Multiple platform build/check report for BioC 3.20 - BUILD results for RTopper on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 RTopper on kjohnson3

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

Version: 1.52.0

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

StartedAt: 2024-11-08 18:54:18 -0500 (Fri, 08 Nov 2024)

EndedAt: 2024-11-08 18:54:45 -0500 (Fri, 08 Nov 2024)

EllapsedTime: 27.3 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 RTopper
###
##############################################################################
##############################################################################


* checking for file ‘RTopper/DESCRIPTION’ ... OK
* preparing ‘RTopper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RTopper.Rnw’ using Sweave
Loading required package: Biobase
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")'.

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



Error: processing vignette 'RTopper.Rnw' failed with diagnostics:
 chunk 7 (label = annotateFGS) 
Error in (function (cond)  : 
  error in evaluating the argument 'X' in selecting a method for function 'sapply': Timeout was reached [rest.kegg.jp]: SSL connection timeout

--- failed re-building ‘RTopper.Rnw’

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

Error: Vignette re-building failed.
Execution halted