##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/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
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 objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: HiCDataHumanIMR90
as(<dsCMatrix>, "dgTMatrix") is deprecated since Matrix 1.5-0; do as(as(., "generalMatrix"), "TsparseMatrix") instead
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