0s autopkgtest [15:47:27]: starting date and time: 2025-10-18 15:47:27+0000 0s autopkgtest [15:47:27]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:47:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3i_k5lsk/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade bedops --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-3.secgroup --name adt-resolute-ppc64el-bedops-20251018-154726-juju-7f2275-prod-proposed-migration-environment-15-df578bd2-fcb0-478f-878c-11c974cdee3d --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-bedops-20251018-154726-juju-7f2275-prod-proposed-migration-environment-15-df578bd2-fcb0-478f-878c-11c974cdee3d from image adt/ubuntu-resolute-ppc64el-server-20251018.img (UUID 746a0a80-14f1-4bf7-89b6-cbb5ab236a4e)... 58s autopkgtest [15:48:25]: testbed dpkg architecture: ppc64el 58s autopkgtest [15:48:25]: testbed apt version: 3.1.8ubuntu1 59s autopkgtest [15:48:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 59s autopkgtest [15:48:26]: testbed release detected to be: None 59s autopkgtest [15:48:26]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 61s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 61s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 61s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [73.4 kB] 61s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 61s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [222 kB] 61s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [3808 B] 61s Fetched 777 kB in 1s (784 kB/s) 61s Reading package lists... 62s Failed to check for VM: Permission denied 62s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Reading package lists... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s The following packages will be upgraded: 63s gir1.2-girepository-2.0 libgirepository-1.0-1 libpython3-stdlib python3 63s python3-minimal 64s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 185 kB of archives. 64s After this operation, 2048 B of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 64s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgirepository-1.0-1 ppc64el 1.86.0-6 [97.4 kB] 64s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el gir1.2-girepository-2.0 ppc64el 1.86.0-6 [25.3 kB] 64s dpkg-preconfigure: unable to re-open stdin: No such file or directory 64s Fetched 185 kB in 0s (370 kB/s) 65s (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 ... 76461 files and directories currently installed.) 65s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 65s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 65s Setting up python3-minimal (3.13.7-2) ... 65s (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 ... 76461 files and directories currently installed.) 65s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 65s running python pre-rtupdate hooks for python3.13... 65s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 65s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 65s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 65s Preparing to unpack .../libgirepository-1.0-1_1.86.0-6_ppc64el.deb ... 65s Unpacking libgirepository-1.0-1:ppc64el (1.86.0-6) over (1.84.0-1) ... 65s Preparing to unpack .../gir1.2-girepository-2.0_1.86.0-6_ppc64el.deb ... 65s Unpacking gir1.2-girepository-2.0:ppc64el (1.86.0-6) over (1.84.0-1) ... 65s Setting up libgirepository-1.0-1:ppc64el (1.86.0-6) ... 65s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 65s Setting up python3 (3.13.7-2) ... 65s running python rtupdate hooks for python3.13... 65s running python post-rtupdate hooks for python3.13... 66s Setting up gir1.2-girepository-2.0:ppc64el (1.86.0-6) ... 66s Processing triggers for man-db (2.13.1-1) ... 67s Processing triggers for libc-bin (2.42-0ubuntu3) ... 67s autopkgtest [15:48:34]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [15:48:38]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 71s autopkgtest [15:48:38]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops 74s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (dsc) [2227 B] 74s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (tar) [13.5 MB] 74s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (diff) [10.9 kB] 74s gpgv: Signature made Tue Dec 17 17:01:06 2024 UTC 74s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 74s gpgv: issuer "crusoe@debian.org" 74s gpgv: Can't check signature: No public key 74s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-3.dsc: no acceptable signature found 75s autopkgtest [15:48:42]: testing package bedops version 2.4.41+dfsg-3 75s autopkgtest [15:48:42]: build not needed 79s autopkgtest [15:48:46]: test run-unit-test: preparing testbed 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Solving dependencies... 79s The following NEW packages will be installed: 79s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 79s libjs-underscore tcsh 79s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 32.1 MB of archives. 79s After this operation, 88.9 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tcsh ppc64el 6.24.13-2 [532 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bedops ppc64el 2.4.41+dfsg-3 [1363 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bedops-doc all 2.4.41+dfsg-3 [21.8 MB] 81s Fetched 32.1 MB in 2s (14.4 MB/s) 81s Selecting previously unselected package tcsh. 82s (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 ... 76461 files and directories currently installed.) 82s Preparing to unpack .../0-tcsh_6.24.13-2_ppc64el.deb ... 82s Unpacking tcsh (6.24.13-2) ... 82s Selecting previously unselected package bedops. 82s Preparing to unpack .../1-bedops_2.4.41+dfsg-3_ppc64el.deb ... 82s Unpacking bedops (2.4.41+dfsg-3) ... 82s Selecting previously unselected package libjs-jquery. 82s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 82s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 82s Selecting previously unselected package libjs-underscore. 82s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 82s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 82s Selecting previously unselected package libjs-sphinxdoc. 82s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 82s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 82s Selecting previously unselected package fonts-mathjax. 82s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 82s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 82s Selecting previously unselected package libjs-mathjax. 82s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 82s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 82s Selecting previously unselected package bedops-doc. 82s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-3_all.deb ... 82s Unpacking bedops-doc (2.4.41+dfsg-3) ... 83s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 83s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 83s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 83s Setting up tcsh (6.24.13-2) ... 83s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode 83s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 83s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 83s Setting up bedops (2.4.41+dfsg-3) ... 83s Setting up bedops-doc (2.4.41+dfsg-3) ... 83s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for debianutils (5.23.2) ... 84s autopkgtest [15:48:51]: test run-unit-test: [----------------------- 84s Testing bedops 84s Testing binary [bedops] and build type [] 84s make[1]: Entering directory '/tmp/autopkgtest.c3DGTq/autopkgtest_tmp/tests/bedops' 84s Missing binary [bedops] for build type [] 84s Writing to [/tmp/tmp.nHJVvqD586] 84s bedops --version 84s bedops 84s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 84s https://doi.org/10.1093/bioinformatics/bts277 84s version: 2.4.41 (typical) 84s authors: Shane Neph & Scott Kuehn 84s [bedops- --merge] - [Test 001] ...passed! 84s [bedops- --merge] - [Test 002] ...passed! 84s [bedops- --merge] - [Test 003] ...passed! 84s [bedops- --merge] - [Test 004] ...passed! 84s [bedops- --merge] - [Test 005] ...passed! 84s [bedops- --merge] - [Test 006] ...passed! 84s [bedops- --merge] - [Test 007] ...passed! 84s [bedops- --merge] - [Test 008] ...passed! 84s [bedops- --merge] - [Test 009] ...passed! 84s [bedops- --complement] - [Test 001] ...passed! 84s [bedops- --complement] - [Test 002] ...passed! 84s [bedops- --complement] - [Test 003] ...passed! 84s [bedops- --complement] - [Test 004] ...passed! 84s [bedops- --complement] - [Test 005] ...passed! 84s [bedops- --complement] - [Test 006] ...passed! 84s [bedops- --complement] - [Test 007] ...passed! 84s [bedops- --complement] - [Test 008] ...passed! 84s [bedops- --complement] - [Test 009] ...passed! 84s [bedops- --intersection] - [Test 001] ...passed! 84s [bedops- --intersection] - [Test 002] ...passed! 84s [bedops- --intersection] - [Test 003] ...passed! 84s [bedops- --intersection] - [Test 004] ...passed! 84s [bedops- --difference] - [Test 001] ...passed! 84s [bedops- --difference] - [Test 002] ...passed! 84s [bedops- --difference] - [Test 003] ...passed! 84s [bedops- --difference] - [Test 004] ...passed! 84s [bedops- --difference] - [Test 005] ...passed! 84s [bedops- --difference] - [Test 006] ...passed! 84s [bedops- --difference] - [Test 007] ...passed! 84s [bedops- --symdiff] - [Test 001] ...passed! 84s [bedops- --symdiff] - [Test 002] ...passed! 84s [bedops- --symdiff] - [Test 003] ...passed! 84s [bedops- --symdiff] - [Test 004] ...passed! 84s [bedops- --symdiff] - [Test 005] ...passed! 84s [bedops- --element-of] - [Test 001] ...passed! 84s [bedops- --element-of] - [Test 002] ...passed! 84s [bedops- --element-of] - [Test 003] ...passed! 85s [bedops- --element-of] - [Test 004] ...passed! 85s [bedops- --not-element-of] - [Test 001] ...passed! 85s [bedops- --not-element-of] - [Test 002] ...passed! 85s [bedops- --not-element-of] - [Test 003] ...passed! 85s [bedops- --union] - [Test 001] ...passed! 85s [bedops- --union] - [Test 002] ...passed! 85s [bedops- --union] - [Test 003] ...passed! 85s [bedops- --union] - [Test 004] ...passed! 85s [bedops- --union] - [Test 005] ...passed! 85s [bedops- --union] - [Test 006] ...passed! 85s [bedops- --union] - [Test 007] ...passed! 85s [bedops- --union] - [Test 008] ...passed! 85s [bedops- --union] - [Test 009] ...passed! 85s [bedops- --partition] - [Test 001] ...passed! 85s [bedops- --partition] - [Test 002] ...passed! 85s [bedops- --partition] - [Test 003] ...passed! 85s [bedops- --partition] - [Test 004] ...passed! 85s [bedops- --partition] - [Test 005] ...passed! 85s [bedops- --chrom] - [Test 001] ...passed! 85s [bedops- --chrom] - [Test 002] ...passed! 85s [bedops- --chrom] - [Test 003] ...passed! 85s [bedops- --chrom] - [Test 004] ...passed! 85s [bedops- --chop] - [Test 001] ...passed! 85s [bedops- --chop] - [Test 002] ...passed! 85s [bedops- --chop] - [Test 003] ...passed! 85s [bedops- --chop] - [Test 004] ...passed! 85s [bedops- --chop] - [Test 005] ...passed! 85s [bedops- --stdin] - [Test 001] ...passed! 85s [bedops- --named-pipe] - [Test 001] ...passed! 85s [bedops- --ec] - [Test 001] ...passed! (not expected to pass) 85s make[1]: Leaving directory '/tmp/autopkgtest.c3DGTq/autopkgtest_tmp/tests/bedops' 85s make[1]: *** [Makefile:380: ec] Error 1 85s make: *** [Makefile:10: all] Error 2 85s Testing starch 85s Testing binary group [starch] and build type [] 85s make[1]: Entering directory '/tmp/autopkgtest.c3DGTq/autopkgtest_tmp/tests/starch' 85s Missing binary [unstarch] for build type [] 85s Writing to [/tmp/tmp.Xhd2LRLNcn] 85s unstarch --version 85s unstarch 85s binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older) 85s [starch-unstarch- --signature] - [Test 001] ...passed! 85s [starch-unstarch- --signature] - [Test 002] ...passed! 85s Missing binary [bedops-starch] for build type [] 85s bedops-starch --version 85s starch 85s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 85s Writing to [/tmp/tmp.Xhd2LRLNcn] 85s Missing binary [bedmap] for build type [] 85s bedmap --help 85s bedmap 85s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 85s https://doi.org/10.1093/bioinformatics/bts277 85s version: 2.4.41 (typical) 85s authors: Shane Neph & Scott Kuehn 85s 85s USAGE: bedmap [process-flags] [overlap-option] [map-file] 85s Any input file must be sorted per the sort-bed utility. 85s The program accepts BED and Starch file formats. 85s You may use '-' for a BED file to indicate the input comes from stdin. 85s 85s Traverse , while applying on qualified, overlapping elements from 85s . Output is one line for each line in , sent to standard output. There 85s is no limit on the number of operations you can specify to compute in one bedmap call. 85s If is omitted, the given file is treated as both the and . 85s This usage is more efficient than specifying the same file twice. 85s Arguments may be given in any order before the input file(s). 85s 85s Process Flags: 85s -------- 85s --chrom Jump to and process data for given only. 85s --delim Change output delimiter from '|' to between columns (e.g. '\t'). 85s --ec Error check all input files (slower). 85s --faster (advanced) Strong input assumptions are made. Compatible with: 85s --bp-ovr, --range, --fraction-both, and --exact overlap options only. 85s --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. 85s --help Print this message and exit successfully. 85s --min-memory Minimize memory usage (slower). 85s --multidelim Change delimiter of multi-value output columns from ';' to . 85s --prec Change the post-decimal precision of scores to . 0 <= . 85s --sci Use scientific notation for score outputs. 85s --skip-unmapped Print no output for a row with no mapped elements. 85s --sweep-all Ensure is read completely (helps to prevent broken pipes). 85s --unmapped-val Print on unmapped --echo-map* and --min/max-element* operations. 85s The default is to print nothing. 85s --version Print program information. 85s 85s 85s Overlap Options (At most, one may be selected. By default, --bp-ovr 1 is used): 85s -------- 85s --bp-ovr Require bp overlap between elements of input files. 85s --exact First 3 fields from must be identical to 's. 85s --fraction-both Both --fraction-ref and --fraction-map must be true to 85s qualify as overlapping. Expect 0 < val <= 1. 85s --fraction-either Either --fraction-ref or --fraction-map must be true to 85s qualify as overlapping. Expect 0 < val <= 1. 85s --fraction-map The fraction of the element's size from that must overlap 85s the element in . Expect 0 < val <= 1. 85s --fraction-ref The fraction of the element's size from that must overlap 85s an element in . Expect 0 < val <= 1. 85s --range Grab elements within bp of 's element, 85s where 0 <= int. --range 0 is an alias for --bp-ovr 1. 85s 85s 85s Operations: (Any number of operations may be used any number of times.) 85s ---------- 85s SCORE: 85s must have at least 3 columns and 5 columns. 85s 85s --cv The result of --stdev divided by the result of --mean. 85s --kth Generalized median. Report the value, x, such that the fraction 85s of overlapping elements' scores from is less than x, 85s and the fraction 1- of scores is greater than x. 0 < val <= 1. 85s --mad The median absolute deviation of overlapping elements in . 85s Multiply mad score by . 0 < mult, and mult is 1 by default. 85s --max The highest score from overlapping elements in . 85s --max-element A (non-random) highest-scoring and overlapping element in . 85s --max-element-rand A random highest-scoring and overlapping element in . 85s --mean The average score from overlapping elements in . 85s --median The median score from overlapping elements in . 85s --min The lowest score from overlapping elements in . 85s --min-element A (non-random) lowest-scoring and overlapping element in . 85s --min-element-rand A random lowest-scoring and overlapping element in . 85s --stdev The square root of the result of --variance. 85s --sum Accumulated scores from overlapping elements in . 85s --tmean The mean score from overlapping elements in , after 85s ignoring the bottom and top fractions of those scores. 85s 0 <= low <= 1. 0 <= hi <= 1. low+hi <= 1. 85s --variance The variance of scores from overlapping elements in . 85s --wmean Weighted mean, scaled in proportion to the coverage of the 85s element by each overlapping element. 85s 85s ---------- 85s NON-SCORE: 85s must have at least 3 columns. 85s For --echo-map-id/echo-map-id-uniq, must have at least 4 columns. 85s For --echo-map-score, must have at least 5 columns. 85s For all others, requires at least 3 columns. 85s 85s --bases The total number of overlapping bases from . 85s --bases-uniq The number of distinct bases from 's element covered by 85s overlapping elements in . 85s --bases-uniq-f The fraction of distinct bases from 's element covered by 85s overlapping elements in . 85s --count The number of overlapping elements in . 85s --echo Print each line from . 85s --echo-map List all overlapping elements from . 85s --echo-map-id List IDs from all overlapping elements. 85s --echo-map-id-uniq List unique IDs from overlapping elements. 85s --echo-map-range Print genomic range of overlapping elements from . 85s --echo-map-score List scores from overlapping elements. 85s --echo-map-size List the full length of every overlapping element. 85s --echo-overlap-size List lengths of overlaps. 85s --echo-ref-name Print the first 3 fields of using chrom:start-end format. 85s --echo-ref-row-id Print 'id-' followed by the line number of . 85s --echo-ref-size Print the length of each line from . 85s --indicator Print 1 if there exists an overlapping element in , 0 otherwise. 85s 85s 85s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed! 85s Missing binary [bedops-starch] for build type [] 85s Writing to [/tmp/tmp.Xhd2LRLNcn] 85s bedops-starch --version 85s starch 85s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 85s Generating random intervals... 85s ./generate_random_intervals.sh /tmp/autopkgtest.c3DGTq/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.Xhd2LRLNcn/random_intervals.bed 87s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001]autopkgtest [15:48:53]: test run-unit-test: -----------------------] 87s ...passed! 87s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed! 87s Removing [/tmp/tmp.Xhd2LRLNcn] 87s make[1]: Leaving directory '/tmp/autopkgtest.c3DGTq/autopkgtest_tmp/tests/starch' 87s autopkgtest [15:48:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 87s run-unit-test PASS 88s autopkgtest [15:48:55]: @@@@@@@@@@@@@@@@@@@@ summary 88s run-unit-test PASS