Your message dated Sun, 14 Jul 2024 18:33:10 +0000
with message-id <[email protected]>
and subject line Bug#1070842: fixed in r-bioc-mutationalpatterns
3.14.0+dfsg-1~0exp
has caused the Debian Bug report #1070842,
regarding r-bioc-mutationalpatterns: autopkgtest regression with r-base 4.4.0
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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--
1070842: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1070842
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: r-bioc-mutationalpatterns
Version: 3.12.0+dfsg-1
Severity: serious
X-Debbugs-Cc: Dirk Eddelbuettel <[email protected]>
User: [email protected]
Usertags: regression
Hi Maintainer
r-bioc-mutationalpatterns' autopkgtest regresses when tested with r-base 4.4.0
[1]. 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/
125s > test_check("MutationalPatterns")
172s [ FAIL 3 | WARN 275 | SKIP 0 | PASS 280 ]
172s
172s ══ Failed tests
════════════════════════════════════════════════════════════════
172s ── Error ('test-fit_to_signatures_bootstrapped.R:12:3'): Output
has correct class ──
172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects
of class NULL
172s Backtrace:
172s ▆
172s 1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at
test-fit_to_signatures_bootstrapped.R:12:3
172s 2. │ └─MutationalPatterns::fit_to_signatures_strict(...)
172s 3. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...)
172s 4. │ └─MutationalPatterns:::.plot_sim_decay(...)
172s 5. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist()
172s 6. │ ├─S4Vectors::isEmpty(sims)
172s 7. │ └─S4Vectors::isEmpty(sims)
172s 8. │ └─base::vapply(x, isEmpty, logical(1L))
172s 9. │ ├─S4Vectors (local) FUN(X[[i]], ...)
172s 10. │ └─S4Vectors (local) FUN(X[[i]], ...)
172s 11. └─base::unlist(.)
172s ── Error ('test-fit_to_signatures_bootstrapped.R:31:3'): Output
is equal to expected ──
172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects
of class NULL
172s Backtrace:
172s ▆
172s 1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at
test-fit_to_signatures_bootstrapped.R:31:3
172s 2. │ └─MutationalPatterns::fit_to_signatures_strict(...)
172s 3. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...)
172s 4. │ └─MutationalPatterns:::.plot_sim_decay(...)
172s 5. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist()
172s 6. │ ├─S4Vectors::isEmpty(sims)
172s 7. │ └─S4Vectors::isEmpty(sims)
172s 8. │ └─base::vapply(x, isEmpty, logical(1L))
172s 9. │ ├─S4Vectors (local) FUN(X[[i]], ...)
172s 10. │ └─S4Vectors (local) FUN(X[[i]], ...)
172s 11. └─base::unlist(.)
172s ── Error ('test-fit_to_signatures_strict.R:11:1'): (code run
outside of `test_that()`) ──
172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects
of class NULL
172s Backtrace:
172s ▆
172s 1. ├─MutationalPatterns::fit_to_signatures_strict(...) at
test-fit_to_signatures_strict.R:11:1
172s 2. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...)
172s 3. │ └─MutationalPatterns:::.plot_sim_decay(...)
172s 4. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist()
172s 5. │ ├─S4Vectors::isEmpty(sims)
172s 6. │ └─S4Vectors::isEmpty(sims)
172s 7. │ └─base::vapply(x, isEmpty, logical(1L))
172s 8. │ ├─S4Vectors (local) FUN(X[[i]], ...)
172s 9. │ └─S4Vectors (local) FUN(X[[i]], ...)
172s 10. └─base::unlist(.)
172s
172s [ FAIL 3 | WARN 275 | SKIP 0 | PASS 280 ]
173s Error: Test failures
173s Execution halted
--- End Message ---
--- Begin Message ---
Source: r-bioc-mutationalpatterns
Source-Version: 3.14.0+dfsg-1~0exp
Done: Michael R. Crusoe <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (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 [email protected])
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Hash: SHA512
Format: 1.8
Date: Thu, 11 Jul 2024 13:42:37 +0200
Source: r-bioc-mutationalpatterns
Architecture: source
Version: 3.14.0+dfsg-1~0exp
Distribution: experimental
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1070842
Changes:
r-bioc-mutationalpatterns (3.14.0+dfsg-1~0exp) experimental; urgency=medium
.
* Team upload
* New upstream version. Closes: #1070842
* d/tests/autopkgtest-pkg-r.conf: skip on 32-bit architectures.
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