Multiple platform build/check report for BioC 3.20 - BUILD results for r3Cseq on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4670
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4355
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4446
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4439
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4306
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 r3Cseq on taishan

To the developers/maintainers of the r3Cseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/r3Cseq.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: r3Cseq

Version: 1.52.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data r3Cseq

StartedAt: 2025-03-07 03:18:05 -0000 (Fri, 07 Mar 2025)

EndedAt: 2025-03-07 03:19:12 -0000 (Fri, 07 Mar 2025)

EllapsedTime: 67.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data r3Cseq
###
##############################################################################
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* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* preparing ‘r3Cseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘r3Cseq.Rnw’ using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
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, saveRDS,
    setdiff, table, tapply, union, unique, unsplit,
    which.max, which.min

Loading required package: S4Vectors

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

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Loading required package: VGAM
Loading required package: splines
Loading required package: qvalue
No methods found in package 'Biostrings' for request: 'DNAString' when loading 'r3Cseq'

Error: processing vignette 'r3Cseq.Rnw' failed with diagnostics:
 chunk 7 
Error in library(BSgenome.Mmusculus.UCSC.mm9.masked) : 
  there is no package called 'BSgenome.Mmusculus.UCSC.mm9.masked'

--- failed re-building 'r3Cseq.Rnw'

SUMMARY: processing the following file failed:
  'r3Cseq.Rnw'

Error: Vignette re-building failed.
Execution halted