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BioC 3.6: BUILD report for HCsnip on malbec1

This page was generated on 2017-08-16 13:20:48 -0400 (Wed, 16 Aug 2017).

Package 623/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HCsnip 1.17.0
Askar Obulkasim
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HCsnip
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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: 1.17.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HCsnip
StartedAt: 2017-08-15 19:18:52 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 19:19:06 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 13.8 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HCsnip
###
##############################################################################
##############################################################################


* checking for file ‘HCsnip/DESCRIPTION’ ... OK
* preparing ‘HCsnip’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... 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 2.5.0 
 
 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
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