Build/check report for BioC 3.23 - BUILD results for gage on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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BUILD results for gage on nebbiolo1

To the developers/maintainers of the gage package:
- 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 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: gage

Version: 2.61.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gage

StartedAt: 2025-10-30 17:11:54 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 17:14:14 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 140.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gage
###
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* checking for file ‘gage/DESCRIPTION’ ... OK
* preparing ‘gage’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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/RtmpCcg5Lb/Rbuild143a98336d13ac/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/RtmpCcg5Lb/Rbuild143a98336d13ac/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/RtmpCcg5Lb/Rbuild143a98336d13ac/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/RtmpCcg5Lb/Rbuild143a98336d13ac/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/RtmpCcg5Lb/Rbuild143a98336d13ac/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/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa04510.pathview.multi.png
Loading required package: S4Vectors
Loading required package: stats4
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


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: GenomicRanges
Loading required package: Seqinfo
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/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa03013.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa03008.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/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

Error: processing vignette 'dataPrep.Rnw' failed with diagnostics:
 chunk 5 (label = gse16873.affyid) 
Error in library(hgu133a.db) : there is no package called ‘hgu133a.db’

--- failed re-building ‘dataPrep.Rnw’

--- re-building ‘gage.Rnw’ using Sweave
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Gene ID type for 'human' is: 'EG'
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa04110.pathview.multi.png
Info: Downloading xml files for hsa00020, 1/1 pathways..
Info: Downloading png files for hsa00020, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa00020.pathview.multi.png
'select()' returned 1:1 mapping between keys and columns
Warning: reconcile groups sharing member nodes!
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa04110.pathview.multi.pdf
Warning in text.default(xloc, yloc, label = labs[sub2grp[sub.idx, 1]], cex = cex) :
  length(labels) > max(length(x), length(y)). labels truncated to length 36.
Warning in .local(from, to, graph) :
  edges replaced: ‘75|36’, ‘69|37’, ‘69|38’, ‘76|39’, ‘76|40’, ‘65|42’, ‘63|42’, ‘69|107’, ‘62|107’, ‘65|46’, ‘63|46’, ‘63|47’, ‘65|91’, ‘63|97’
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /tmp/RtmpCcg5Lb/Rbuild143a98336d13ac/gage/vignettes
Info: Writing image file hsa00020.pathview.multi.pdf
Warning: file stem ‘gage-heter.gage’ is not portable
--- finished re-building ‘gage.Rnw’

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

Error: Vignette re-building failed.
Execution halted