############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pathview ### ############################################################################## ############################################################################## * checking for file ‘pathview/DESCRIPTION’ ... OK * preparing ‘pathview’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘pathview.Rnw’ using Sweave ############################################################################## 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). ############################################################################## 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 /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.2layer.png 'select()' returned 1:1 mapping between keys and columns Warning: reconcile groups sharing member nodes! Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.pdf 'select()' returned 1:1 mapping between keys and columns Warning: reconcile groups sharing member nodes! Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.2layer.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.split.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa04110.gse16873.split.expanded.pdf Info: Downloading xml files for hsa00640, 1/1 pathways.. Info: Downloading png files for hsa00640, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.png Warning in .local(from, to, graph) : edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’ 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.pdf 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.match.multi.png Warning in .local(from, to, graph) : edges replaced: ‘180|60’, ‘122|119’, ‘122|120’, ‘84|77’, ‘84|199’ 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gse16873.cpd.3-2s.multi.pdf Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.sel.genes.sel.cpd.png 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.sel.genes.cpd.png Note: "CAS Registry Number" has only 4643 unique IDs! Note: "ENSEMBLPROT" has only 22648 unique IDs! 'select()' returned 1:many mapping between keys and columns Note: multiple compounds may map to a input ID, only the first one kept! 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gene.ensprot.cpd.cas.png Note: multiple compounds may map to a input ID, only the first one kept! 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file hsa00640.gene.entrez.cpd.kc.png Info: Downloading xml files for eco00640, 1/1 pathways.. Info: Downloading png files for eco00640, 1/1 pathways.. Info: Working in directory /home/biocbuild/tmp/Rtmpw4kkSg/Rbuild28f94e25018102/pathview/vignettes Info: Writing image file eco00640.eco.kegg.png Loading required namespace: org.EcK12.eg.db Error: processing vignette 'pathview.Rnw' failed with diagnostics: chunk 34 (label = eco.dat.kegg) Error : incomplete input --- failed re-building ‘pathview.Rnw’ SUMMARY: processing the following file failed: ‘pathview.Rnw’ Error: Vignette re-building failed. Execution halted