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lcolladotor/der2R-oVSy.run2-v0.0.46.e659794

Created April 23, 2014 20:08
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der2R-oVSy.run2-v0.0.46.e659794
Warning message:
In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
Loading required package: GenomicFeatures
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 object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: AnnotationDbi
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")'.
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
Writing 1 Bibtex entries ... OK
Results written to file 'run2-v0.0.46/basicExploration/references.bib'
processing file: basicExploration.Rmd
citation already in database
citation already in database
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
citation already in database
citation already in database
citation already in database
citation already in database
citation already in database
output file: basicExploration.knit.md
Output created: basicExploration.html
Error in tools::file_path_as_absolute(output_file) :
file 'basicExploration.html' does not exist
Calls: generateReport -> render -> <Anonymous>
In addition: Warning messages:
1: In png(tempfile()) : unable to open connection to X11 display ''
2: 'metadata' object already exists in knit environment so won't be accessible during knit
Execution halted
Raw
der2R-oVSy.run2-v0.0.46.o659794
**** Job starts ****
Wed Apr 23 14:48:52 EDT 2014
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/jhpce/shared/jhpce/core/JHPCE_tools/1.0/bin/pandoc basicExploration.utf8.md --to html --from markdown-hard_line_breaks+superscript+tex_math_dollars+raw_html+markdown_in_html_blocks-implicit_figures --output basicExploration.html --filter /jhpce/shared/jhpce/core/JHPCE_tools/1.0/bin/pandoc-citeproc -H /scratch/temp/659794.1.shared.q/RtmpQYJuqJ/knitr_bootstrap_full.html
**** Job ends ****
Wed Apr 23 15:54:02 EDT 2014
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