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CHECK report for IntEREst on merida2

This page was generated on 2018-10-17 08:57:54 -0400 (Wed, 17 Oct 2018).

Package 742/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntEREst 1.4.1
Ali Oghabian , Mikko Frilander
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IntEREst
Branch: RELEASE_3_7
Last Commit: 58b2cf4
Last Changed Date: 2018-05-02 07:06:36 -0400 (Wed, 02 May 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IntEREst
Version: 1.4.1
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_1.4.1.tar.gz
StartedAt: 2018-10-16 22:06:55 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:12:30 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 334.7 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_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/IntEREst.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.4.1’
* 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 39.694  0.366  40.226
* 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
DEXSeqIntEREst39.694 0.36640.226
addAnnotation0.0370.0020.038
annotateU122.9030.0512.966
attributes0.0540.0010.055
boxplot-method0.0810.0010.082
buildSsTypePwms0.0030.0010.004
counts-method0.0980.0020.100
deseqInterest2.7060.0122.730
exactTestInterest0.1230.0010.125
getRepeatTable0.0010.0000.002
glmInterest0.1960.0080.205
interest2.2040.0512.262
interest.sequential2.0940.0152.119
interestResult0.0280.0010.029
interestResultIntEx0.1630.0010.164
intexIndex0.0050.0000.005
lfc0.1570.0010.158
mergeInterestResult0.3070.0010.311
plot-method0.3730.0030.386
psi1.1510.0071.170
qlfInterest0.1910.0060.200
readInterestResults0.0490.0020.052
referencePrepare1.1950.0051.209
subInterestResult0.0900.0020.092
treatInterest0.2080.0100.218
u12Boxplot0.1190.0010.121
u12BoxplotNb0.1360.0010.138
u12DensityPlot1.0600.0201.085
u12Index0.0120.0000.012
u12NbIndex0.1130.0010.117
unionRefTr0.0210.0000.022
updateRowDataCol0.0280.0010.030