Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).

CHECK results for CancerSubtypes on nebbiolo1

To the developers/maintainers of the CancerSubtypes package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CancerSubtypes.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 238/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerSubtypes 1.18.0  (landing page)
Taosheng Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CancerSubtypes
git_branch: RELEASE_3_13
git_last_commit: 66e771e
git_last_commit_date: 2021-05-19 12:22:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CancerSubtypes
Version: 1.18.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CancerSubtypes_1.18.0.tar.gz
StartedAt: 2021-10-14 09:08:27 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:11:07 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 159.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CancerSubtypes.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CancerSubtypes.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CancerSubtypes_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CancerSubtypes.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.18.0’
* 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 ... NOTE
displayClusters: no visible global function definition for ‘grey’
Undefined global functions or variables:
  grey
Consider adding
  importFrom("grDevices", "grey")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
                user system elapsed
sigclustTest  24.839  0.024  24.868
ExecuteCNMF   18.389  5.833   9.671
ExecuteSNF.CC 14.228  0.468  14.697
survAnalysis  10.599  0.026  10.624
FSbyCox        7.820  0.013   7.833
ExecuteCC      6.198  0.100   6.299
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CancerSubtypes.Rcheck/00check.log’
for details.



Installation output

CancerSubtypes.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CancerSubtypes
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 71/72
  To enable shared memory capabilities, try: install.extras('
NMF
')


RUNIT TEST PROTOCOL -- Thu Oct 14 09:11:04 2021 
*********************************************** 
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 
  3.144   0.181   3.310 

Example timings

CancerSubtypes.Rcheck/CancerSubtypes-Ex.timings

nameusersystemelapsed
DiffExp.limma0.2830.0200.303
ExecuteCC6.1980.1006.299
ExecuteCNMF18.389 5.833 9.671
ExecuteSNF.CC14.228 0.46814.697
ExecuteSNF0.5000.0160.516
ExecuteWSNF1.6830.0281.711
ExecuteiCluster3.4550.0183.474
FSbyCox7.8200.0137.833
FSbyMAD0.1600.0040.163
FSbyPCA0.1520.0120.164
FSbyVar0.0490.0040.053
GeneExp0.0140.0030.017
Ranking0.0270.0080.034
affinityMatrix0.0210.0000.022
data.checkDistribution0.2660.0080.274
data.imputation0.0050.0000.006
data.normalization0.0750.0040.079
dist20.0110.0000.012
drawHeatmap3.6760.0683.746
miRNAExp0.0050.0000.005
saveFigure0.7670.0080.776
sigclustTest24.839 0.02424.868
silhouette_SimilarityMatrix0.2260.0040.229
spectralAlg0.0050.0000.005
status0.0000.0010.002
survAnalysis10.599 0.02610.624
time0.0020.0000.001