Package: IntEREst

Version: 1.10.2

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IntEREst_1.10.2.tar.gz

StartedAt: 2020-04-15 04:39:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:46:12 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 386.6 seconds

RetCode: 0

Status:  OK

CheckDir: IntEREst.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IntEREst_1.10.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/IntEREst.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.2’
* 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 or elapsed time > 5s
                 user system elapsed
DEXSeqIntEREst 35.996  0.168  36.412
deseqInterest   8.892  0.004   9.000
annotateU12     4.888  0.028   5.018
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/IntEREst.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL IntEREst
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

name	user	system	elapsed
DEXSeqIntEREst	35.996	0.168	36.412
addAnnotation	0.048	0.000	0.047
annotateU12	4.888	0.028	5.018
applyOverlap	0.244	0.000	0.244
attributes	0.052	0.000	0.053
boxplot-method	0.104	0.000	0.107
buildSsTypePwms	0.000	0.000	0.001
counts-method	0.040	0.000	0.038
deseqInterest	8.892	0.004	9.000
exactTestInterest	0.172	0.000	0.173
getRepeatTable	0	0	0
glmInterest	0.244	0.000	0.244
interest	2.044	0.004	2.162
interest.sequential	1.844	0.016	1.871
interestResult	0.020	0.000	0.022
interestResultIntEx	0.212	0.000	0.210
intexIndex	0.004	0.000	0.006
lfc	0.360	0.000	0.364
mergeInterestResult	0.332	0.000	0.333
plot-method	0.440	0.000	0.442
psi	1.324	0.012	1.338
qlfInterest	0.328	0.012	0.339
readInterestResults	0.036	0.000	0.038
referencePrepare	1.532	0.008	1.545
subInterestResult	0.036	0.000	0.035
treatInterest	0.204	0.000	0.202
u12Boxplot	0.092	0.000	0.094
u12BoxplotNb	0.128	0.000	0.126
u12DensityPlot	0.372	0.004	0.377
u12Index	0.008	0.000	0.010
u12NbIndex	0.096	0.000	0.096
unionRefTr	0.020	0.000	0.018
updateRowDataCol	0.052	0.000	0.052