Multiple platform build/check report for BioC 3.22 - BUILD results for graphite on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 graphite on taishan

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

Version: 1.56.0

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

StartedAt: 2025-11-18 02:08:17 -0000 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 02:08:56 -0000 (Tue, 18 Nov 2025)

EllapsedTime: 39.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


* checking for file ‘graphite/DESCRIPTION’ ... OK
* preparing ‘graphite’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘metabolites.pdf.asis’ using asis
--- finished re-building ‘metabolites.pdf.asis’

--- re-building ‘graphite.Rnw’ using Sweave
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

Warning: Local storage of pathway data using format v1 was deprecated in graphite
1.55.1.
✔ graphite will automatically migrate to and use format v2 going forward.
ℹ If you no longer need compatibility with older graphite versions, run
  purgeCacheV1() to reclaim disk space.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Resolving timed out after 10001 milliseconds

Error: processing vignette 'graphite.Rnw' failed with diagnostics:
 chunk 3 (label = base1) 
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?

--- failed re-building ‘graphite.Rnw’

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

Error: Vignette re-building failed.
Execution halted