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This page was generated on 2025-01-24 11:42 -0500 (Fri, 24 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4609
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4393
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3839
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 3835
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4408
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

Package 900/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.53.0  (landing page)
Gabriele Sales
Snapshot Date: 2025-01-23 13:40 -0500 (Thu, 23 Jan 2025)
git_url: https://git.bioconductor.org/packages/graphite
git_branch: devel
git_last_commit: e301772
git_last_commit_date: 2024-10-31 03:15:43 -0500 (Thu, 31 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

BUILD results for graphite on kjohnson3

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.

raw results


Summary

Package: graphite
Version: 1.53.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data graphite
StartedAt: 2025-01-23 16:04:50 -0500 (Thu, 23 Jan 2025)
EndedAt: 2025-01-23 16:05:07 -0500 (Thu, 23 Jan 2025)
EllapsedTime: 17.2 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 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


Loading required package: KEGGgraph

Attaching package: ‘KEGGgraph’

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

    plot

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

    plot

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: Biobase
Welcome to Bioconductor

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

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: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns

Error: processing vignette 'graphite.Rnw' failed with diagnostics:
 chunk 17 (label = tg1) 
Error in library(topologyGSA) : there is no package called ‘topologyGSA’

--- failed re-building ‘graphite.Rnw’

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

Error: Vignette re-building failed.
Execution halted