Multiple platform build/check report for BioC 3.24 - BUILD results for sva on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4878
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4663
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 sva on taishan

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

Version: 3.61.0

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

StartedAt: 2026-05-05 06:22:16 -0000 (Tue, 05 May 2026)

EndedAt: 2026-05-05 06:22:54 -0000 (Tue, 05 May 2026)

EllapsedTime: 38.0 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 sva
###
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* checking for file ‘sva/DESCRIPTION’ ... OK
* preparing ‘sva’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sva.Rnw’ using Sweave
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-3. For overview type 'help("mgcv-package")'.
Loading required package: genefilter
Loading required package: BiocParallel
Loading required package: Biobase
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

Welcome to Bioconductor

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


Attaching package: ‘limma’

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

    plotMA


Error: processing vignette 'sva.Rnw' failed with diagnostics:
 chunk 14 (label = input) 
Error in topTableF(eb, adjust = "BH") : 
  could not find function "topTableF"

--- failed re-building ‘sva.Rnw’

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

Error: Vignette re-building failed.
Execution halted