Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:28 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 708/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.47.0  (landing page)
Weijun Luo
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/gage
git_branch: master
git_last_commit: d33ece3
git_last_commit_date: 2022-04-26 11:06:03 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: gage
Version: 2.47.0
Command: chmod a+r gage -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gage
StartedAt: 2022-06-23 18:42:39 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 18:45:10 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 151.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r gage -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe 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..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa03013/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa03013 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa03013, 1/1 pathways..
Warning: Download of hsa03013 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa03013 skipped!
Info: Downloading xml files for hsa03008, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa03008/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa03008 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa03008, 1/1 pathways..
Warning: Download of hsa03008 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa03008 skipped!
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
Info: Downloading xml files for hsa04610, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04610/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04610 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04610, 1/1 pathways..
Warning: Download of hsa04610 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04610 skipped!
Info: Downloading xml files for hsa04512, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04512/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04512 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04512, 1/1 pathways..
Warning: Download of hsa04512 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04512 skipped!
Info: Downloading xml files for hsa04510, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04510/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04510 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04510, 1/1 pathways..
Warning: Download of hsa04510 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04510 skipped!
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, 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

Attaching package: 'IRanges'

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

    windows

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
Info: Downloading xml files for hsa03013, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa03013/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa03013 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa03013, 1/1 pathways..
Warning: Download of hsa03013 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa03013 skipped!
Info: Downloading xml files for hsa03008, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa03008/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa03008 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa03008, 1/1 pathways..
Warning: Download of hsa03008 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa03008 skipped!
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
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

texify: major issue: So far, you have not checked for updates as a MiKTeX user.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "RNA-seqWorkflow.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.16-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.16-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'RNA-seqWorkflow.Rnw' failed with diagnostics:
running 'texi2dvi' on 'RNA-seqWorkflow.tex' failed

LaTeX errors:
RNA-seqWorkflow.tex:311: Package pdftex.def Error: File `hsa03013.pathview.mult
i.png' not found: using draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
RNA-seqWorkflow.tex:319: Package pdftex.def Error: File `hsa04512.pathview.mult
i.png' not found: using draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.

--- failed 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
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
--- finished re-building 'dataPrep.Rnw'

--- re-building 'gage.Rnw' using Sweave
Gene ID type for 'human' is: 'EG'
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
Info: Downloading xml files for hsa00020, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa00020/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa00020 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa00020, 1/1 pathways..
Warning: Download of hsa00020 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa00020 skipped!
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
Info: Downloading xml files for hsa00020, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa00020/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa00020 xml file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa00020 skipped!
Warning: file stem 'gage-heter.gage' is not portable
texify: major issue: So far, you have not checked for updates as a MiKTeX user.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "gage.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.16-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.16-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'gage.Rnw' failed with diagnostics:
running 'texi2dvi' on 'gage.tex' failed

LaTeX errors:
gage.tex:781: Package pdftex.def Error: File `hsa00020.pathview.multi.png' not 
found: using draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
gage.tex:789: Package pdftex.def Error: File `hsa04110.pathview.multi.pdf' not 
found: using draft setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.

--- failed re-building 'gage.Rnw'

SUMMARY: processing the following files failed:
  'RNA-seqWorkflow.Rnw' 'gage.Rnw'

Error: Vignette re-building failed.
Execution halted