Multiple platform build/check report for BioC 3.11 - CHECK report for IntEREst on celaya2

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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_1.11.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IntEREst.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.2’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.InterestResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 42.116  0.680  42.825
deseqInterest  11.137  0.067  11.207
annotateU12     4.996  0.200   5.195
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/IntEREst.Rcheck/00check.log’
for details.

Installation output

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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/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	42.116	0.680	42.825
addAnnotation	0.046	0.002	0.048
annotateU12	4.996	0.200	5.195
applyOverlap	0.372	0.013	0.384
attributes	0.086	0.005	0.092
boxplot-method	0.157	0.007	0.163
buildSsTypePwms	0.001	0.001	0.002
counts-method	0.056	0.004	0.061
deseqInterest	11.137	0.067	11.207
exactTestInterest	0.152	0.002	0.154
getRepeatTable	0.001	0.000	0.001
glmInterest	0.358	0.040	0.398
interest	3.611	0.050	3.665
interest.sequential	2.680	0.030	2.712
interestResult	0.029	0.002	0.031
interestResultIntEx	0.316	0.002	0.318
intexIndex	0.011	0.001	0.011
lfc	0.426	0.042	0.468
mergeInterestResult	0.099	0.002	0.102
plot-method	0.519	0.006	0.527
psi	1.726	0.034	1.759
qlfInterest	0.288	0.011	0.299
readInterestResults	0.057	0.004	0.062
referencePrepare	2.150	0.038	2.188
subInterestResult	0.055	0.002	0.057
treatInterest	0.225	0.006	0.230
u12Boxplot	0.158	0.002	0.161
u12BoxplotNb	0.222	0.002	0.224
u12DensityPlot	0.537	0.039	0.576
u12Index	0.019	0.000	0.020
u12NbIndex	0.183	0.003	0.184
unionRefTr	0.033	0.001	0.034
updateRowDataCol	0.086	0.002	0.089

CHECK report for IntEREst on celaya2

Summary

Command output

Installation output

Tests output

Example timings