Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:06:12 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 EnrichmentBrowser on tokay2


To the developers/maintainers of the EnrichmentBrowser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichmentBrowser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 581/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.24.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/EnrichmentBrowser
git_branch: RELEASE_3_14
git_last_commit: 30747bc
git_last_commit_date: 2021-12-15 18:46:45 -0500 (Wed, 15 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnrichmentBrowser
Version: 2.24.1
Command: chmod a+r EnrichmentBrowser -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data EnrichmentBrowser
StartedAt: 2022-01-23 10:00:03 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 10:03:04 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 180.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r EnrichmentBrowser -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data EnrichmentBrowser
###
##############################################################################
##############################################################################


* checking for file 'EnrichmentBrowser/DESCRIPTION' ... OK
* preparing 'EnrichmentBrowser':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'EnrichmentBrowser.Rnw' using knitr
Loading required package: SummarizedExperiment
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: GenomicRanges
Loading required package: stats4
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, 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, sort, table, tapply, union, unique, unsplit, which.max,
    which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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: 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: graph

Attaching package: 'EnrichmentBrowser'

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

    normalize



Encountered 448 from.IDs with >1 corresponding to.ID
(the first to.ID was chosen for each of them)
Excluding 8818 genes not satisfying min.cpm threshold

Attaching package: 'Biostrings'

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

    complement

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

    strsplit

Excluding 389 genes not satisfying min.cpm threshold
Encountered 98 from.IDs with >1 corresponding to.ID
(the first to.ID was chosen for each of them)
Excluded 1997 from.IDs without a corresponding to.ID
Encountered 13 to.IDs with >1 from.ID (the first from.ID was chosen for each of them)
Mapped from.IDs have been added to the rowData column ENSEMBL
Excluding 23 genes not satisfying min.cpm threshold
Quitting from lines 734-739 (EnrichmentBrowser.Rnw) 
Error: processing vignette 'EnrichmentBrowser.Rnw' failed with diagnostics:
Timeout was reached: [rest.kegg.jp] Resolving timed out after 10000 milliseconds
--- failed re-building 'EnrichmentBrowser.Rnw'

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

Error: Vignette re-building failed.
Execution halted