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:29:259s 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
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