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This page was generated on 2024-02-18 02:28:28 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 646/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ensemblVEP 1.45.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/ensemblVEP
git_branch: devel
git_last_commit: 7e6d1d2
git_last_commit_date: 2024-01-26 07:26:55 -0500 (Fri, 26 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

BUILD results for ensemblVEP on merida1


To the developers/maintainers of the ensemblVEP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ensemblVEP.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: ensemblVEP
Version: 1.45.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ensemblVEP
StartedAt: 2024-02-16 18:51:30 -0500 (Fri, 16 Feb 2024)
EndedAt: 2024-02-16 18:53:53 -0500 (Fri, 16 Feb 2024)
EllapsedTime: 142.9 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 ensemblVEP
###
##############################################################################
##############################################################################


* checking for file ‘ensemblVEP/DESCRIPTION’ ... OK
* preparing ‘ensemblVEP’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ensemblVEP.Rnw’ using Sweave
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: GenomicRanges
Loading required package: stats4
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: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: SummarizedExperiment
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")'.


Attaching package: ‘Biobase’

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

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit


Attaching package: ‘VariantAnnotation’

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

    tabulate

Warning: Package 'ensemblVEP' is deprecated and will be removed from
  Bioconductor version 3.20; Functionality has been moved to
  VariantAnnotation

Attaching package: ‘ensemblVEP’

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

    cache

install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (you may need to install the DBD::mysql module) (@INC contains: /usr/local/ensembl-vep/modules /usr/local/ensembl-vep ##PATH_TO##/bioperl-1.6.924 /Users/biocbuild/perl5/perlbrew/perls/5.26.2/lib/site_perl/5.26.2/darwin-thread-multi-2level /Users/biocbuild/perl5/perlbrew/perls/5.26.2/lib/site_perl/5.26.2 /Users/biocbuild/perl5/perlbrew/perls/5.26.2/lib/5.26.2/darwin-thread-multi-2level /Users/biocbuild/perl5/perlbrew/perls/5.26.2/lib/5.26.2) at (eval 31) line 3.
Perhaps the DBD::mysql perl module hasn't been fully installed,
or perhaps the capitalisation of 'mysql' isn't right.
Available drivers: DBM, ExampleP, File, Gofer, Mem, Proxy, Sponge.
 at /usr/local/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1771.

Error: processing vignette 'ensemblVEP.Rnw' failed with diagnostics:
 chunk 5 (label = rtn_GRanges) 
Error in .io_check_exists(path(con)) : file(s) do not exist:
  '/tmp/Rtmp7eEH6H/file128c470a8943a'

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

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

Error: Vignette re-building failed.
Execution halted