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This page was generated on 2024-03-28 11:38:07 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1377/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mygene 1.39.1  (landing page)
Adam Mark, Cyrus Afrasiabi, Chunlei Wu
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/mygene
git_branch: devel
git_last_commit: a13fe29
git_last_commit_date: 2024-03-22 12:45:04 -0400 (Fri, 22 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for mygene on palomino3


To the developers/maintainers of the mygene package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mygene.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: mygene
Version: 1.39.1
Command: chmod a+r mygene -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data mygene
StartedAt: 2024-03-27 20:49:02 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:50:05 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 62.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r mygene -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data mygene
###
##############################################################################
##############################################################################


* checking for file 'mygene/DESCRIPTION' ... OK
* preparing 'mygene':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'mygene.Rnw' using Sweave
Loading required package: GenomicFeatures
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, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: txdbmaker

Attaching package: 'txdbmaker'

The following objects are masked from 'package:GenomicFeatures':

    UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart,
    makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName,
    makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl,
    makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC,
    makeTxDbPackage, makeTxDbPackageFromBiomart,
    makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues,
    supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks,
    supportedUCSCtables


Error: processing vignette 'mygene.Rnw' failed with diagnostics:
 chunk 7 
Error in rename(df, c(X_id = "_id")) : 
  Some 'from' names in value not found on 'x': X_id

--- failed re-building 'mygene.Rnw'

SUMMARY: processing the following file failed:
  'mygene.Rnw'

Error: Vignette re-building failed.
Execution halted