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CHECK report for IntEREst on merida1

This page was generated on 2019-04-16 12:00:28 -0400 (Tue, 16 Apr 2019).

Package 784/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.6.2
Ali Oghabian , Mikko Frilander
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/IntEREst
Branch: RELEASE_3_8
Last Commit: 8b33290
Last Changed Date: 2019-02-11 05:11:26 -0400 (Mon, 11 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: IntEREst
Version: 1.6.2
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_1.6.2.tar.gz
StartedAt: 2019-04-16 00:43:42 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:49:13 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 331.4 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_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/IntEREst.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntEREst/DESCRIPTION’ ... OK
* this is package ‘IntEREst’ version ‘1.6.2’
* 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 or elapsed time > 5s
                 user system elapsed
DEXSeqIntEREst 41.674  0.442  42.288
* 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/3.5/Resources/library’
* installing *source* package ‘IntEREst’ ...
** 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
* DONE (IntEREst)

Tests output


Example timings

IntEREst.Rcheck/IntEREst-Ex.timings

nameusersystemelapsed
DEXSeqIntEREst41.674 0.44242.288
addAnnotation0.0420.0030.045
annotateU122.7470.0772.836
attributes0.0360.0010.038
boxplot-method0.0650.0010.066
buildSsTypePwms0.0010.0000.001
counts-method0.1010.0010.102
deseqInterest2.8730.0322.920
exactTestInterest0.1070.0010.109
getRepeatTable000
glmInterest0.2050.0050.212
interest2.5350.0232.568
interest.sequential1.6260.0221.653
interestResult0.0240.0010.025
interestResultIntEx0.1740.0020.182
intexIndex0.0050.0000.005
lfc0.1390.0010.139
mergeInterestResult0.2970.0010.300
plot-method0.3950.0040.401
psi1.0720.0061.088
qlfInterest0.1890.0100.201
readInterestResults0.0370.0020.039
referencePrepare1.2050.0081.217
subInterestResult0.0500.0010.050
treatInterest0.1650.0070.172
u12Boxplot0.0850.0020.088
u12BoxplotNb0.1330.0010.134
u12DensityPlot0.3430.0120.356
u12Index0.0080.0010.008
u12NbIndex0.1220.0020.125
unionRefTr0.020.000.02
updateRowDataCol0.0380.0010.041