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CHECK report for IntEREst on malbec1

This page was generated on 2021-05-05 12:10:04 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings IntEREst_1.14.0.tar.gz
StartedAt: 2021-05-05 02:44:22 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 02:51:02 -0400 (Wed, 05 May 2021)
EllapsedTime: 400.0 seconds
RetCode: 0
Status:   OK  
CheckDir: IntEREst.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings IntEREst_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/IntEREst.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 30.792  0.176  31.047
deseqInterest   7.268  0.016   7.307
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL IntEREst
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
DEXSeqIntEREst30.792 0.17631.047
addAnnotation0.0640.0000.061
annotateU124.7160.1764.897
applyOverlap0.2200.0000.222
attributes0.0520.0040.058
boxplot-method0.1160.0000.116
buildSsTypePwms0.0000.0000.001
counts-method0.0480.0000.046
deseqInterest7.2680.0167.307
exactTestInterest0.1600.0000.161
getRepeatTable000
glmInterest0.2280.0080.243
interest2.1520.0042.178
interest.sequential1.4200.0041.424
interestResult0.0200.0000.018
interestResultIntEx0.2160.0000.218
intexIndex0.0080.0000.009
lfc0.2120.0040.217
mergeInterestResult0.0560.0000.057
plot-method0.4160.0040.420
psi0.7120.0040.714
qlfInterest0.2120.0040.216
readInterestResults0.0360.0000.036
referencePrepare1.2560.0001.256
subInterestResult0.0520.0000.050
treatInterest1.3080.0081.318
u12Boxplot0.1560.0000.160
u12BoxplotNb0.2000.0000.201
u12DensityPlot0.2720.0000.271
u12Index0.0160.0000.015
u12NbIndex0.1520.0000.153
unionRefTr0.0240.0000.026
updateRowDataCol0.0680.0000.066