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BioC 3.6: CHECK report for CancerSubtypes on malbec1

This page was generated on 2017-08-16 13:24:52 -0400 (Wed, 16 Aug 2017).

Package 171/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.3.7
Taosheng Xu
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CancerSubtypes
Last Changed Rev: 131885 / Revision: 131943
Last Changed Date: 2017-08-10 13:03:23 -0400 (Thu, 10 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerSubtypes
Version: 1.3.7
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz
StartedAt: 2017-08-15 21:44:20 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:47:34 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 193.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CancerSubtypes_1.3.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CancerSubtypes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerSubtypes’ version ‘1.3.7’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CancerSubtypes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
sigclustTest  44.780  0.020  44.829
ExecuteCNMF   25.588  1.020  10.945
ExecuteSNF.CC 16.292  0.024  16.328
survAnalysis  11.044  0.004  11.068
ExecuteCC      8.752  0.020   8.776
drawHeatmap    5.476  0.028   5.522
FSbyCox        5.348  0.000   5.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

CancerSubtypes.Rcheck/00install.out:

* installing *source* package ‘CancerSubtypes’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CancerSubtypes)

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings:

nameusersystemelapsed
DiffExp.limma1.1320.0201.150
ExecuteCC8.7520.0208.776
ExecuteCNMF25.588 1.02010.945
ExecuteSNF.CC16.292 0.02416.328
ExecuteSNF0.2640.0040.265
ExecuteWSNF1.9480.0081.962
ExecuteiCluster3.6880.0003.686
FSbyCox5.3480.0005.353
FSbyMAD0.2160.0000.216
FSbyPCA0.1360.0000.133
FSbyVar0.0880.0000.089
GeneExp0.040.000.04
Ranking0.0240.0000.025
data.checkDistribution0.3360.0000.333
data.imputation0.0040.0000.006
data.normalization0.1280.0000.126
drawHeatmap5.4760.0285.522
miRNAExp0.0040.0000.006
saveFigure1.7040.0121.717
sigclustTest44.780 0.02044.829
silhouette_SimilarityMatrix0.3040.0000.303
spectralAlg0.0280.0000.029
status0.0000.0000.003
survAnalysis11.044 0.00411.068
time0.0000.0000.002