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### Running command:
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###   /Library/Frameworks/R.framework/Resources/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RNA-seqWorkflow.Rnw’ using Sweave
Loading required package: gageData


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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).
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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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/gage/vignettes
Info: Writing image file hsa04510.pathview.multi.png

Error: processing vignette 'RNA-seqWorkflow.Rnw' failed with diagnostics:
 chunk 15 (label = deseq2) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

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

--- re-building ‘dataPrep.Rnw’ using Sweave
Loading required package: AnnotationDbi
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: 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 objects are masked from ‘package:base’:

    I, expand.grid, unname

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
Gene ID type for 'human' is: 'EG'
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/gage/vignettes
Info: Writing image file hsa00020.pathview.multi.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/gage/vignettes
Info: Writing image file hsa04110.pathview.multi.pdf
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 /private/tmp/Rtmp4O5ITc/Rbuild13741b3c2a9c/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:
  ‘RNA-seqWorkflow.Rnw’

Error: Vignette re-building failed.
Execution halted