############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiTC ### ############################################################################## ############################################################################## * checking for file ‘HiTC/DESCRIPTION’ ... OK * preparing ‘HiTC’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘HiC_analysis.Rnw’ using Sweave Loading required package: HiTC Loading required package: IRanges 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: 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: HiCDataHumanIMR90 'as(, "dgTMatrix")' is deprecated. Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated"). Warning: file stem ‘./HiTC-plot1’ is not portable Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Plotting chr5chr5... minrange= 2 - maxrange= 569 Plotting chr5chr6... minrange= 1 - maxrange= 8 Plotting chr5chr7... minrange= 1 - maxrange= 8 Plotting chr6chr6... minrange= 3 - maxrange= 593.02 Plotting chr6chr7... minrange= 1 - maxrange= 8 Plotting chr7chr7... minrange= 2 - maxrange= 571 Warning: file stem ‘./HiTC-plot2’ is not portable Plotting chr5chr5... minrange= 1 - maxrange= 200 Plotting chr5chr6... minrange= 1 - maxrange= 200 Plotting chr5chr7... minrange= 1 - maxrange= 119 Plotting chr6chr5... minrange= 1 - maxrange= 200 Plotting chr6chr6... minrange= 1 - maxrange= 200 Plotting chr6chr7... minrange= 1 - maxrange= 81 Plotting chr7chr5... minrange= 1 - maxrange= 119 Plotting chr7chr6... minrange= 1 - maxrange= 81 Plotting chr7chr7... minrange= 1 - maxrange= 200 Loading required package: BSgenome.Hsapiens.UCSC.hg18 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’ Error: processing vignette 'HiC_analysis.Rnw' failed with diagnostics: chunk 6 (label = resFrag) Error in getRestrictionFragmentsPerChromosome(resSite = "AAGCTT", overhangs5 = 1, : require(genomePack, character.only = TRUE) is not TRUE --- failed re-building ‘HiC_analysis.Rnw’ --- re-building ‘HiTC.Rnw’ using Sweave Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Warning: file stem ‘./HiTC-qcc’ is not portable Get data ... Generate quality control plots ... minrange= 1 - maxrange= 741 Warning: file stem ‘./HiTC-bin5C’ is not portable Bin size 'xgi' =102420 [3x34140] Bin size 'ygi' =102420 [3x34140] minrange= 3 - maxrange= 477.2 Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... minrange= 0.027 - maxrange= 2.139 Warning: file stem ‘./HiTC-annot5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] Loading required package: rtracklayer minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-comp5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] minrange= 0.5 - maxrange= 10 minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-mapClist’ is not portable Plotting chr12chr12... minrange= 1 - maxrange= 100 Plotting chr12chr13... minrange= 1 - maxrange= 20 Plotting chr12chr14... minrange= 1 - maxrange= 39 Plotting chr13chr13... minrange= 1 - maxrange= 100 Plotting chr13chr14... minrange= 1 - maxrange= 18 Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapChic’ is not portable Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapNormhic’ is not portable Lowess fit ... Plotting chr14chr14... minrange= 0.015 - maxrange= 2.519 Warning: file stem ‘./HiTC-mapCorhic’ is not portable Plotting chr14chr14... minrange= 0 - maxrange= 1 Warning: file stem ‘./HiTC-mapPCAhic’ is not portable Lowess fit ... --- finished re-building ‘HiTC.Rnw’ SUMMARY: processing the following file failed: ‘HiC_analysis.Rnw’ Error: Vignette re-building failed. Execution halted