############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r rRDP -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data rRDP ### ############################################################################## ############################################################################## * checking for file 'rRDP/DESCRIPTION' ... OK * preparing 'rRDP': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building 'rRDP.Rnw' using Sweave Loading required package: Biostrings Loading required package: BiocGenerics 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Warning in system(exe, ignore.stdout = TRUE, ignore.stderr = TRUE, intern = FALSE) : '\bin\java.exe' not found Error: processing vignette 'rRDP.Rnw' failed with diagnostics: chunk 8 (label = predict) Error in predict.RDPClassifier(rdp(), seq) : Error executing: \bin\java.exe -Xmx1g -jar F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpMzamWw\Rinst3054431f6751\rRDP\java\rdp_classifier.jar classify -t F:\biocbuild\bbs-3.18-bioc\R\library\rRDPData\extdata\16srrna\rRNAClassifier.properties -o F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpEH6Cla\file3dd470035e75_tax_assignments.txt -c 0.8 -format fixrank F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpEH6Cla\file3dd470035e75.fasta --- failed re-building 'rRDP.Rnw' SUMMARY: processing the following file failed: 'rRDP.Rnw' Error: Vignette re-building failed. Execution halted