BioC 3.2: BUILD report for gage on moscato1

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### Running command:
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###   chmod a+r gage -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe 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 ...Warning: running command '"D:/biocbld/bbs-3.2-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: gageData
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

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
Loading required package: DBI

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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.

The pathview downloads and uses KEGG data. Academic users may freely use the
KEGG website at http://www.kegg.jp/ or its mirror site at GenomeNet
http://www.genome.jp/kegg/. Academic users may also freely link to the KEGG
website. Non-academic users may use the KEGG website as end users for
non-commercial purposes, but any other use requires a license agreement
(details at http://www.kegg.jp/kegg/legal.html).
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Info: Downloading xml files for hsa03013, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 45848 != reported length 200
Info: Downloading png files for hsa03013, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpADZQqY/Rbuild221c23201bef/gage/vignettes
Info: Writing image file hsa03013.pathview.multi.png
Info: Downloading xml files for hsa03008, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 8573 != reported length 200
Info: Downloading png files for hsa03008, 1/1 pathways..
Warning: Parsing ./hsa03008.xml file failed, please check the file!
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 15872 != reported length 200
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Parsing ./hsa04110.xml file failed, please check the file!
Info: Downloading xml files for hsa04610, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 14412 != reported length 200
Info: Downloading png files for hsa04610, 1/1 pathways..
Warning: Parsing ./hsa04610.xml file failed, please check the file!
Info: Downloading xml files for hsa04512, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 5653 != reported length 200
Info: Downloading png files for hsa04512, 1/1 pathways..
Warning: Parsing ./hsa04512.xml file failed, please check the file!
Info: Downloading xml files for hsa04510, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  downloaded length 36991 != reported length 200
Info: Downloading png files for hsa04510, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpADZQqY/Rbuild221c23201bef/gage/vignettes
Info: Writing image file hsa04510.pathview.multi.png
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Rcpp
Loading required package: RcppArmadillo
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 D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpADZQqY/Rbuild221c23201bef/gage/vignettes
Info: Writing image file hsa03013.deseq2.png
Warning: Parsing ./hsa03008.xml file failed, please check the file!
Warning: Parsing ./hsa04110.xml file failed, please check the file!
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

Warning: running command '"c:\MikTex2.9\miktex\bin\texify.exe" --quiet --pdf "RNA-seqWorkflow.tex" --max-iterations=20 -I "D:/biocbld/bbs-3.2-bioc/R/share/texmf/tex/latex" -I "D:/biocbld/bbs-3.2-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'RNA-seqWorkflow.tex' failed

LaTeX errors:
-seqWorkflow.tex:338: Package pdftex.def Error: File `hsa04512.pathview.multi.p
ng' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help
Execution halted
BioC 3.2: BUILD report for gage on moscato1

Summary

Command output
