Multiple platform build/check report for BioC 3.11 - CHECK report for IntEREst on machv2

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IntEREst.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.12.0’
* 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 35.368  0.285  35.686
deseqInterest   8.195  0.013   8.212
* 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

##############################################################################
##############################################################################
###
### 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

name	user	system	elapsed
DEXSeqIntEREst	35.368	0.285	35.686
addAnnotation	0.063	0.002	0.065
annotateU12	4.230	0.098	4.331
applyOverlap	0.326	0.002	0.328
attributes	0.063	0.004	0.067
boxplot-method	0.110	0.002	0.112
buildSsTypePwms	0.001	0.000	0.001
counts-method	0.036	0.002	0.038
deseqInterest	8.195	0.013	8.212
exactTestInterest	0.142	0.003	0.144
getRepeatTable	0.001	0.001	0.001
glmInterest	0.228	0.003	0.231
interest	2.502	0.023	2.528
interest.sequential	3.266	0.021	3.289
interestResult	0.030	0.002	0.033
interestResultIntEx	0.271	0.002	0.273
intexIndex	0.009	0.000	0.010
lfc	0.348	0.005	0.353
mergeInterestResult	0.103	0.003	0.105
plot-method	0.561	0.045	0.608
psi	1.276	0.070	1.346
qlfInterest	0.186	0.006	0.193
readInterestResults	0.045	0.003	0.048
referencePrepare	1.605	0.007	1.613
subInterestResult	0.051	0.001	0.052
treatInterest	0.245	0.013	0.259
u12Boxplot	0.143	0.002	0.145
u12BoxplotNb	0.165	0.001	0.177
u12DensityPlot	0.395	0.008	0.404
u12Index	0.01	0.00	0.01
u12NbIndex	0.146	0.002	0.149
unionRefTr	0.028	0.001	0.029
updateRowDataCol	0.068	0.002	0.071

CHECK report for IntEREst on machv2

Summary

Command output

Installation output

Tests output

Example timings