| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:58 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the YAPSA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/YAPSA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2035/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| YAPSA 1.18.0 (landing page) Daniel Huebschmann
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: YAPSA |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data YAPSA |
| StartedAt: 2021-10-14 15:42:00 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 15:46:19 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 258.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data YAPSA
###
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##############################################################################
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* preparing ‘YAPSA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘YAPSA.Rmd’ using rmarkdown
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Registered S3 methods overwritten by 'proxy':
method from
print.registry_field registry
print.registry_entry registry
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
pandoc-citeproc: reference ComplexHeatmap2015 not found
--- finished re-building ‘YAPSA.Rmd’
--- re-building ‘vignette_confidenceIntervals.Rmd’ using rmarkdown
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--- finished re-building ‘vignette_confidenceIntervals.Rmd’
--- re-building ‘vignette_exomes.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
--- finished re-building ‘vignette_exomes.Rmd’
--- re-building ‘vignette_signature_specific_cutoffs.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
Warning: `offset` is deprecated, use `location` instead.
Warning: The label(s) tab:Table1 not found
--- finished re-building ‘vignette_signature_specific_cutoffs.Rmd’
--- re-building ‘vignette_stratifiedAnalysis.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Quitting from lines 301-306 (vignette_stratifiedAnalysis.Rmd)
Error: processing vignette 'vignette_stratifiedAnalysis.Rmd' failed with diagnostics:
'posthoc.kruskal.nemenyi.test.default' is defunct.
Use 'PMCMRplus::kwAllPairsNemenyiTest' instead.
See help("Defunct") and help("PMCMR-defunct").
--- failed re-building ‘vignette_stratifiedAnalysis.Rmd’
--- re-building ‘vignettes_Indel.Rmd’ using rmarkdown
Warning: `offset` is deprecated, use `location` instead.
--- finished re-building ‘vignettes_Indel.Rmd’
SUMMARY: processing the following file failed:
‘vignette_stratifiedAnalysis.Rmd’
Error: Vignette re-building failed.
Execution halted