Back to Multiple platform build/check report for BioC 3.12
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for IntEREst on merida1

This page was generated on 2021-05-05 12:14:30 -0400 (Wed, 05 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: 2021-05-04 14:50:13 -0400 (Tue, 04 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: 2021-05-05 03:32:56 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 03:40:19 -0400 (Wed, 05 May 2021)
EllapsedTime: 442.6 seconds
RetCode: 0
Status:   OK  
CheckDir: IntEREst.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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 32.057  0.292  32.398
deseqInterest   7.412  0.023   7.445
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IntEREst
###
##############################################################################
##############################################################################


* 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
DEXSeqIntEREst32.057 0.29232.398
addAnnotation0.0520.0020.053
annotateU123.7040.0833.792
applyOverlap0.2950.0020.297
attributes0.0430.0030.047
boxplot-method0.0880.0010.089
buildSsTypePwms0.0010.0000.000
counts-method0.0440.0030.047
deseqInterest7.4120.0237.445
exactTestInterest0.1720.0030.174
getRepeatTable000
glmInterest0.1910.0040.196
interest2.2920.0232.319
interest.sequential2.1370.0182.157
interestResult0.0210.0010.023
interestResultIntEx0.2100.0020.211
intexIndex0.0060.0000.006
lfc0.2470.0070.254
mergeInterestResult0.0640.0010.066
plot-method0.4510.0140.466
psi1.2470.0131.262
qlfInterest0.2240.0070.231
readInterestResults0.0520.0040.055
referencePrepare1.4750.0101.487
subInterestResult0.0760.0020.077
treatInterest0.1680.0040.172
u12Boxplot0.1420.0020.144
u12BoxplotNb0.1850.0010.186
u12DensityPlot0.3830.0110.395
u12Index0.0130.0000.013
u12NbIndex0.1270.0020.129
unionRefTr0.0240.0010.025
updateRowDataCol0.0680.0020.070