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BioC 3.4: BUILD report for HiTC on moscato1

This page was generated on 2016-09-21 03:44:09 -0700 (Wed, 21 Sep 2016).

Package 579/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.17.2
Nicolas Servant
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HiTC
Last Changed Rev: 121144 / Revision: 121152
Last Changed Date: 2016-09-19 10:40:00 -0700 (Mon, 19 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded [ ERROR ] skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: HiTC
Version: 1.17.2
Command: chmod a+r HiTC -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HiTC
StartedAt: 2016-09-19 23:25:15 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 23:27:06 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 110.3 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r HiTC -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe 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 ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: HiTC
Loading required package: IRanges
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 objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame,
    cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: HiCDataHumanIMR90
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
Note: method with signature 'CsparseMatrix#Matrix#missing#replValue' chosen for function '[<-',
 target signature 'dgCMatrix#lgCMatrix#missing#numeric'.
 "Matrix#lsparseMatrix#missing#replValue" would also be valid

Error: processing vignette 'HiC_analysis.Rnw' failed with diagnostics:
 chunk 4 (label = plot1) 
Error in base::which(x, arr.ind, useNames, ...) : 
  argument to 'which' is not logical
Execution halted