BioC 3.2: BUILD report for gage on oaxaca

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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/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
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) :
cannot open URL 'http://rest.kegg.jp/get/hsa03013/kgml': HTTP status was '0 (null)'
Warning: Download of hsa03013 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa03013, 1/1 pathways..
Warning: Failed to download KEGG xml/png files, hsa03013 skipped!
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/Rtmp2g5OfR/Rbuild55e0484d09e7/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/Rtmp2g5OfR/Rbuild55e0484d09e7/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/Rtmp2g5OfR/Rbuild55e0484d09e7/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/Rtmp2g5OfR/Rbuild55e0484d09e7/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/Rtmp2g5OfR/Rbuild55e0484d09e7/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
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/Rtmp2g5OfR/Rbuild55e0484d09e7/gage/vignettes
Info: Writing image file hsa03013.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/Rtmp2g5OfR/Rbuild55e0484d09e7/gage/vignettes
Info: Writing image file hsa03008.deseq2.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /private/tmp/Rtmp2g5OfR/Rbuild55e0484d09e7/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

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'RNA-seqWorkflow.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `hsa03013.pathview.multi.png' not found.

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

l.307 ....png,read=.png]{hsa03013.pathview.multi}}

! ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted

BioC 3.2: BUILD report for gage on oaxaca

Summary

Command output