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CHECK report for CancerSubtypes on malbec2

This page was generated on 2019-04-09 11:46:35 -0400 (Tue, 09 Apr 2019).

Package 206/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.9.0
Taosheng Xu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CancerSubtypes
Branch: master
Last Commit: 0e61488
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CancerSubtypes
Version: 1.9.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CancerSubtypes_1.9.0.tar.gz
StartedAt: 2019-04-08 23:12:14 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:15:46 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 211.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CancerSubtypes_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CancerSubtypes.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.0’
* 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 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  37.522  0.040  37.606
ExecuteCNMF   33.402  1.879  14.748
ExecuteSNF.CC 31.022  0.307  19.291
survAnalysis  17.210  0.008  17.225
FSbyCox        8.811  0.007   8.822
ExecuteCC      6.910  0.027   7.144
drawHeatmap    5.029  0.036   5.067
* 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


Installation output

CancerSubtypes.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CancerSubtypes
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CancerSubtypes’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CancerSubtypes)

Tests output

CancerSubtypes.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("CancerSubtypes")

Attaching package: 'pkgmaker'

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

    isFALSE

NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Mon Apr  8 23:15:42 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CancerSubtypes RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.204   0.165   3.485 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.3750.0000.375
ExecuteCC6.9100.0277.144
ExecuteCNMF33.402 1.87914.748
ExecuteSNF.CC31.022 0.30719.291
ExecuteSNF0.2230.0000.223
ExecuteWSNF1.8340.0191.855
ExecuteiCluster4.3760.0134.388
FSbyCox8.8110.0078.822
FSbyMAD0.2140.0000.214
FSbyPCA0.1260.0000.126
FSbyVar0.0660.0000.066
GeneExp0.0360.0040.040
Ranking0.0270.0000.027
data.checkDistribution0.2560.0040.260
data.imputation0.0060.0000.006
data.normalization0.1370.0000.137
drawHeatmap5.0290.0365.067
miRNAExp0.0060.0000.006
saveFigure1.1080.0041.112
sigclustTest37.522 0.04037.606
silhouette_SimilarityMatrix0.3410.0000.341
spectralAlg0.0260.0000.027
status0.0010.0000.002
survAnalysis17.210 0.00817.225
time0.0020.0000.002