Your message dated Thu, 06 Jul 2023 15:19:57 +0000
with message-id <e1qhqlx-00enw1...@fasolo.debian.org>
and subject line Bug#1039510: fixed in r-cran-pammtools 0.5.91-3
has caused the Debian Bug report #1039510,
regarding mvtnorm breaks r-cran-pammtools autopkgtest: missing Breaks and/or
versioned (test) Depends?
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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--
1039510: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1039510
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: mvtnorm, r-cran-pammtools
Control: found -1 mvtnorm/1.2-2-1
Control: found -1 r-cran-pammtools/0.5.8-1
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of mvtnorm the autopkgtest of r-cran-pammtools
fails in testing when that autopkgtest is run with the binary packages
of mvtnorm from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
mvtnorm from testing 1.2-2-1
r-cran-pammtools from testing 0.5.8-1
versioned deps [0] from testing from unstable
all others from testing from testing
I note that with both versions from unstable the test also passes, which
hints at either a missing *versioned* test dependency in
r-cran-pammtools (if it *only* breaks the test), or missing versioned
Breaks in mvtnorm *and* a missing versioned Depends in r-cran-pammtools
if r-cran-pammtools is really broken with the wrong version of mvtnorm.
I copied some of the output at the bottom of this report.
Currently this regression is blocking both the migration of mvtnorm to
testing [1] and the migration of r-cran-pammtools to testing [2]. Due to
the nature of this issue, I filed this bug report against both packages.
Can you please investigate the situation and reassign the bug to the
right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[0] You can see what packages were added from the second line of the log
file quoted below. The migration software adds source package from
unstable to the list if they are needed to install packages from
mvtnorm/1.2-2-1. I.e. due to versioned dependencies or breaks/conflicts.
[1] https://qa.debian.org/excuses.php?package=mvtnorm
[2] https://qa.debian.org/excuses.php?package=r-cran-pammtools
https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-pammtools/34886689/log.gz
46s BEGIN TEST testthat.R
46s 46s R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
46s Copyright (C) 2023 The R Foundation for Statistical Computing
46s Platform: x86_64-pc-linux-gnu (64-bit)
46s 46s R is free software and comes with ABSOLUTELY NO WARRANTY.
46s You are welcome to redistribute it under certain conditions.
46s Type 'license()' or 'licence()' for distribution details.
46s 46s R is a collaborative project with many contributors.
46s Type 'contributors()' for more information and
46s 'citation()' on how to cite R or R packages in publications.
46s 46s Type 'demo()' for some demos, 'help()' for on-line help, or
46s 'help.start()' for an HTML browser interface to help.
46s Type 'q()' to quit R.
46s 46s > Sys.setenv("R_TESTS" = "") # see
https://github.com/hadley/testthat/issues/86
46s > library(testthat)
46s > library(checkmate)
46s > library(dplyr)
47s 47s Attaching package: ‘dplyr’
47s 47s The following object is masked from ‘package:testthat’:
47s 47s matches
47s 47s The following objects are masked from ‘package:stats’:
47s 47s filter, lag
47s 47s The following objects are masked from ‘package:base’:
47s 47s intersect, setdiff, setequal, union
47s 47s > library(purrr)
47s 47s Attaching package: ‘purrr’
47s 47s The following object is masked from ‘package:testthat’:
47s 47s is_null
47s 47s > library(tidyr)
47s 47s Attaching package: ‘tidyr’
47s 47s The following object is masked from ‘package:testthat’:
47s 47s matches
47s 47s > # library(pammtools)
47s > 47s > test_check("pammtools")
47s Loading required package: pammtools
48s 48s Attaching package: ‘pammtools’
48s 48s The following object is masked from ‘package:stats’:
48s 48s filter
48s 59s [ FAIL 2 | WARN 8 | SKIP 0 | PASS 341 ]
59s 59s ══ Failed tests
════════════════════════════════════════════════════════════════
59s ── Error ('test-cumulative-effect.R:29'): LL helpers and as_ped
produce equivalent LL windows ──
59s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL
requires the use of native symbols
59s Backtrace:
59s ▆
59s 1. ├─pammtools::sim_pexp(...) at test-cumulative-effect.R:29:2
59s 2. │ ├─base::suppressMessages(ped <- ped %>%
left_join(reduce(df2, full_join)))
59s 3. │ │ └─base::withCallingHandlers(...)
59s 4. │ └─ped %>% left_join(reduce(df2, full_join))
59s 5. ├─dplyr::left_join(., reduce(df2, full_join))
59s 6. ├─pammtools:::left_join.ped(., reduce(df2, full_join))
59s 7. │ └─pammtools:::ped_classes(y)
59s 8. │ └─class(ped) %in% ...
59s 9. └─purrr::reduce(df2, full_join)
59s 10. └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
59s 11. ├─dplyr (local) fn(out, elt, ...)
59s 12. └─dplyr:::full_join.data.frame(out, elt, ...)
59s 13. └─dplyr:::join_mutate(...)
59s 14. ├─base::`[<-`(`*tmp*`, new_rows, names(y_key), value
= `<tibble[,2]>`)
59s 15. └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows,
names(y_key), value = `<tibble[,2]>`)
59s 16. └─tibble:::tbl_subassign(x, i, j, value, i_arg,
j_arg, substitute(value))
59s 17. └─tibble:::tbl_subassign_row(xj, i, value, i_arg,
value_arg)
59s 18. ├─base::withCallingHandlers(...)
59s 19. └─tibble:::vectbl_assign(x[[j]], i,
recycled_value[[j]])
59s ── Error ('test-simple-transform.R:50'): Transformation of regular
survival data works ──
59s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL
requires the use of native symbols
59s Backtrace:
59s ▆
59s 1. ├─base::`[<-`(`*tmp*`, 6, "days", value = `<dbl>`) at
test-simple-transform.R:50:2
59s 2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 6, "days", value = `<dbl>`)
at test-simple-transform.R:50:2
59s 3. └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg,
substitute(value))
59s 4. └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg)
59s 5. ├─base::withCallingHandlers(...)
59s 6. └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
59s 59s [ FAIL 2 | WARN 8 | SKIP 0 | PASS 341 ]
59s Error: Test failures
59s Execution halted
60s autopkgtest [14:19:07]: test run-unit-test
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: r-cran-pammtools
Source-Version: 0.5.91-3
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
r-cran-pammtools, 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 1039...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated r-cran-pammtools 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: SHA256
Format: 1.8
Date: Thu, 06 Jul 2023 16:29:59 +0200
Source: r-cran-pammtools
Architecture: source
Version: 0.5.91-3
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1039510
Changes:
r-cran-pammtools (0.5.91-3) unstable; urgency=medium
.
* Artificial versioned Depends r-cran-mvtnorm (>= 1.2-2-1~) to enable
migration to testing
Closes: #1039510
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