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CHECK report for CancerSubtypes on malbec1

This page was generated on 2020-04-15 12:11:43 -0400 (Wed, 15 Apr 2020).

Package 223/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.12.1
Taosheng Xu
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CancerSubtypes
Branch: RELEASE_3_10
Last Commit: 68df12d
Last Changed Date: 2020-04-04 04:40:16 -0400 (Sat, 04 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CancerSubtypes
Version: 1.12.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CancerSubtypes_1.12.1.tar.gz
StartedAt: 2020-04-15 04:03:37 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:07:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 248.3 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-3.10-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CancerSubtypes_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CancerSubtypes.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.1’
* 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  42.988  0.036  43.494
ExecuteCNMF   31.560  1.808  17.657
ExecuteSNF.CC 32.924  0.340  21.999
survAnalysis  18.408  0.000  18.617
FSbyCox       10.604  0.004  10.643
ExecuteCC      9.464  0.064  10.464
drawHeatmap    6.560  0.040   6.675
* 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-3.10-bioc/R/bin/R CMD INSTALL CancerSubtypes
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Wed Apr 15 04:07:42 2020 
*********************************************** 
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 
  4.368   0.172   4.576 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.4000.0360.502
ExecuteCC 9.464 0.06410.464
ExecuteCNMF31.560 1.80817.657
ExecuteSNF.CC32.924 0.34021.999
ExecuteSNF0.3720.0120.386
ExecuteWSNF2.9960.0243.030
ExecuteiCluster4.2480.0084.288
FSbyCox10.604 0.00410.643
FSbyMAD0.3040.0000.302
FSbyPCA0.1920.0000.201
FSbyVar0.0960.0000.099
GeneExp0.0640.0000.062
Ranking0.0440.0000.045
data.checkDistribution0.3880.0000.387
data.imputation0.0080.0000.008
data.normalization0.1640.0080.169
drawHeatmap6.5600.0406.675
miRNAExp0.0080.0000.007
saveFigure1.5000.0081.561
sigclustTest42.988 0.03643.494
silhouette_SimilarityMatrix0.3520.0040.362
spectralAlg0.0480.0000.047
status0.0000.0000.002
survAnalysis18.408 0.00018.617
time0.0040.0000.002