Your message dated Fri, 09 May 2014 09:19:12 +0000
with message-id <[email protected]>
and subject line Bug#747337: fixed in bedtools 2.19.1-2
has caused the Debian Bug report #747337,
regarding broken autopkgtest: missing dependency, not testing installed
package, test failures
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
747337: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=747337
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: bedtools
Version: 2.19.1-1
User: [email protected]
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
signature.asc
Description: Digital signature
--- End Message ---
--- Begin Message ---
Source: bedtools
Source-Version: 2.19.1-2
We believe that the bug you reported is fixed in the latest version of
bedtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated bedtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 09 May 2014 09:48:05 +0200
Source: bedtools
Binary: bedtools bedtools-test
Architecture: source amd64 all
Version: 2.19.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
bedtools - suite of utilities for comparing genomic features
bedtools-test - test data for the bedtools package
Closes: 747337
Changes:
bedtools (2.19.1-2) unstable; urgency=medium
.
* debian/tests/control: Add "Depends: @, samtools" as advised in
#747337
* debian/tests/upstream: Use content from bedtools-test package to
actually run the test suite
Closes: #747337
* debian/rules: Use dh to easily enable unit tests at package build
time
* Build-Depends: samtools to run the full test suite
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