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BUILD report for HCsnip on tokay1

This page was generated on 2018-04-12 13:30:57 -0400 (Thu, 12 Apr 2018).

Package 640/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HCsnip 1.18.0
Askar Obulkasim
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/HCsnip
Branch: RELEASE_3_6
Last Commit: 74e8a83
Last Changed Date: 2017-10-30 12:40:00 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded [ ERROR ] skipped  skipped 
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: HCsnip
Version: 1.18.0
Command: chmod a+r HCsnip -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HCsnip
StartedAt: 2018-04-11 21:52:38 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:53:13 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 35.2 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   chmod a+r HCsnip -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HCsnip
###
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* checking for file 'HCsnip/DESCRIPTION' ... OK
* preparing 'HCsnip':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
 ERROR
Loading required package: survival
Loading required package: coin
Loading required package: fpc
Loading required package: clusterRepro
Loading required package: impute
Loading required package: randomForestSRC

 randomForestSRC 2.5.1 
 
 Type rfsrc.news() to see new features, changes, and bug fixes. 
 

Loading required package: sm
Package 'sm', version 2.2-5.4: type help(sm) for summary information
Loading required package: sigaR
Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: mvtnorm
Warning: Package 'HCsnip' is deprecated and will be removed from Bioconductor
  version 3.7
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

Error: processing vignette 'HCsnip.Rnw' failed with diagnostics:
 chunk 6 (label = chunk6) 
Error : 'surv_test' is defunct.  Use 'logrank_test' instead.
Execution halted