Package: bedtools Version: 2.19.1-1 User: autopkgtest-de...@lists.alioth.debian.org Usertags: autopkgtest
Hello, bedtools' autopkgtest currently fails [1] with a lot of "samtools: command not found" errors. I checked the source, and it seems samtools is only being used in the tests and appears in the documentation, so it primarily needs to become a new test dependency: --- bedtools-2.19.1/debian/tests/control 2014-03-21 05:20:33.000000000 +0100 +++ bedtools-2.19.1/debian/tests/control 2014-05-07 17:29:17.000000000 +0200 @@ -1 +1,2 @@ Tests: upstream +Depends: @, samtools But after fixing that there are still errors: | general.t06...\c | 0a1 | > Error: The requested file (idontexist.bed) could not be opened. Error message: (No such file or directory). Exiting! | fail | general.t07...\c Well, that certainly isn't *supposed* to exist? | ok | general.t08...\c | 0a1 | > chr1 10 21 | fail No idea about that one | map.t46...\c | 1c1,3 | < test-map.sh: line 697: ../../bin/bedtools: No such file or directory | --- | > | > ***** | > ***** ERROR: There are 1 columns given, but there are 2 operations. That indicates that it tries to run bedtools from the build tree, but it should use the installed package. There are a lot more errors, attaching full log for convenience. Thanks, Martin [1] http://ci.debian.net/#package/bedtools -- Martin Pitt | http://www.piware.de Ubuntu Developer (www.ubuntu.com) | Debian Developer (www.debian.org)
adt-run [2014-05-07 17:31:35]: version @devel@ adt-run: $ vserver: adt-virt-qemu /home/martin-scratch/adt-utopic-amd64-cloud.img adt-run: testbed dpkg architecture: amd64 adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds ... adt-run: @@@@@@@@@@@@@@@@@@@@ ubtree ubtree0 adt-run: $ ubtree0-extract: sh -ec <SCRIPT> adt-run: testing package bedtools version 2.19.1-1ubuntu1 adt-run: * <ubtree:ubtree0> build not needed adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds done. adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests ... adt-run: @@@@@@@@@@@@@@@@@@@@ test ubtree ubtree0 adt-run: @@@@@@@@@@ run_tests ... adt-run [2014-05-07 17:31:55]: & ubtree0t-upstream: preparing adt-run: & ubtree0t-upstream: processing dependency @ adt-run: & ubtree0t-upstream: synthesised dependency bedtools adt-run: & ubtree0t-upstream: synthesised dependency bedtools-test adt-run: & ubtree0t-upstream: processing dependency samtools adt-run: & ubtree0t-upstream: literal dependency samtools Reading package lists... Building dependency tree... Reading state information... Correcting dependencies...Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done Done Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done The following extra packages will be installed: bedtools bedtools-test samtools Suggested packages: filo The following NEW packages will be installed: bedtools bedtools-test samtools 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 3459 kB of archives. After this operation, 6314 kB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu/ utopic/universe bedtools amd64 2.19.1-1 [512 kB] Get:2 http://archive.ubuntu.com/ubuntu/ utopic/universe bedtools-test all 2.19.1-1 [2387 kB] Get:3 http://archive.ubuntu.com/ubuntu/ utopic/universe samtools amd64 0.1.19-1 [560 kB] Fetched 3459 kB in 0s (33.2 MB/s) Selecting previously unselected package bedtools. (Reading database ... 56253 files and directories currently installed.) Preparing to unpack .../bedtools_2.19.1-1_amd64.deb ... Unpacking bedtools (2.19.1-1) ... Selecting previously unselected package bedtools-test. Preparing to unpack .../bedtools-test_2.19.1-1_all.deb ... Unpacking bedtools-test (2.19.1-1) ... Selecting previously unselected package samtools. Preparing to unpack .../samtools_0.1.19-1_amd64.deb ... Unpacking samtools (0.1.19-1) ... Processing triggers for man-db (2.6.7.1-1) ... Setting up bedtools (2.19.1-1) ... Setting up bedtools-test (2.19.1-1) ... Setting up samtools (0.1.19-1) ... Setting up adt-satdep (0) ... adt-run [2014-05-07 17:32:04]: & ubtree0t-upstream: running... adt-run [2014-05-07 17:32:07]: & ubtree0t-upstream: finished adt-run: & ubtree0t-upstream: - - - - - - - - - - results - - - - - - - - - -ubtree0t-upstream FAIL non-zero exit status 1 adt-run: & ubtree0t-upstream: - - - - - - - - - - stdout - - - - - - - - - - Performing general tests: general.t01...\c ok general.t02...\c ok general.t03...\c ok general.t04...\c ok general.t05...\c ok general.t06...\c 0a1 > Error: The requested file (idontexist.bed) could not be opened. Error > message: (No such file or directory). Exiting! fail general.t07...\c ok general.t08...\c 0a1 > chr1 10 21 fail Testing bedtools bed12tobed6: bed12tobed6.t1...\c ok bed12tobed6.t2...\c ok bed12tobed6.t3...\c ok bed12tobed6.t4...\c ok bed12tobed6.t5...\c ok Testing bedtools bamtobed: bamtobed.t1...\c ok bamtobed.t2...\c ok bamtobed.t3...\c ok bamtobed.t4...\c ok bamtobed.t5...\c ok bamtobed.t6...\c ok bamtobed.t7...\c ok bamtobed.t8...\c ok bamtobed.t9...\c ok bamtobed.t10...\c ok bamtobed.t9...\c ok bamtobed.t11...\c ok Testing bedtools closest: closest.t1...\c ok closest.t2...\c ok closest.t3...\c ok closest.t4...\c ok closest.t5...\c ok closest.t6...\c ok closest.t7...\c ok closest.t8...\c ok closest.t9...\c ok closest.t10...\c ok closest.t11...\c ok closest.t12...\c ok Testing bedtools cluster: cluster.t1...\c ok cluster.t2...\c ok Testing bedtools coverage: Testing bedtools expand: expand.t1...\c ok expand.t2...\c ok expand.t3...\c ok Testing bedtools flank: flank.t1...\c ok flank.t2...\c ok flank.t3...\c ok flank.t4...\c ok flank.t5...\c ok flank.t6...\c ok flank.t7...\c ok flank.t8...\c ok flank.t9...\c ok flank.t10...\c ok flank.t11...\c ok Testing bedtools genomecov: genomecov.t1...\c ok genomecov.t2...\c ok genomecov.t3...\c ok genomecov.t4...\c ok genomecov.t5...\c ok genomecov.t6...\c ok genomecov.t7...\c ok Testing bedtools getfasta: getfasta.t01...\c ok getfasta.t02...\c ok getfasta.t03...\c ok getfasta.t04...\c ok getfasta.t05...\c ok getfasta.t06...\c ok getfasta.t07...\c ok Testing bedtools intersect: intersect.t01...\c ok intersect.t02...\c ok intersect.t03...\c ok intersect.t04...\c ok intersect.t05...\c ok intersect.t06...\c ok intersect.t07...\c ok intersect.t08...\c ok intersect.t09...\c ok intersect.t10...\c ok intersect.t11...\c ok intersect.t12...\c ok intersect.t13...\c ok intersect.t14...\c ok intersect.t15...\c ok intersect.t16...\c ok intersect.t17...\c ok intersect.t18...\c ok intersect.t19...\c ok intersect.t20...\c ok intersect.t21...\c ok intersect.t22...\c ok intersect.t22.a...\c ok intersect.t22.b...\c ok intersect.t22.c...\c ok intersect.t22.d...\c ok intersect.t22.e...\c ok intersect.t22.f...\c ok intersect.t23...\c ok intersect.t24...\c ok intersect.t25...\c ok intersect.t26...\c ok intersect.t27...\c ok intersect.t28...\c ok intersect.t29...\c ok intersect.t30...\c ok intersect.t31...\c ok intersect.t32...\c ok intersect.t33...\c ok intersect.t34...\c ok intersect.t35...\c ok intersect.t36...\c ok intersect.t37...\c intersect.new.t01...\c ok intersect.new.t02...\c ok intersect.new.t03...\c ok intersect.new.t04...\c ok intersect.new.t05...\c ok intersect.new.t06...\c ok intersect.new.t07...\c ok intersect.new.t08...\c ok intersect.new.t09...\c ok intersect.new.t10...\c ok intersect.new.t11...\c ok intersect.new.t12...\c ok intersect.new.t13...\c ok intersect.new.t14...\c ok intersect.new.t15...\c ok intersect.new.t16...\c ok intersect.new.t17...\c ok intersect.new.t18...\c ok intersect.new.t19...\c ok intersect.new.t20...\c ok intersect.new.t20.b...\c ok intersect.new.t20.c...\c ok intersect.new.t21...\c ok intersect.new.t22...\c ok intersect.new.t23...\c ok intersect.new.t24...\c ok intersect.new.t25...\c ok intersect.new.t26...\c ok intersect.new.t27...\c ok intersect.new.t28...\c ok intersect.new.t29...\c ok intersect.new.t30...\c ok intersect.new.t31...\c ok intersect.new.t32...\c ok intersect.new.t33...\c ok intersect.new.t34...\c ok intersect.new.t35...\c ok intersect.new.t36...\c ok intersect.new.t37...\c ok intersect.new.t38...\c ok intersect.new.t39...\c ok intersect.new.t40...\c ok intersect.new.t41...\c ok intersect.new.t42...\c ok intersect.new.t43...\c ok intersect.new.t44...\c ok intersect.new.t45...\c ok intersect.new.t46...\c ok intersect.new.t47...\c ok intersect.new.t48...\c ok intersect.new.t49...\c ok intersect.new.t50...\c ok intersect.new.t51...\c ok intersect.new.t52...\c ok intersect.new.t53...\c ok intersect.new.t54...\c ok intersect.new.t55...\c ok Testing bedtools jaccard: jaccard.t01...\c ok jaccard.t02...\c ok jaccard.t03...\c ok jaccard.t04...\c ok jaccard.t05...\c ok jaccard.t06...\c ok Testing bedtools map: map.t01...\c ok map.t02...\c ok map.t03...\c ok map.t04...\c ok map.t05...\c ok map.t06...\c ok map.t07...\c ok map.t08...\c ok map.t09...\c ok map.t10...\c ok map.t11...\c ok map.t12...\c ok map.t13...\c ok map.t14...\c ok map.t15...\c ok map.t16...\c ok map.t17...\c ok map.t18...\c ok map.t19...\c ok map.t20...\c ok map.t21...\c ok map.t22..\c ok map.t23..\c ok map.t24..\c ok map.t25..\c ok map.t26..\c ok map.t27..\c ok map.t28..\c ok map.t29..\c ok map.t30..\c ok map.t31..\c ok map.t32..\c ok map.t33..\c ok map.t33..\c ok map.t33..\c ok map.t34..\c ok map.t35..\c ok map.t36..\c ok map.t37..\c ok map.t38..\c ok map.t39..\c ok map.t40..\c ok map.t41..\c ok map.t42..\c ok map.t43..\c ok map.t44...\c ok map.t45...\c ok map.t46...\c 1c1,3 < test-map.sh: line 697: ../../bin/bedtools: No such file or directory --- > > ***** > ***** ERROR: There are 1 columns given, but there are 2 operations. fail map.t47...\c 1c1,3 < test-map.sh: line 711: ../../bin/bedtools: No such file or directory --- > > ***** > ***** ERROR: There are 3 columns given, but there are 2 operations. fail map.t48...\c 1c1,3 < test-map.sh: line 724: ../../bin/bedtools: No such file or directory --- > > ***** > ***** ERROR: Column 1 is not a numeric field for database file values.bed. fail map.t49...\c 0a1,6 > chr1 0 100 65 9 > chr1 100 200 1 7 > chr2 0 100 . . > chr2 100 200 . . > chr3 0 100 6 7 > chr3 100 200 8 23 fail map.t50...\c 0a1,6 > chr1 0 100 13.5 65 9 > chr1 100 200 120 1 7 > chr2 0 100 . . . > chr2 100 200 . . . > chr3 0 100 10 6 7 > chr3 100 200 120 8 23 fail map.t51...\c 0a1,6 > chr1 0 100 12.9167 > chr1 100 200 0 > chr2 0 100 . > chr2 100 200 . > chr3 0 100 76.2222 > chr3 100 200 0.25 fail map.t52...\c 0a1,6 > chr1 0 100 15.5 > chr1 100 200 . > chr2 0 100 . > chr2 100 200 . > chr3 0 100 114.333 > chr3 100 200 0.5 fail Testing bedtools merge: merge.t1...\c ok merge.t2...\c /usr/bin/tac ok merge.t3...\c ok merge.t4...\c ok merge.t5...\c ok merge.t6...\c ok merge.t7...\c ok merge.t8...\c ok merge.t9...\c ok merge.t10...\c ok Testing bedtools multicov: multicov.t1...\c ok multicov.t2...\c ok multicov.t3...\c ok multicov.t4...\c ok multicov.t5...\c ok multicov.t6...\c ok multicov.t7...\c ok multicov.t8...\c ok multicov.t9...\c ok Testing bedtools reldist: reldist.t01...\c 1a2 > 0.00 43424 43424 1.000 fail reldist.t02...\c 1a2,51 > 0.00 164 43408 0.004 > 0.01 551 43408 0.013 > 0.02 598 43408 0.014 > 0.03 637 43408 0.015 > 0.04 793 43408 0.018 > 0.05 688 43408 0.016 > 0.06 874 43408 0.020 > 0.07 765 43408 0.018 > 0.08 685 43408 0.016 > 0.09 929 43408 0.021 > 0.10 876 43408 0.020 > 0.11 959 43408 0.022 > 0.12 860 43408 0.020 > 0.13 851 43408 0.020 > 0.14 903 43408 0.021 > 0.15 893 43408 0.021 > 0.16 883 43408 0.020 > 0.17 828 43408 0.019 > 0.18 917 43408 0.021 > 0.19 875 43408 0.020 > 0.20 897 43408 0.021 > 0.21 986 43408 0.023 > 0.22 903 43408 0.021 > 0.23 944 43408 0.022 > 0.24 904 43408 0.021 > 0.25 867 43408 0.020 > 0.26 943 43408 0.022 > 0.27 933 43408 0.021 > 0.28 1132 43408 0.026 > 0.29 881 43408 0.020 > 0.30 851 43408 0.020 > 0.31 963 43408 0.022 > 0.32 950 43408 0.022 > 0.33 965 43408 0.022 > 0.34 907 43408 0.021 > 0.35 884 43408 0.020 > 0.36 965 43408 0.022 > 0.37 944 43408 0.022 > 0.38 911 43408 0.021 > 0.39 939 43408 0.022 > 0.40 921 43408 0.021 > 0.41 950 43408 0.022 > 0.42 935 43408 0.022 > 0.43 919 43408 0.021 > 0.44 915 43408 0.021 > 0.45 934 43408 0.022 > 0.46 843 43408 0.019 > 0.47 850 43408 0.020 > 0.48 1006 43408 0.023 > 0.49 937 43408 0.022 fail reldist.t03...\c 1a2,52 > 0.00 20629 43422 0.475 > 0.01 2629 43422 0.061 > 0.02 1427 43422 0.033 > 0.03 985 43422 0.023 > 0.04 897 43422 0.021 > 0.05 756 43422 0.017 > 0.06 667 43422 0.015 > 0.07 557 43422 0.013 > 0.08 603 43422 0.014 > 0.09 487 43422 0.011 > 0.10 461 43422 0.011 > 0.11 423 43422 0.010 > 0.12 427 43422 0.010 > 0.13 435 43422 0.010 > 0.14 375 43422 0.009 > 0.15 367 43422 0.008 > 0.16 379 43422 0.009 > 0.17 371 43422 0.009 > 0.18 346 43422 0.008 > 0.19 389 43422 0.009 > 0.20 377 43422 0.009 > 0.21 411 43422 0.009 > 0.22 377 43422 0.009 > 0.23 352 43422 0.008 > 0.24 334 43422 0.008 > 0.25 315 43422 0.007 > 0.26 370 43422 0.009 > 0.27 330 43422 0.008 > 0.28 330 43422 0.008 > 0.29 280 43422 0.006 > 0.30 309 43422 0.007 > 0.31 326 43422 0.008 > 0.32 287 43422 0.007 > 0.33 294 43422 0.007 > 0.34 306 43422 0.007 > 0.35 307 43422 0.007 > 0.36 309 43422 0.007 > 0.37 271 43422 0.006 > 0.38 293 43422 0.007 > 0.39 311 43422 0.007 > 0.40 331 43422 0.008 > 0.41 320 43422 0.007 > 0.42 299 43422 0.007 > 0.43 327 43422 0.008 > 0.44 321 43422 0.007 > 0.45 326 43422 0.008 > 0.46 306 43422 0.007 > 0.47 354 43422 0.008 > 0.48 365 43422 0.008 > 0.49 336 43422 0.008 > 0.50 38 43422 0.001 fail Testing bedtools slop: slop.t1...\c ok slop.t2...\c ok slop.t3...\c ok slop.t4...\c ok slop.t5...\c ok slop.t6...\c ok slop.t7...\c ok slop.t8...\c ok slop.t9...\c ok slop.t10...\c ok slop.t11...\c ok Testing bedtools subtract: subtract.t1...\c ok subtract.t2...\c ok subtract.t3...\c ok subtract.t4...\c ok subtract.t5...\c ok subtract.t6...\c ok subtract.t7...\c ok subtract.t8...\c ok subtract.t9...\c ok subtract.t10...\c ok Testing bedtools sample: sample.t01...\c ok sample.new.t02...\c ok sample.new.t03...\c ok sample.new.t04...\c ok sample.new.t05...\c ok sample.new.t06...\c ok sample.new.t07...\c ok sample.new.t08...\c ok sample.new.t09...\c ok adt-run: & ubtree0t-upstream: - - - - - - - - - - stderr - - - - - - - - - - [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] EOF marker is absent. The input is probably truncated. test-map.sh: line 741: ../../bin/bedtools: No such file or directory test-map.sh: line 758: ../../bin/bedtools: No such file or directory test-map.sh: line 774: ../../bin/bedtools: No such file or directory test-map.sh: line 789: ../../bin/bedtools: No such file or directory adt-run: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests done. qemu: terminating on signal 15 from pid 6227
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