Your message dated Tue, 26 May 2020 17:48:40 +0000
with message-id <e1jddgu-000638...@fasolo.debian.org>
and subject line Bug#961572: fixed in r-bioc-mutationalpatterns 2.0.0-2
has caused the Debian Bug report #961572,
regarding r-bioc-mutationalpatterns: autopkgtest regression
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.
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--
961572: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961572
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: r-bioc-mutationalpatterns
Version: 2.0.0-1
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: regression
Hi Maintainer
Since the upload of 2.0.0-1, r-bioc-mutationalpatterns has been
failing its own autopkgtests [1]. This now prevents the migration of
r-base.
I've copied what I hope is the relevant part of the log below.
Regards
Graham
[1] https://ci.debian.net/packages/r/r-bioc-mutationalpatterns/testing/amd64/
> test_check("MutationalPatterns")
── 1. Error: (unknown) (@test_mut_matrix_stranded.R#3) ────────────────────────
there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Backtrace:
1. base::library("TxDb.Hsapiens.UCSC.hg19.knownGene")
── 2. Error: (unknown) (@test_mut_matrix.R#5) ─────────────────────────────────
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
1. base::library(ref_genome, character.only = TRUE)
── 3. Error: (unknown) (@test_read_vcfs_as_granges.R#5) ───────────────────────
there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Backtrace:
1. base::library(ref_genome, character.only = TRUE)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
1. Error: (unknown) (@test_mut_matrix_stranded.R#3)
2. Error: (unknown) (@test_mut_matrix.R#5)
3. Error: (unknown) (@test_read_vcfs_as_granges.R#5)
Error: testthat unit tests failed
Execution halted
autopkgtest [09:41:10]: test pkg-r-autopkgtest: -----------------------]
autopkgtest [09:41:10]: test pkg-r-autopkgtest: - - - - - - - - - -
results - - - - - - - - - -
pkg-r-autopkgtest FAIL non-zero exit status 1
--- End Message ---
--- Begin Message ---
Source: r-bioc-mutationalpatterns
Source-Version: 2.0.0-2
Done: =?utf-8?q?Dylan_A=C3=AFssi?= <dai...@debian.org>
We believe that the bug you reported is fixed in the latest version of
r-bioc-mutationalpatterns, 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 961...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dylan Aïssi <dai...@debian.org> (supplier of updated r-bioc-mutationalpatterns
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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 26 May 2020 19:12:49 +0200
Source: r-bioc-mutationalpatterns
Architecture: source
Version: 2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Dylan Aïssi <dai...@debian.org>
Closes: 961572
Changes:
r-bioc-mutationalpatterns (2.0.0-2) unstable; urgency=medium
.
* Team upload.
* Add patch to skip tests requiring packages not in Debian (Closes: #961572)
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