Last updated on 2024-06-13 05:59:05 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.11-1 | 7.68 | 250.61 | 258.29 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.11-1 | 7.48 | 138.28 | 145.76 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.11-1 | 316.36 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.11-1 | 312.69 | OK | |||
| r-devel-windows-x86_64 | 0.11-1 | 10.00 | 191.00 | 201.00 | OK | |
| r-patched-linux-x86_64 | 0.11-1 | 12.17 | 238.09 | 250.26 | OK | |
| r-release-linux-x86_64 | 0.11-1 | 8.59 | 237.63 | 246.22 | OK | |
| r-release-macos-arm64 | 0.11-1 | 83.00 | OK | |||
| r-release-macos-x86_64 | 0.11-1 | 144.00 | OK | |||
| r-release-windows-x86_64 | 0.11-1 | 9.00 | 191.00 | 200.00 | OK | |
| r-oldrel-macos-arm64 | 0.11-1 | 94.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.11-1 | 255.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.11-1 | 11.00 | 239.00 | 250.00 | OK |
Version: 0.11-1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘dplyr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.11-1
Check: examples
Result: ERROR
Running examples in ‘gadget3-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: likelihood_catchdistribution
> ### Title: Gadget3 likelihood actions
> ### Aliases: g3l_distribution_sumofsquares g3l_distribution_multinomial
> ### g3l_distribution_multivariate g3l_distribution_surveyindices_log
> ### g3l_distribution_surveyindices_linear
> ### g3l_distribution_sumofsquaredlogratios g3_distribution_preview
> ### g3l_abundancedistribution g3l_catchdistribution
>
> ### ** Examples
>
> ## Don't show:
> library(magrittr)
> ## End(Don't show)
> ling_imm <- g3_stock('ling_imm', seq(20, 156, 4)) %>% g3s_age(3, 10)
> ling_mat <- g3_stock('ling_mat', seq(20, 156, 4)) %>% g3s_age(5, 15)
> lln <- g3_fleet('lln')
>
> # Invent a ldist.lln table for our tests
> ldist.lln.raw <- data.frame(
+ year = c(1999, 2000),
+ age = sample(5:9, 100, replace = TRUE),
+ length = sample(10:70, 100, replace = TRUE),
+ number = 1,
+ stringsAsFactors = FALSE)
>
> # Group length into 10-long bins
> # NB: The last 2 bins will be empty, but gadget3 will use the factor levels, include them as zero
> # NB: Generally one would use mfdb::mfdb_sample_count() source and group data for you
> ldist.lln.raw |> dplyr::group_by(
+ year = year, age = age,
+ length = cut(length, breaks = seq(10, 100, by = 10), right = FALSE)
+ ) |> dplyr::summarise(number = sum(number), .groups = 'keep') -> ldist.lln
Error in loadNamespace(x) : there is no package called ‘dplyr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.11-1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘incorporating-observation-data.Rmd’ using rmarkdown
Quitting from lines 26-29 [unnamed-chunk-2] (incorporating-observation-data.Rmd)
Error: processing vignette 'incorporating-observation-data.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘incorporating-observation-data.Rmd’
--- re-building ‘introduction-single-stock.Rmd’ using rmarkdown
Quitting from lines 101-103 [unnamed-chunk-6] (introduction-single-stock.Rmd)
Error: processing vignette 'introduction-single-stock.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘introduction-single-stock.Rmd’
--- re-building ‘model-customisation.Rmd’ using rmarkdown
--- finished re-building ‘model-customisation.Rmd’
--- re-building ‘model-debugging.Rmd’ using rmarkdown
--- finished re-building ‘model-debugging.Rmd’
--- re-building ‘model-structure.Rmd’ using rmarkdown
--- finished re-building ‘model-structure.Rmd’
--- re-building ‘multiple-substocks.Rmd’ using rmarkdown
Quitting from lines 58-73 [unnamed-chunk-4] (multiple-substocks.Rmd)
Error: processing vignette 'multiple-substocks.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘multiple-substocks.Rmd’
--- re-building ‘random-effects.Rmd’ using rmarkdown
Quitting from lines 59-74 [unnamed-chunk-4] (random-effects.Rmd)
Error: processing vignette 'random-effects.Rmd' failed with diagnostics:
there is no package called 'dplyr'
--- failed re-building ‘random-effects.Rmd’
--- re-building ‘writing_actions.Rmd’ using rmarkdown
--- finished re-building ‘writing_actions.Rmd’
SUMMARY: processing the following files failed:
‘incorporating-observation-data.Rmd’ ‘introduction-single-stock.Rmd’
‘multiple-substocks.Rmd’ ‘random-effects.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.11-1
Check: Rd cross-references
Result: NOTE
Undeclared package ‘mfdb’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang