Last updated on 2025-05-22 05:50:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 10.46 | 139.71 | 150.17 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 5.64 | 100.20 | 105.84 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 257.38 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 242.51 | OK | |||
| r-devel-windows-x86_64 | 1.1.0 | 15.00 | 159.00 | 174.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 10.99 | 133.53 | 144.52 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 11.43 | 133.23 | 144.66 | OK | |
| r-release-macos-arm64 | 1.1.0 | 96.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.0 | 127.00 | ERROR | |||
| r-release-windows-x86_64 | 1.1.0 | 16.00 | 159.00 | 175.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 78.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 105.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 19.00 | 211.00 | 230.00 | NOTE |
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:
> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ### matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
>
> ### ** Examples
>
> expression.matrix.preproc <- as.matrix(read.csv(
+ system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
+ row.names = 1
+ ))[1:100, 1:4]
>
> anno <- AnnotationDbi::select(
+ getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+ keys = rownames(expression.matrix.preproc),
+ keytype = 'ENSEMBL',
+ columns = 'SYMBOL'
+ ) %>%
+ dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+ dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘GEO_App.Rmd’ using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178620&format=file&file=GSE178620%5Fraw%5Fabundances%2Ecsv%2Egz'
Content type 'application/octet-stream' length 1892945 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
--- finished re-building ‘GEO_App.Rmd’
--- re-building ‘IntegratingMultiomics.Rmd’ using rmarkdown
--- finished re-building ‘IntegratingMultiomics.Rmd’
--- re-building ‘bulkAnalyseR.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpWZPt3X/Rf1389609a2f6a': No space left on device
Quitting from bulkAnalyseR.Rmd:76-80 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$weave(file, quiet = quiet, encoding = enc)
7. └─knitr:::vweave_rmarkdown(...)
8. └─rmarkdown::render(...)
9. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. └─knitr:::process_file(text, output)
11. ├─xfun:::handle_error(...)
12. ├─base::withCallingHandlers(...)
13. └─knitr:::process_group(group)
14. └─knitr:::call_block(x)
15. └─knitr:::block_exec(params)
16. └─knitr:::eng_r(options)
17. ├─knitr:::in_input_dir(...)
18. │ └─knitr:::in_dir(input_dir(), expr)
19. └─knitr (local) evaluate(...)
20. └─evaluate::evaluate(...)
21. └─evaluate:::watchout(...)
22. └─evaluate:::local_persistent_sink_connection(debug, frame)
23. └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'bulkAnalyseR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘bulkAnalyseR.Rmd’
SUMMARY: processing the following file failed:
‘bulkAnalyseR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 3.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64