[Debian-med-packaging] Bug#747337: broken autopkgtest: missing dependency, not testing installed package, test failures
Martin Pitt
mpitt at debian.org
Wed May 7 15:35:47 UTC 2014
Package: bedtools
Version: 2.19.1-1
User: autopkgtest-devel at 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)
-------------- next part --------------
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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