Build/check report for BioC 3.23 - BUILD results for a4 on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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 a4 on nebbiolo1

To the developers/maintainers of the a4 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4.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.

raw results

Summary

Package: a4

Version: 1.59.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data a4

StartedAt: 2025-10-30 15:59:06 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 15:59:36 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 30.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data a4
###
##############################################################################
##############################################################################


* checking for file ‘a4/DESCRIPTION’ ... OK
* preparing ‘a4’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘a4vignette.Rnw’ using Sweave
Loading required package: a4Base
Loading required package: a4Preproc
Loading required package: a4Core

a4Base version 1.59.0

Loading required package: a4Classif

a4Classif version 1.59.0

Loading required package: a4Reporting

a4 version 1.59.0

Loading required package: ALL
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")'.

Loading required package: nlcv
Loading required package: MLInterfaces
Loading required package: Rcpp
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
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: XML
Loading required package: cluster
Loading required package: xtable

Attaching package: ‘xtable’

The following object is masked from ‘package:a4Reporting’:

    xtable


nlcv version 0.3.6


Error: processing vignette 'a4vignette.Rnw' failed with diagnostics:
 chunk 4 (label = prepareALL) 
Error in library("hgu95av2.db") : 
  there is no package called ‘hgu95av2.db’

--- failed re-building ‘a4vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘a4vignette.Rnw’

Error: Vignette re-building failed.
Execution halted