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This page was generated on 2023-02-06 11:06:28 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

BUILD results for BSgenome on merida1


To the developers/maintainers of the BSgenome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BSgenome.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 225/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.67.3  (landing page)
Hervé Pagès
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/BSgenome
git_branch: master
git_last_commit: 4f6d830
git_last_commit_date: 2023-02-02 21:52:38 -0500 (Thu, 02 Feb 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: BSgenome
Version: 1.67.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BSgenome
StartedAt: 2023-02-05 16:59:41 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 17:02:34 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 172.8 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 BSgenome
###
##############################################################################
##############################################################################


* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* preparing ‘BSgenome’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BSgenomeForge.Rnw’ using Sweave
Loading required package: BiocGenerics

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, 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
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: GenomicRanges
Loading required package: rtracklayer
--- finished re-building ‘BSgenomeForge.Rnw’

--- re-building ‘GenomeSearching.Rnw’ using Sweave
Loading required package: AnnotationDbi
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")'.

Loading required package: BSgenome.Hsapiens.UCSC.hg38

Error: processing vignette 'GenomeSearching.Rnw' failed with diagnostics:
 chunk 24 (label = f1) 
Error : package or namespace load failed for ‘BSgenome.Hsapiens.UCSC.hg38.masked’:
 .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg38.masked', details:
  call: validObject(.Object)
  error: invalid class “RdaCollection” object: 
    files
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273333v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273334v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273335v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273336v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273341v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273342v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273343v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273344v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr2_MU273345v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273346v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273347v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr3_MU273348v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr4_MU273350v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr4_MU273351v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273352v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273353v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273354v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr5_MU273355v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273359v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273360v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273361v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273362v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr8_MU273363v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273364v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273365v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr9_MU273366v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr10_MU273367v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_KQ759759v2_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273369v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273370v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr11_MU273371v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr12_MU273372v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr14_MU273373v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr15_MU273374v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr16_MU273376v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr16_MU273377v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273379v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273380v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273381v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273382v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr17_MU273383v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273384v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273385v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr19_MU273386v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr20_MU273388v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr20_MU273389v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr21_MU273390v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr21_MU273391v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr21_MU273392v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr22_KQ759762v2_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chrX_MU273393v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chrX_MU273394v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chrY_MU273398v1_fix.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273330v1_alt.masks.rda',
    '/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BSgenome.Hsapiens.UCSC.hg38.masked/extdata/chr1_MU273331v1_alt.masks.rda',
    '/Library
--- failed re-building ‘GenomeSearching.Rnw’

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

Error: Vignette re-building failed.
Execution halted