Re: Package rpact has issues in autopkgtest
Hi Friedrich,
thanks a lot for the super-speedy and helpful response
Andreas.
On Tue, Sep 21, 2021 at 12:14:15PM +0200, Friedrich Pahlke (RPACT) wrote:
> Hi Andreas,
>
> Thank you for the problem report.
>
> We first heard of this issue a week ago. The problem occurs if you enable fancy quotes.
> Please execute
> options(useFancyQuotes = FALSE)
> before you run the tests.
>
> In the next version of rpact we will handle that inside the test files.
>
> Best regards,
>
> Friedrich
>
>
> Friedrich Pahlke, Ph.D.
> RPACT
>
> phone +49 451 1217116
> mobile +49 151 72928193
> fax +49 451 1216993
> e-mail friedrich.pahlke@rpact.com
>
> CEOs: Prof. Dr. Gernot Wassmer, Dr. Friedrich Pahlke
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> _______________________________________________________
> RPACT - R Programming for Adaptive Clinical Trials
> www.rpact.com
>
> Am 21.09.2021 um 11:40 schrieb Andreas Tille:
> > Hi Friedrich,
> >
> > when trying to upgrade the rpact package in Debian the test suite has
> > some failures:
> >
> >
> > ══ Failed tests ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
> > ── Failure (test-class_analysis_dataset.R:2190:2): Illegal creation of a dataset of means with subsets: wrong deselection (one group) ──
> > `getDataset(S1 = S1, R = R)` threw an error with unexpected message.
> > Expected match: "Conflicting arguments: if S1 is deselected (NA) then R also must be deselected (NA) but, e.g., 'sampleSize' R is 21 in group 1 at stage 2"
> > Actual message: "Conflicting arguments: if S1 is deselected (NA) then R also must be deselected (NA) but, e.g., ‘sampleSize’ R is 21 in group 1 at stage 2"
> > Backtrace:
> > █
> > 1. ├─testthat::expect_error(...) test-class_analysis_dataset.R:2190:8
> > 2. │ └─testthat:::quasi_capture(...)
> > 3. │ ├─testthat:::.capture(...)
> > 4. │ │ └─base::withCallingHandlers(...)
> > 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
> > 6. └─rpact::getDataset(S1 = S1, R = R)
> > 7. └─rpact:::.getEnrichmentDatasetFromArgs(...)
> > 8. └─rpact:::.validateEnrichmentDataFrame(dataFrame)
> > ── Failure (test-class_analysis_dataset.R:2331:2): Illegal creation of a dataset of means with subsets: wrong deselection (three subsets) ──
> > `getDataset(S1 = S1, S2 = S2, S12 = S12, R = R)` threw an error with unexpected message.
> > Expected match: "Conflicting arguments: if S2 is deselected (NA) then R also must be deselected (NA) but, e.g., 'sampleSize' R is 19 in group 1 at stage 2"
> > Actual message: "Conflicting arguments: if S2 is deselected (NA) then R also must be deselected (NA) but, e.g., ‘sampleSize’ R is 19 in group 1 at stage 2"
> > Backtrace:
> > █
> > 1. ├─testthat::expect_error(...) test-class_analysis_dataset.R:2331:8
> > 2. │ └─testthat:::quasi_capture(...)
> > 3. │ ├─testthat:::.capture(...)
> > 4. │ │ └─base::withCallingHandlers(...)
> > 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
> > 6. └─rpact::getDataset(S1 = S1, S2 = S2, S12 = S12, R = R)
> > 7. └─rpact:::.getEnrichmentDatasetFromArgs(...)
> > 8. └─rpact:::.validateEnrichmentDataFrame(dataFrame)
> > ...
> > 12. └─rpact:::.getEnrichmentDatasetFromArgs(...)
> > 13. └─rpact:::.validateEnrichmentDataFrame(dataFrame)
> > ── Failure (test-class_analysis_dataset.R:2618:2): Illegal creation of a dataset of survival data with subsets: wrong deselection (one group) ──
> > `getDataset(S1 = S1, R = R)` threw an error with unexpected message.
> > Expected match: "Conflicting arguments: if S1 is deselected (NA) then R also must be deselected (NA) but, e.g., 'overallEvent' R is 38 in group 1 at stage 2"
> > Actual message: "Conflicting arguments: if S1 is deselected (NA) then R also must be deselected (NA) but, e.g., ‘overallEvent’ R is 38 in group 1 at stage 2"
> > Backtrace:
> > █
> > 1. ├─testthat::expect_error(...) test-class_analysis_dataset.R:2618:8
> > 2. │ └─testthat:::quasi_capture(...)
> > 3. │ ├─testthat:::.capture(...)
> > 4. │ │ └─base::withCallingHandlers(...)
> > 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
> > 6. └─rpact::getDataset(S1 = S1, R = R)
> > 7. └─rpact:::.getEnrichmentDatasetFromArgs(...)
> > 8. └─rpact:::.validateEnrichmentDataFrame(dataFrame)
> >
> > [ FAIL 6 | WARN 0 | SKIP 187 | PASS 1998 ]
> > Error: Test failures
> >
> >
> > Any hint how to work around this?
> >
> > Kind regards
> >
> > Andreas.
> >
>
--
http://fam-tille.de
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