Galaxy Tool "r_bioc_depgen_r_3_1_2" run at 21/01/2015 11:25:22
r log output
Loading required package: BiocInstaller
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
Loading required package: pkgDepTools
Loading required package: methods
Loading required package: graph
Loading required package: RBGL
Loading required package: Biobase
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
trying URL 'http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc/src/contrib/DESeq2_1.6.3.tar.gz'
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Warning messages:
1: In .local(from, to, graph) :
edges replaced: 'MafDb.ALL.wgs.phase1.release.v3.20101123|VariantFiltering', 'NA|RSQLite', 'NA|Biobase', 'NA|AnnotationDbi', 'NA|IRanges', 'NA|Biostrings', 'NA|Rsamtools', 'NA|GenomicRanges', 'NA|VariantAnnotation'
2: In .local(from, to, graph) :
edges replaced: 'MafDb.ESP6500SI.V2.SSA137.dbSNP138|VariantFiltering', 'NA|RSQLite', 'NA|Biobase', 'NA|AnnotationDbi', 'NA|IRanges', 'NA|Biostrings', 'NA|GenomicRanges', 'NA|VariantAnnotation'
3: In .local(from, to, graph) :
edges replaced: 'phastCons100way.UCSC.hg19|VariantFiltering', 'NA|IRanges', 'NA|GenomicRanges', 'NA|BSgenome'
4: In .local(from, to, graph) : edges replaced: 'SNPRelate|gdsfmt'
5: In .local(from, to, graph) : edges replaced: 'RCurl|bitops'
Warning messages:
1: In if (grepl("*.gz", fullname)) { :
the condition has length > 1 and only the first element will be used
2: In if (grepl("*.gz", fullname)) { :
the condition has length > 1 and only the first element will be used
Other log output
## Toolfactory generated command line = Rscript /mnt/galaxy/tmp/143.1.all.q/r_bioc_depgen_r_3_1_2gRKYSn.Rscript OUTPATH="/mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat" tardir="/tmp" ourpackages="DESeq2" xmlprefix="https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/"
[1] "tardir= /tmp xmlprefix= https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ ourpackages= DESeq2 OUTPATH= /mnt/galaxy/tmp/job_working_directory/000/225/galaxy_dataset_508.dat"
[1] "BiocInstaller is loaded correctly"
[1] "pkgDepTools is loaded correctly"
[1] "Biobase is loaded correctly"
[1] Greetings! The R you have chosen is using the following repositories:
BioCsoft
http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/bioc
BioCann
http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/annotation
BioCexp
http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/data/experiment
BioCextra
http://mirror.aarnet.edu.au/pub/bioconductor//packages/3.0/extra
CRAN
http://cran.at.r-project.org
[,1] [,2]
[1,] "DESeq2" "/tmp/DESeq2_1.6.3.tar.gz"
[2,] "S4Vectors" "/tmp/S4Vectors_0.4.0.tar.gz"
[3,] "IRanges" "/tmp/IRanges_2.0.1.tar.gz"
[4,] "GenomicRanges" "/tmp/GenomicRanges_1.18.4.tar.gz"
[5,] "Rcpp" "/tmp/Rcpp_0.11.3.tar.gz"
[6,] "RcppArmadillo" "/tmp/RcppArmadillo_0.4.600.0.tar.gz"
[7,] "BiocGenerics" "/tmp/BiocGenerics_0.12.1.tar.gz"
[8,] "Biobase" "/tmp/Biobase_2.26.0.tar.gz"
[9,] "BiocParallel" "/tmp/BiocParallel_1.0.0.tar.gz"
[10,] "genefilter" "/tmp/genefilter_1.48.1.tar.gz"
[11,] "locfit" "/tmp/locfit_1.5-9.1.tar.gz"
[12,] "geneplotter" "/tmp/geneplotter_1.44.0.tar.gz"
[13,] "ggplot2" "/tmp/ggplot2_1.0.0.tar.gz"
[14,] "Hmisc" "/tmp/Hmisc_3.14-6.tar.gz"
[15,] "foreach" "/tmp/foreach_1.4.2.tar.gz"
[16,] "BatchJobs" "/tmp/BatchJobs_1.5.tar.gz"
[17,] "BBmisc" "/tmp/BBmisc_1.8.tar.gz"
[18,] "GenomeInfoDb" "/tmp/GenomeInfoDb_1.2.4.tar.gz"
[19,] "XVector" "/tmp/XVector_0.6.0.tar.gz"
[20,] "lattice" "/tmp/lattice_0.20-29.tar.gz"
[21,] "survival" "/tmp/survival_2.37-7.tar.gz"
[22,] "Formula" "/tmp/Formula_1.2-0.tar.gz"
[23,] "latticeExtra" "/tmp/latticeExtra_0.6-26.tar.gz"
[24,] "cluster" "/tmp/cluster_1.15.3.tar.gz"
[25,] "rpart" "/tmp/rpart_4.1-8.tar.gz"
[26,] "nnet" "/tmp/nnet_7.3-8.tar.gz"
[27,] "acepack" "/tmp/acepack_1.3-3.3.tar.gz"
[28,] "foreign" "/tmp/foreign_0.8-62.tar.gz"
[29,] "AnnotationDbi" "/tmp/AnnotationDbi_1.28.1.tar.gz"
[30,] "annotate" "/tmp/annotate_1.44.0.tar.gz"
[31,] "RColorBrewer" "/tmp/RColorBrewer_1.1-2.tar.gz"
[32,] "plyr" "/tmp/plyr_1.8.1.tar.gz"
[33,] "digest" "/tmp/digest_0.6.8.tar.gz"
[34,] "gtable" "/tmp/gtable_0.1.2.tar.gz"
[35,] "reshape2" "/tmp/reshape2_1.4.1.tar.gz"
[36,] "scales" "/tmp/scales_0.2.4.tar.gz"
[37,] "proto" "/tmp/proto_0.3-10.tar.gz"
[38,] "MASS" "/tmp/MASS_7.3-37.tar.gz"
[39,] "DBI" "/tmp/DBI_0.3.1.tar.gz"
[40,] "RSQLite" "/tmp/RSQLite_1.0.0.tar.gz"
[41,] "checkmate" "/tmp/checkmate_1.5.1.tar.gz"
[42,] "brew" "/tmp/brew_1.0-6.tar.gz"
[43,] "fail" "/tmp/fail_1.2.tar.gz"
[44,] "sendmailR" "/tmp/sendmailR_1.2-1.tar.gz"
[45,] "stringr" "/tmp/stringr_0.6.2.tar.gz"
[46,] "XML" "/tmp/XML_3.98-1.1.tar.gz"
[47,] "xtable" "/tmp/xtable_1.7-4.tar.gz"
[48,] "codetools" "/tmp/codetools_0.2-10.tar.gz"
[49,] "iterators" "/tmp/iterators_1.0.7.tar.gz"
[50,] "dichromat" "/tmp/dichromat_2.0-0.tar.gz"
[51,] "munsell" "/tmp/munsell_0.4.2.tar.gz"
[52,] "labeling" "/tmp/labeling_0.3.tar.gz"
[53,] "colorspace" "/tmp/colorspace_1.2-4.tar.gz"
[54,] "base64enc" "/tmp/base64enc_0.1-2.tar.gz"
[1] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true
[2] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true
[3] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true
[4] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true
[5] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true
[6] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.4.tar.gz?raw=true
[7] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true
[8] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true
[9] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true
[10] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true
[11] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true
[12] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true
[13] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true
[14] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true
[15] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true
[16] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true
[17] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true
[18] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true
[19] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true
[20] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true
[21] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true
[22] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true
[23] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true
[24] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true
[25] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true
[26] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true
[27] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true
[28] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true
[29] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true
[30] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true
[31] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true
[32] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true
[33] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true
[34] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true
[35] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true
[36] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true
[37] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true
[38] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true
[39] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true
[40] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true
[41] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true
[42] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true
[43] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true
[44] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.2-0.tar.gz?raw=true
[45] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true
[46] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true
[47] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true
[48] https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] parallel methods stats graphics grDevices utils datasets
[8] base
other attached packages:
[1] Biobase_2.26.0 BiocGenerics_0.12.1 pkgDepTools_1.32.0
[4] RBGL_1.42.0 graph_1.44.1 BiocInstaller_1.16.1
loaded via a namespace (and not attached):
[1] stats4_3.1.2 tools_3.1.2
[1] Wed Jan 21 11:25:22 2015
All output files available for downloading