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 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data YAPSA ### ############################################################################## ############################################################################## * 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 Warning: `offset` is deprecated, use `location` instead. 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delta: 0.1 Warning in value[[3L]](cond) : lower; delta: 0.2 Warning in value[[3L]](cond) : upper; delta: 0.2 Warning in value[[3L]](cond) : lower; delta: 0.2 --- 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