0s autopkgtest [15:58:37]: starting date and time: 2025-10-18 15:58:37+0000 0s autopkgtest [15:58:37]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:58:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2jwfcc5r/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-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-6.secgroup --name adt-resolute-amd64-bedops-20251018-155837-juju-7f2275-prod-proposed-migration-environment-2-e7dc0f2d-2adb-4536-a36c-e981d9da7ded --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-bedops-20251018-155837-juju-7f2275-prod-proposed-migration-environment-2-e7dc0f2d-2adb-4536-a36c-e981d9da7ded from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 30s autopkgtest [15:59:07]: testbed dpkg architecture: amd64 30s autopkgtest [15:59:07]: testbed apt version: 3.1.6ubuntu2 31s autopkgtest [15:59:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [15:59:08]: testbed release detected to be: None 31s autopkgtest [15:59:08]: updating testbed package index (apt update) 31s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 31s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 32s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 32s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 32s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 32s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 32s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 32s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 32s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 32s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 32s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 32s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 32s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 32s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 32s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 32s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 32s Fetched 972 kB in 1s (1638 kB/s) 33s Reading package lists... 33s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 33s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 33s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 33s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 34s Reading package lists... 34s Reading package lists... 34s Building dependency tree... 34s Reading state information... 34s Calculating upgrade... 34s The following packages will be upgraded: 34s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 34s libpython3-stdlib python3 python3-minimal 34s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 34s Need to get 2751 kB of archives. 34s After this operation, 2048 B of additional disk space will be used. 34s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 34s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 34s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 34s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 34s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 34s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 34s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 35s dpkg-preconfigure: unable to re-open stdin: No such file or directory 35s Fetched 2751 kB in 0s (8035 kB/s) 35s (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 ... 78439 files and directories currently installed.) 35s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 35s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 35s Setting up python3-minimal (3.13.7-2) ... 35s (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 ... 78439 files and directories currently installed.) 35s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 35s running python pre-rtupdate hooks for python3.13... 35s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 35s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 35s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 35s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 35s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 35s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 35s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 35s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 35s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 35s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 35s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 35s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 35s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 35s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 35s Setting up apt (3.1.8ubuntu1) ... 36s Setting up python3 (3.13.7-2) ... 36s running python rtupdate hooks for python3.13... 36s running python post-rtupdate hooks for python3.13... 36s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 36s Processing triggers for man-db (2.13.1-1) ... 37s Processing triggers for libc-bin (2.42-0ubuntu3) ... 37s autopkgtest [15:59:14]: upgrading testbed (apt dist-upgrade and autopurge) 37s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Calculating upgrade... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Solving dependencies... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s autopkgtest [15:59:15]: rebooting testbed after setup commands that affected boot 52s autopkgtest [15:59:29]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 54s autopkgtest [15:59:31]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops 56s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (dsc) [2227 B] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (tar) [13.5 MB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (diff) [10.9 kB] 56s gpgv: Signature made Tue Dec 17 17:01:06 2024 UTC 56s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 56s gpgv: issuer "crusoe@debian.org" 56s gpgv: Can't check signature: No public key 56s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-3.dsc: no acceptable signature found 57s autopkgtest [15:59:34]: testing package bedops version 2.4.41+dfsg-3 57s autopkgtest [15:59:34]: build not needed 58s autopkgtest [15:59:35]: test run-unit-test: preparing testbed 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 58s The following NEW packages will be installed: 58s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 58s libjs-underscore tcsh 59s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 32.2 MB of archives. 59s After this operation, 89.3 MB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 tcsh amd64 6.24.13-2 [451 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 bedops amd64 2.4.41+dfsg-3 [1519 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 59s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 59s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 59s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 bedops-doc all 2.4.41+dfsg-3 [21.8 MB] 60s Fetched 32.2 MB in 1s (32.1 MB/s) 60s Selecting previously unselected package tcsh. 60s (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 ... 78439 files and directories currently installed.) 60s Preparing to unpack .../0-tcsh_6.24.13-2_amd64.deb ... 60s Unpacking tcsh (6.24.13-2) ... 60s Selecting previously unselected package bedops. 60s Preparing to unpack .../1-bedops_2.4.41+dfsg-3_amd64.deb ... 60s Unpacking bedops (2.4.41+dfsg-3) ... 60s Selecting previously unselected package libjs-jquery. 60s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 60s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 60s Selecting previously unselected package libjs-underscore. 60s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 60s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 60s Selecting previously unselected package libjs-sphinxdoc. 60s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 60s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 60s Selecting previously unselected package fonts-mathjax. 60s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 60s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 60s Selecting previously unselected package libjs-mathjax. 60s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 60s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 60s Selecting previously unselected package bedops-doc. 60s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-3_all.deb ... 60s Unpacking bedops-doc (2.4.41+dfsg-3) ... 60s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 60s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 60s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 60s Setting up tcsh (6.24.13-2) ... 60s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode 60s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 60s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 60s Setting up bedops (2.4.41+dfsg-3) ... 60s Setting up bedops-doc (2.4.41+dfsg-3) ... 60s Processing triggers for man-db (2.13.1-1) ... 61s Processing triggers for debianutils (5.23.2) ... 62s autopkgtest [15:59:39]: test run-unit-test: [----------------------- 62s Testing bedops 62s Testing binary [bedops] and build type [] 62s make[1]: Entering directory '/tmp/autopkgtest.PARUk6/autopkgtest_tmp/tests/bedops' 62s Missing binary [bedops] for build type [] 62s Writing to [/tmp/tmp.rSb3u5zXEW] 62s bedops --version 62s bedops 62s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 62s https://doi.org/10.1093/bioinformatics/bts277 62s version: 2.4.41 (typical) 62s authors: Shane Neph & Scott Kuehn 62s [bedops- --merge] - [Test 001] ...passed! 62s [bedops- --merge] - [Test 002] ...passed! 62s [bedops- --merge] - [Test 003] ...passed! 62s [bedops- --merge] - [Test 004] ...passed! 62s [bedops- --merge] - [Test 005] ...passed! 62s [bedops- --merge] - [Test 006] ...passed! 62s [bedops- --merge] - [Test 007] ...passed! 62s [bedops- --merge] - [Test 008] ...passed! 62s [bedops- --merge] - [Test 009] ...passed! 62s [bedops- --complement] - [Test 001] ...passed! 62s [bedops- --complement] - [Test 002] ...passed! 62s [bedops- --complement] - [Test 003] ...passed! 62s [bedops- --complement] - [Test 004] ...passed! 62s [bedops- --complement] - [Test 005] ...passed! 62s [bedops- --complement] - [Test 006] ...passed! 62s [bedops- --complement] - [Test 007] ...passed! 62s [bedops- --complement] - [Test 008] ...passed! 62s [bedops- --complement] - [Test 009] ...passed! 62s [bedops- --intersection] - [Test 001] ...passed! 62s [bedops- --intersection] - [Test 002] ...passed! 62s [bedops- --intersection] - [Test 003] ...passed! 62s [bedops- --intersection] - [Test 004] ...passed! 62s [bedops- --difference] - [Test 001] ...passed! 62s [bedops- --difference] - [Test 002] ...passed! 62s [bedops- --difference] - [Test 003] ...passed! 62s [bedops- --difference] - [Test 004] ...passed! 62s [bedops- --difference] - [Test 005] ...passed! 62s [bedops- --difference] - [Test 006] ...passed! 62s [bedops- --difference] - [Test 007] ...passed! 62s [bedops- --symdiff] - [Test 001] ...passed! 62s [bedops- --symdiff] - [Test 002] ...passed! 62s [bedops- --symdiff] - [Test 003] ...passed! 62s [bedops- --symdiff] - [Test 004] ...passed! 62s [bedops- --symdiff] - [Test 005] ...passed! 62s [bedops- --element-of] - [Test 001] ...passed! 62s [bedops- --element-of] - [Test 002] ...passed! 62s [bedops- --element-of] - [Test 003] ...passed! 62s [bedops- --element-of] - [Test 004] ...passed! 62s [bedops- --not-element-of] - [Test 001] ...passed! 62s [bedops- --not-element-of] - [Test 002] ...passed! 62s [bedops- --not-element-of] - [Test 003] ...passed! 62s [bedops- --union] - [Test 001] ...passed! 62s [bedops- --union] - [Test 002] ...passed! 62s [bedops- --union] - [Test 003] ...passed! 62s [bedops- --union] - [Test 004] ...passed! 62s [bedops- --union] - [Test 005] ...passed! 62s [bedops- --union] - [Test 006] ...passed! 62s [bedops- --union] - [Test 007] ...passed! 62s [bedops- --union] - [Test 008] ...passed! 62s [bedops- --union] - [Test 009] ...passed! 62s [bedops- --partition] - [Test 001] ...passed! 62s [bedops- --partition] - [Test 002] ...passed! 62s [bedops- --partition] - [Test 003] ...passed! 62s [bedops- --partition] - [Test 004] ...passed! 62s [bedops- --partition] - [Test 005] ...passed! 62s [bedops- --chrom] - [Test 001] ...passed! 62s [bedops- --chrom] - [Test 002] ...passed! 62s [bedops- --chrom] - [Test 003] ...passed! 62s [bedops- --chrom] - [Test 004] ...passed! 62s [bedops- --chop] - [Test 001] ...passed! 62s [bedops- --chop] - [Test 002] ...passed! 62s [bedops- --chop] - [Test 003] ...passed! 62s [bedops- --chop] - [Test 004] ...passed! 62s [bedops- --chop] - [Test 005] ...passed! 62s [bedops- --stdin] - [Test 001] ...passed! 62s [bedops- --named-pipe] - [Test 001] ...passed! 62s [bedops- --ec] - [Test 001] ...passed! (not expected to pass) 62s make[1]: Leaving directory '/tmp/autopkgtest.PARUk6/autopkgtest_tmp/tests/bedops' 62s Testing starch 62s make[1]: *** [Makefile:380: ec] Error 1 62s make: *** [Makefile:10: all] Error 2 62s Testing binary group [starch] and build type [] 62s make[1]: Entering directory '/tmp/autopkgtest.PARUk6/autopkgtest_tmp/tests/starch' 62s Missing binary [unstarch] for build type [] 62s Writing to [/tmp/tmp.Vn33FSLXVM] 62s unstarch --version 62s unstarch 62s binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older) 62s [starch-unstarch- --signature] - [Test 001] ...passed! 62s [starch-unstarch- --signature] - [Test 002] ...passed! 62s Missing binary [bedops-starch] for build type [] 62s bedops-starch --version 62s starch 62s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 62s Writing to [/tmp/tmp.Vn33FSLXVM] 62s Missing binary [bedmap] for build type [] 62s bedmap --help 62s bedmap 62s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 62s https://doi.org/10.1093/bioinformatics/bts277 62s version: 2.4.41 (typical) 62s authors: Shane Neph & Scott Kuehn 62s 62s USAGE: bedmap [process-flags] [overlap-option] [map-file] 62s Any input file must be sorted per the sort-bed utility. 62s The program accepts BED and Starch file formats. 62s You may use '-' for a BED file to indicate the input comes from stdin. 62s 62s Traverse , while applying on qualified, overlapping elements from 62s . Output is one line for each line in , sent to standard output. There 62s is no limit on the number of operations you can specify to compute in one bedmap call. 62s If is omitted, the given file is treated as both the and . 62s This usage is more efficient than specifying the same file twice. 62s Arguments may be given in any order before the input file(s). 62s 62s Process Flags: 62s -------- 62s --chrom Jump to and process data for given only. 62s --delim Change output delimiter from '|' to between columns (e.g. '\t'). 62s --ec Error check all input files (slower). 62s --faster (advanced) Strong input assumptions are made. Compatible with: 62s --bp-ovr, --range, --fraction-both, and --exact overlap options only. 62s --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. 62s --help Print this message and exit successfully. 62s --min-memory Minimize memory usage (slower). 62s --multidelim Change delimiter of multi-value output columns from ';' to . 62s --prec Change the post-decimal precision of scores to . 0 <= . 62s --sci Use scientific notation for score outputs. 62s --skip-unmapped Print no output for a row with no mapped elements. 62s --sweep-all Ensure is read completely (helps to prevent broken pipes). 62s --unmapped-val Print on unmapped --echo-map* and --min/max-element* operations. 62s The default is to print nothing. 62s --version Print program information. 62s 62s 62s Overlap Options (At most, one may be selected. By default, --bp-ovr 1 is used): 62s -------- 62s --bp-ovr Require bp overlap between elements of input files. 62s --exact First 3 fields from must be identical to 's. 62s --fraction-both Both --fraction-ref and --fraction-map must be true to 62s qualify as overlapping. Expect 0 < val <= 1. 62s --fraction-either Either --fraction-ref or --fraction-map must be true to 62s qualify as overlapping. Expect 0 < val <= 1. 62s --fraction-map The fraction of the element's size from that must overlap 62s the element in . Expect 0 < val <= 1. 62s --fraction-ref The fraction of the element's size from that must overlap 62s an element in . Expect 0 < val <= 1. 62s --range Grab elements within bp of 's element, 62s where 0 <= int. --range 0 is an alias for --bp-ovr 1. 62s 62s 62s Operations: (Any number of operations may be used any number of times.) 62s ---------- 62s SCORE: 62s must have at least 3 columns and 5 columns. 62s 62s --cv The result of --stdev divided by the result of --mean. 62s --kth Generalized median. Report the value, x, such that the fraction 62s of overlapping elements' scores from is less than x, 62s and the fraction 1- of scores is greater than x. 0 < val <= 1. 62s --mad The median absolute deviation of overlapping elements in . 62s Multiply mad score by . 0 < mult, and mult is 1 by default. 62s --max The highest score from overlapping elements in . 62s --max-element A (non-random) highest-scoring and overlapping element in . 62s --max-element-rand A random highest-scoring and overlapping element in . 62s --mean The average score from overlapping elements in . 62s --median The median score from overlapping elements in . 62s --min The lowest score from overlapping elements in . 62s --min-element A (non-random) lowest-scoring and overlapping element in . 62s --min-element-rand A random lowest-scoring and overlapping element in . 62s --stdev The square root of the result of --variance. 62s --sum Accumulated scores from overlapping elements in . 62s --tmean The mean score from overlapping elements in , after 62s ignoring the bottom and top fractions of those scores. 62s 0 <= low <= 1. 0 <= hi <= 1. low+hi <= 1. 62s --variance The variance of scores from overlapping elements in . 62s --wmean Weighted mean, scaled in proportion to the coverage of the 62s element by each overlapping element. 62s 62s ---------- 62s NON-SCORE: 62s must have at least 3 columns. 62s For --echo-map-id/echo-map-id-uniq, must have at least 4 columns. 62s For --echo-map-score, must have at least 5 columns. 62s For all others, requires at least 3 columns. 62s 62s --bases The total number of overlapping bases from . 62s --bases-uniq The number of distinct bases from 's element covered by 62s overlapping elements in . 62s --bases-uniq-f The fraction of distinct bases from 's element covered by 62s overlapping elements in . 62s --count The number of overlapping elements in . 62s --echo Print each line from . 62s --echo-map List all overlapping elements from . 62s --echo-map-id List IDs from all overlapping elements. 62s --echo-map-id-uniq List unique IDs from overlapping elements. 62s --echo-map-range Print genomic range of overlapping elements from . 62s --echo-map-score List scores from overlapping elements. 62s --echo-map-size List the full length of every overlapping element. 62s --echo-overlap-size List lengths of overlaps. 62s --echo-ref-name Print the first 3 fields of using chrom:start-end format. 62s --echo-ref-row-id Print 'id-' followed by the line number of . 62s --echo-ref-size Print the length of each line from . 62s --indicator Print 1 if there exists an overlapping element in , 0 otherwise. 62s 62s 62s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed! 62s Missing binary [bedops-starch] for build type [] 62s Writing to [/tmp/tmp.Vn33FSLXVM] 62s bedops-starch --version 62s starch 62s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 62s Generating random intervals... 62s ./generate_random_intervals.sh /tmp/autopkgtest.PARUk6/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.Vn33FSLXVM/random_intervals.bed 63s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001] ...passed! 63s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed! 63s Removing [/tmp/tmp.Vn33FSLXVM] 63s make[1]: Leaving directory '/tmp/autopkgtest.PARUk6/autopkgtest_tmp/tests/starch' 63s autopkgtest [15:59:40]: test run-unit-test: -----------------------] 64s run-unit-test PASS 64s autopkgtest [15:59:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 64s autopkgtest [15:59:41]: @@@@@@@@@@@@@@@@@@@@ summary 64s run-unit-test PASS