory '/tmp/autopkgtest.p57FWy/autopkgtest_tmp/tests/bedops' 431s Testing starch 431s make[1]: *** [Makefile:380: ec] Error 1 431s make: *** [Makefile:10: all] Error 2 431s Testing binary group [starch] and build type [] 431s make[1]: Entering directory '/tmp/autopkgtest.p57FWy/autopkgtest_tmp/tests/starch' 431s Missing binary [unstarch] for build type [] 431s Writing to [/tmp/tmp.rObeSyxrPd] 431s unstarch --version 431s unstarch 431s binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older) 431s [starch-unstarch- --signature] - [Test 001] ...passed! 431s [starch-unstarch- --signature] - [Test 002]starch 431s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 431s ...passed! 431s Missing binary [bedops-starch] for build type [] 431s bedops-starch --version 431s Writing to [/tmp/tmp.rObeSyxrPd] 431s Missing binary [bedmap] for build type [] 431s bedmap --help 431s bedmap 431s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 431s https://doi.org/10.1093/bioinformatics/bts277 431s version: 2.4.41 (typical) 431s authors: Shane Neph & Scott Kuehn 431s 431s USAGE: bedmap [process-flags] [overlap-option] [map-file] 431s Any input file must be sorted per the sort-bed utility. 431s The program accepts BED and Starch file formats. 431s You may use '-' for a BED file to indicate the input comes from stdin. 431s 431s Traverse , while applying on qualified, overlapping elements from 431s . Output is one line for each line in , sent to standard output. There 431s is no limit on the number of operations you can specify to compute in one bedmap call. 431s If is omitted, the given file is treated as both the and . 431s This usage is more efficient than specifying the same file twice. 431s Arguments may be given in any order before the input file(s). 431s 431s Process Flags: 431s -------- 431s --chrom Jump to and process data for given only. 431s --delim Change output delimiter from '|' to between columns (e.g. '\t'). 431s --ec Error check all input files (slower). 431s --faster (advanced) Strong input assumptions are made. Compatible with: 431s --bp-ovr, --range, --fraction-both, and --exact overlap options only. 431s --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. 431s --help Print this message and exit successfully. 431s --min-memory Minimize memory usage (slower). 431s --multidelim Change delimiter of multi-value output columns from ';' to . 431s --prec Change the post-decimal precision of scores to . 0 <= . 431s --sci Use scientific notation for score outputs. 431s --skip-unmapped Print no output for a row with no mapped elements. 431s --sweep-all Ensure is read completely (helps to prevent broken pipes). 431s --unmapped-val Print on unmapped --echo-map* and --min/max-element* operations. 431s The default is to print nothing. 431s --version Print program information. 431s 431s 431s Overlap Options (At most, one may be selected. By default, --bp-ovr 1 is used): 431s -------- 431s --bp-ovr Require bp overlap between elements of input files. 431s --exact First 3 fields from must be identical to 's. 431s --fraction-both Both --fraction-ref and --fraction-map must be true to 431s qualify as overlapping. Expect 0 < val <= 1. 431s --fraction-either Either --fraction-ref or --fraction-map must be true to 431s qualify as overlapping. Expect 0 < val <= 1. 431s --fraction-map The fraction of the element's size from that must overlap 431s the element in . Expect 0 < val <= 1. 431s --fraction-ref The fraction of the element's size from that must overlap 431s an element in . Expect 0 < val <= 1. 431s --range Grab elements within bp of 's element, 431s where 0 <= int. --range 0 is an alias for --bp-ovr 1. 431s 431s 431s Operations: (Any number of operations may be used any number of times.) 431s ---------- 431s SCORE: 431s must have at least 3 columns and 5 columns. 431s 431s --cv The result of --stdev divided by the result of --mean. 431s --kth Generalized median. Report the value, x, such that the fraction 431s of overlapping elements' scores from is less than x, 431s and the fraction 1- of scores is greater than x. 0 < val <= 1. 431s --mad The median absolute deviation of overlapping elements in . 431s Multiply mad score by . 0 < mult, and mult is 1 by default. 431s --max The highest score from overlapping elements in . 431s --max-element A (non-random) highest-scoring and overlapping element in . 431s --max-element-rand A random highest-scoring and overlapping element in . 431s --mean The average score from overlapping elements in . 431s --median The median score from overlapping elements in . 431s --min The lowest score from overlapping elements in . 431s --min-element A (non-random) lowest-scoring and overlapping element in . 431s --min-element-rand A random lowest-scoring and overlapping element in . 431s --stdev The square root of the result of --variance. 431s --sum Accumulated scores from overlapping elements in . 431s --tmean The mean score from overlapping elements in , after 431s ignoring the bottom and top fractions of those scores. 431s 0 <= low <= 1. 0 <= hi <= 1. low+hi <= 1. 431s --variance The variance of scores from overlapping elements in . 431s --wmean Weighted mean, scaled in proportion to the coverage of the 431s element by each overlapping element. 431s 431s ---------- 431s NON-SCORE: 431s must have at least 3 columns. 431s For --echo-map-id/echo-map-id-uniq, must have at least 4 columns. 431s For --echo-map-score, must have at least 5 columns. 431s For all others, requires at least 3 columns. 431s 431s --bases The total number of overlapping bases from . 431s --bases-uniq The number of distinct bases from 's element covered by 431s overlapping elements in . 431s --bases-uniq-f The fraction of distinct bases from 's element covered by 431s overlapping elements in . 431s --count The number of overlapping elements in . 431s --echo Print each line from . 431s --echo-map List all overlapping elements from . 431s --echo-map-id List IDs from all overlapping elements. 431s --echo-map-id-uniq List unique IDs from overlapping elements. 431s --echo-map-range Print genomic range of overlapping elements from . 431s --echo-map-score List scores from overlapping elements. 431s --echo-map-size List the full length of every overlapping element. 431s --echo-overlap-size List lengths of overlaps. 431s --echo-ref-name Print the first 3 fields of using chrom:start-end format. 431s --echo-ref-row-id Print 'id-' followed by the line number of . 431s --echo-ref-size Print the length of each line from . 431s --indicator Print 1 if there exists an overlapping element in , 0 otherwise. 431s 431s 431s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed! 431s Missing binary [bedops-starch] for build type [] 431s Writing to [/tmp/tmp.rObeSyxrPd] 431s bedops-starch --version 431s starch 431s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 431s Generating random intervals... 431s ./generate_random_intervals.sh /tmp/autopkgtest.p57FWy/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.rObeSyxrPd/random_intervals.bed 432s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001] ...passed! 432s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed! 432s Removing [/tmp/tmp.rObeSyxrPd] 432s make[1]: Leaving directory '/tmp/autopkgtest.p57FWy/autopkgtest_tmp/tests/starch' 432s autopkgtest [10:39:01]: test run-unit-test: -----------------------] 433s autopkgtest [10:39:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 433s run-unit-test PASS 433s autopkgtest [10:39:02]: @@@@@@@@@@@@@@@@@@@@ summary 433s run-unit-test PASS 452s Creating nova instance adt-noble-ppc64el-bedops-20240322-103149-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...