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This page was generated on 2023-03-24 11:05:27 -0400 (Fri, 24 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4286
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4276
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4303
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 gage on nebbiolo2


To the developers/maintainers of the gage package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gage.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 729/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.48.0  (landing page)
Weijun Luo
Snapshot Date: 2023-03-22 14:00:04 -0400 (Wed, 22 Mar 2023)
git_url: https://git.bioconductor.org/packages/gage
git_branch: RELEASE_3_16
git_last_commit: d067e0a
git_last_commit_date: 2022-11-01 11:05:20 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: gage
Version: 2.48.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gage
StartedAt: 2023-03-22 16:56:41 -0400 (Wed, 22 Mar 2023)
EndedAt: 2023-03-22 17:00:44 -0400 (Wed, 22 Mar 2023)
EllapsedTime: 243.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gage
###
##############################################################################
##############################################################################


* checking for file ‘gage/DESCRIPTION’ ... OK
* preparing ‘gage’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RNA-seqWorkflow.Rnw’ using Sweave
Loading required package: gageData


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Info: Downloading xml files for hsa03013, 1/1 pathways..
Info: Downloading png files for hsa03013, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa03013.pathview.multi.png
Info: Downloading xml files for hsa03008, 1/1 pathways..
Info: Downloading png files for hsa03008, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa03008.pathview.multi.png
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa04110.pathview.multi.png
Info: Downloading xml files for hsa04610, 1/1 pathways..
Info: Downloading png files for hsa04610, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa04610.pathview.multi.png
Info: Downloading xml files for hsa04512, 1/1 pathways..
Info: Downloading png files for hsa04512, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa04512.pathview.multi.png
Info: Downloading xml files for hsa04510, 1/1 pathways..
Info: Downloading png files for hsa04510, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa04510.pathview.multi.png
Loading required package: S4Vectors
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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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: 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

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa03013.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa03008.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpxBBrBv/Rbuild2e2cb2234310d7/gage/vignettes
Info: Writing image file hsa04110.deseq2.png
Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:DESeq2’:

    plotMA

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

    plotMA

--- finished re-building ‘RNA-seqWorkflow.Rnw’

--- re-building ‘dataPrep.Rnw’ using Sweave
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db

'select()' returned 1:1 mapping between keys and columns
--- finished re-building ‘dataPrep.Rnw’

--- re-building ‘gage.Rnw’ using Sweave

Error: processing vignette 'gage.Rnw' failed with diagnostics:
 chunk 12 (label = kegg.gsets) 
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received

--- failed re-building ‘gage.Rnw’

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

Error: Vignette re-building failed.
Execution halted