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BUILD report for pathview on merida1

This page was generated on 2021-05-05 12:14:56 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the pathview package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1309/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.30.3  (landing page)
Weijun Luo
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/pathview
Branch: RELEASE_3_12
Last Commit: bf29875
Last Changed Date: 2021-04-29 18:38:47 -0400 (Thu, 29 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    ERROR  skipped
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: pathview
Version: 1.30.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pathview
StartedAt: 2021-05-04 21:08:40 -0400 (Tue, 04 May 2021)
EndedAt: 2021-05-04 21:10:39 -0400 (Tue, 04 May 2021)
EllapsedTime: 119.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pathview
###
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* checking for file ‘pathview/DESCRIPTION’ ... OK
* preparing ‘pathview’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘pathview.Rnw’ using Sweave

##############################################################################
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 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 /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.2layer.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.2layer.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.split.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa04110.gse16873.split.expanded.pdf
Info: Downloading xml files for hsa00640, 1/1 pathways..
Info: Downloading png files for hsa00640, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.png
Warning in .local(from, to, graph) :
  edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.pdf
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.3-2s.match.multi.png
Warning in .local(from, to, graph) :
  edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.pdf
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    expand.grid

'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.sel.genes.sel.cpd.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.sel.genes.cpd.png
Note: "CAS Registry Number" has only 4643 unique IDs!
Note: "ENSEMBLPROT" has only 21951 unique IDs!
'select()' returned 1:many mapping between keys and columns
Note: multiple compounds may map to a input ID, only the first one kept!
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gene.ensprot.cpd.cas.png
Note: multiple compounds may map to a input ID, only the first one kept!
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file hsa00640.gene.entrez.cpd.kc.png
Info: Downloading xml files for eco00640, 1/1 pathways..
Info: Downloading png files for eco00640, 1/1 pathways..
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file eco00640.eco.kegg.png
Loading required namespace: org.EcK12.eg.db

Info: Getting gene ID data from KEGG...
Info: Done with data retrieval!
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file eco00640.eco.entrez.png
Note: Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
Note: Mapping via KEGG gene ID (not Entrez) is supported for this species,
it looks like "K01488"!
Info: Downloading xml files for ko04112, 1/1 pathways..
Info: Downloading png files for ko04112, 1/1 pathways..
Info: Working in directory /private/tmp/RtmpjO7PBa/Rbuild66af6edbc48b/pathview/vignettes
Info: Writing image file ko04112.ko.data.png

Error: processing vignette 'pathview.Rnw' failed with diagnostics:
 chunk 37 (label = GAGE.Pathview.pipeline) 
Error in attempt to use zero-length variable name

--- failed re-building ‘pathview.Rnw’

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

Error: Vignette re-building failed.
Execution halted