Multiple platform build/check report for BioC 3.23 - BUILD results for ArrayExpress on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4989
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4719
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 ArrayExpress on kjohnson3

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

Version: 1.72.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress

StartedAt: 2026-05-04 15:41:23 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 15:42:03 -0400 (Mon, 04 May 2026)

EllapsedTime: 40.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
###
##############################################################################
##############################################################################


* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* preparing ‘ArrayExpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ArrayExpress.Rnw’ using Sweave
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")'.


Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
 chunk 1 (label = queryAE) 
Error in get_request(paste(query, "&page=", page, sep = "")) : 
  Error running query. Received HTTP error code 500 from server. Please try again later. If you continue to experience 
        problems please contact us 
        at https://www.ebi.ac.uk/about/contact/support/arrayexpress

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

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

Error: Vignette re-building failed.
Execution halted