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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4358
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 BSgenomeForge on taishan

To the developers/maintainers of the BSgenomeForge package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BSgenomeForge.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: BSgenomeForge

Version: 1.6.0

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

StartedAt: 2025-01-08 21:20:43 -0000 (Wed, 08 Jan 2025)

EndedAt: 2025-01-08 21:21:35 -0000 (Wed, 08 Jan 2025)

EllapsedTime: 52.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data BSgenomeForge
###
##############################################################################
##############################################################################


* checking for file ‘BSgenomeForge/DESCRIPTION’ ... OK
* preparing ‘BSgenomeForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘QuickBSgenomeForge.Rmd’ using rmarkdown
Error: processing vignette 'QuickBSgenomeForge.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building ‘QuickBSgenomeForge.Rmd’

--- re-building ‘AdvancedBSgenomeForge.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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

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

    FileForFormat


Attaching package: ‘BSgenomeForge’

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

    forgeBSgenomeDataPkg, forgeMaskedBSgenomeDataPkg, forgeMasksFiles,
    forgeSeqFiles, forgeSeqlengthsRdaFile, forgeSeqlengthsRdsFile

--- finished re-building ‘AdvancedBSgenomeForge.Rnw’

SUMMARY: processing the following file failed:
  ‘QuickBSgenomeForge.Rmd’

Error: Vignette re-building failed.
Execution halted