Package: IntEREst

Version: 1.8.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IntEREst_1.8.0.tar.gz

StartedAt: 2019-10-16 02:33:53 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:39:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 340.0 seconds

RetCode: 0

Status:  OK

CheckDir: IntEREst.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IntEREst.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IntEREst_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IntEREst.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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 ... 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 40.089  0.139  40.251
* 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-3.9-bioc/meat/IntEREst.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IntEREst
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* installing to library ‘/home/biocbuild/bbs-3.9-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	40.089	0.139	40.251
addAnnotation	0.041	0.000	0.041
annotateU12	3.350	0.013	3.610
attributes	0.054	0.000	0.054
boxplot-method	0.09	0.00	0.09
buildSsTypePwms	0.001	0.000	0.000
counts-method	0.075	0.000	0.075
deseqInterest	4.878	0.000	4.878
exactTestInterest	0.091	0.000	0.091
getRepeatTable	0.000	0.000	0.001
glmInterest	0.141	0.000	0.141
interest	1.053	0.008	1.074
interest.sequential	1.323	0.004	1.327
interestResult	0.020	0.000	0.021
interestResultIntEx	0.176	0.000	0.175
intexIndex	0.005	0.000	0.006
lfc	0.155	0.000	0.155
mergeInterestResult	0.349	0.004	0.353
plot-method	0.433	0.000	0.433
psi	1.210	0.000	1.209
qlfInterest	0.253	0.000	0.254
readInterestResults	0.038	0.000	0.038
referencePrepare	1.338	0.000	1.339
subInterestResult	0.041	0.000	0.040
treatInterest	0.223	0.000	0.223
u12Boxplot	0.129	0.000	0.128
u12BoxplotNb	0.124	0.000	0.125
u12DensityPlot	0.367	0.004	0.371
u12Index	0.010	0.000	0.011
u12NbIndex	0.078	0.000	0.078
unionRefTr	0.015	0.000	0.014
updateRowDataCol	0.034	0.000	0.033