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CHECK report for ImpulseDE2 on malbec2

This page was generated on 2019-04-09 11:47:58 -0400 (Tue, 09 Apr 2019).

Package 797/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ImpulseDE2 1.7.1
David S Fischer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ImpulseDE2
Branch: master
Last Commit: 933737f
Last Changed Date: 2019-01-04 13:15:10 -0400 (Fri, 04 Jan 2019)
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: ImpulseDE2
Version: 1.7.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ImpulseDE2_1.7.1.tar.gz
StartedAt: 2019-04-09 01:22:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:28:47 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 365.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ImpulseDE2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ImpulseDE2_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ImpulseDE2.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 ‘ImpulseDE2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImpulseDE2’ version ‘1.7.1’
* package encoding: UTF-8
* 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 ‘ImpulseDE2’ 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
plotGenes: no visible global function definition for ‘error’
plotGenes: no visible binding for global variable ‘normCounts’
plotGenes: no visible binding for global variable ‘Condition’
plotGenes: no visible binding for global variable ‘Batch’
plotGenes: no visible binding for global variable ‘value’
plotGenes: no visible binding for global variable ‘BatchFit’
Undefined global functions or variables:
  Batch BatchFit Condition error normCounts value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotHeatmap       35.158  0.156  35.361
updateDEAnalysis  32.016  0.048  32.068
plotGenes         28.372  0.059  28.437
fitSigmoidModels  20.350  0.276  20.659
get_accessors     19.007  0.024  19.031
runImpulseDE2     17.413  0.035  17.451
list_accession    16.930  0.032  16.980
writeReportToFile 15.975  0.040  16.017
* 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-3.9-bioc/meat/ImpulseDE2.Rcheck/00check.log’
for details.



Installation output

ImpulseDE2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ImpulseDE2
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ImpulseDE2’ ...
** using staged installation
** R
** 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 (ImpulseDE2)

Tests output


Example timings

ImpulseDE2.Rcheck/ImpulseDE2-Ex.timings

nameusersystemelapsed
computeNormConst0.1500.0040.154
fitSigmoidModels20.350 0.27620.659
get_accessors19.007 0.02419.031
list_accession16.930 0.03216.980
plotGenes28.372 0.05928.437
plotHeatmap35.158 0.15635.361
runImpulseDE217.413 0.03517.451
simulateDataSetImpulseDE20.0220.0000.021
updateDEAnalysis32.016 0.04832.068
writeReportToFile15.975 0.04016.017