Last updated on 2020-08-07 01:50:12 CEST.
| Package | ERROR | OK |
|---|---|---|
| ctDNAtools | 1 | 11 |
Current CRAN status: ERROR: 1, OK: 11
Version: 0.4.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Flavor: r-oldrel-macos-x86_64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘ctDNAtools-Ex.R’ failed
The error most likely occurred in:
> ### Name: get_mutations_read_counts
> ### Title: Counts ref and alt reads for a set of mutations
> ### Aliases: get_mutations_read_counts
>
> ### ** Examples
>
> data("mutations", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘GenomeInfoDbData’
Calls: get_mutations_read_counts ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
5. base::getNamespace(ns)
6. base::loadNamespace(name)
9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
12. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
13. base:::withOneRestart(expr, restarts[[1L]])
14. base:::doWithOneRestart(return(expr), restart)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
1. Error: (unknown) (@test-ctDNAtest.R#3)
2. Error: (unknown) (@test-fragment_size.R#13)
Error: testthat unit tests failed
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.4.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘ctDNAtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-69 (ctDNAtools.Rmd)
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘ctDNAtools.Rmd’
SUMMARY: processing the following file failed:
‘ctDNAtools.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64