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CHECK report for IntEREst on merida1

This page was generated on 2021-05-06 12:35:23 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the IntEREst package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 904/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.14.0  (landing page)
Ali Oghabian , Mikko Frilander
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/IntEREst
Branch: RELEASE_3_12
Last Commit: 514e896
Last Changed Date: 2020-10-27 11:22:16 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: IntEREst
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IntEREst_1.14.0.tar.gz
StartedAt: 2021-05-06 02:54:25 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:01:16 -0400 (Thu, 06 May 2021)
EllapsedTime: 411.1 seconds
RetCode: 0
Status:   OK  
CheckDir: IntEREst.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IntEREst_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/IntEREst.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.14.0’
* 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 ‘IntEREst’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DEXSeqIntEREst 30.242  0.254  30.538
deseqInterest   7.259  0.020   7.286
* 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

IntEREst.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IntEREst
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘IntEREst’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (IntEREst)

Tests output


Example timings

IntEREst.Rcheck/IntEREst-Ex.timings

nameusersystemelapsed
DEXSeqIntEREst30.242 0.25430.538
addAnnotation0.0590.0030.063
annotateU123.2750.0673.347
applyOverlap0.2680.0020.268
attributes0.0470.0030.051
boxplot-method0.0880.0010.089
buildSsTypePwms0.0010.0010.001
counts-method0.0410.0030.044
deseqInterest7.2590.0207.286
exactTestInterest0.1540.0030.157
getRepeatTable0.0010.0010.001
glmInterest0.1460.0040.150
interest1.9020.0201.925
interest.sequential1.9050.0171.926
interestResult0.0280.0010.030
interestResultIntEx0.1870.0010.189
intexIndex0.0050.0010.005
lfc0.2790.0040.284
mergeInterestResult0.0610.0020.062
plot-method0.3730.0080.381
psi1.1570.0081.167
qlfInterest0.1760.0040.180
readInterestResults0.0350.0030.039
referencePrepare1.4440.0091.454
subInterestResult0.0710.0020.073
treatInterest0.1770.0050.182
u12Boxplot0.1160.0010.117
u12BoxplotNb0.1680.0020.170
u12DensityPlot0.3870.0130.400
u12Index0.0110.0000.012
u12NbIndex0.1280.0020.130
unionRefTr0.0240.0010.026
updateRowDataCol0.0600.0020.062