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

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

Version: 2.66.0

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

StartedAt: 2025-01-08 21:16:31 -0000 (Wed, 08 Jan 2025)

EndedAt: 2025-01-08 21:16:46 -0000 (Wed, 08 Jan 2025)

EllapsedTime: 15.0 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 Biobase
###
##############################################################################
##############################################################################


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

--- re-building ‘esApply.Rmd’ using rmarkdown
Error: processing vignette 'esApply.Rmd' failed with diagnostics:
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- failed re-building ‘esApply.Rmd’

--- re-building ‘ExpressionSetIntroduction.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

Welcome to Bioconductor

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

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

SUMMARY: processing the following files failed:
  ‘BiobaseDevelopment.Rmd’ ‘esApply.Rmd’

Error: Vignette re-building failed.
Execution halted