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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1663/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.57.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/R453Plus1Toolbox
git_branch: devel
git_last_commit: 8d481bd
git_last_commit_date: 2024-10-29 09:35:04 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


BUILD results for R453Plus1Toolbox on lconway

To the developers/maintainers of the R453Plus1Toolbox package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R453Plus1Toolbox.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: R453Plus1Toolbox
Version: 1.57.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data R453Plus1Toolbox
StartedAt: 2025-03-16 18:11:26 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 18:13:02 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 96.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data R453Plus1Toolbox
###
##############################################################################
##############################################################################


* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* preparing ‘R453Plus1Toolbox’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rnw’ using Sweave
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect,
    is.element, setdiff, setequal, union


Attaching package: ‘BiocGenerics’

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, aperm, append, as.data.frame,
    basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl,
    is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, saveRDS, table, tapply,
    unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet,
    colCollapse, colCounts, colCummaxs, colCummins,
    colCumprods, colCumsums, colDiffs, colIQRDiffs,
    colIQRs, colLogSumExps, colMadDiffs, colMads,
    colMaxs, colMeans2, colMedians, colMins,
    colOrderStats, colProds, colQuantiles, colRanges,
    colRanks, colSdDiffs, colSds, colSums2,
    colTabulates, colVarDiffs, colVars,
    colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys,
    rowAvgsPerColSet, rowCollapse, rowCounts,
    rowCummaxs, rowCummins, rowCumprods, rowCumsums,
    rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2,
    rowMedians, rowMins, rowOrderStats, rowProds,
    rowQuantiles, rowRanges, rowRanks, rowSdDiffs,
    rowSds, rowSums2, rowTabulates, rowVarDiffs,
    rowVars, rowWeightedMads, rowWeightedMeans,
    rowWeightedMedians, rowWeightedSds,
    rowWeightedVars

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view
    with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages
    'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit


Attaching package: ‘VariantAnnotation’

The following object is masked from ‘package:base’:

    tabulate

Loading required package: pwalign

Attaching package: ‘pwalign’

The following objects are masked from ‘package:Biostrings’:

    PairwiseAlignments,
    PairwiseAlignmentsSingleSubject, aligned,
    alignedPattern, alignedSubject, compareStrings,
    deletion, errorSubstitutionMatrices, indel,
    insertion, mismatchSummary, mismatchTable, nedit,
    nindel, nucleotideSubstitutionMatrix,
    pairwiseAlignment, pattern, pid,
    qualitySubstitutionMatrices, stringDist,
    unaligned, writePairwiseAlignments

Warning in .local(dirname) : 'AVASet(dirname)' is deprecated.
Use 'AVASet(dirname, avaBin)' instead.
See help("Deprecated")
Reading sample data ... done
Reading reference sequences ... done
Reading variant data ... done
Reading amplicon data ... done
Variants: 

Amplicons: 
assayDataAmp:4 features,  6 samples
  element names:forwCountrevCount
featureDataAmp: 

Reference sequences: 
Loading required package: BiocParallel
Loading required package: GenomicAlignments
combined forward & reverse filter set to 0.05
forward filter set to 0.1
reverse filter set to 0.05
combined forward & reverse filter set to 0
combined forward & reverse filter set to 0
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Reading data ... 
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N01
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N03
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N04
done

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 45 (label = demultiplex) 
Error in unlist(substitutionMatrix, substitutionMatrix) : 
  'recursive' must be a length-1 vector

--- failed re-building ‘vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vignette.Rnw’

Error: Vignette re-building failed.
Execution halted