Package: IntEREst

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2019-10-16 03:52:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:00:15 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 481.4 seconds

RetCode: 0

Status:  OK

CheckDir: IntEREst.Rcheck

Warnings: 0

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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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IntEREst.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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 49.234  0.588  49.943
deseqInterest   6.533  0.056   6.590
* 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-3.9-bioc/meat/IntEREst.Rcheck/00check.log’
for details.

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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/3.6/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)

name	user	system	elapsed
DEXSeqIntEREst	49.234	0.588	49.943
addAnnotation	0.038	0.002	0.040
annotateU12	4.015	0.142	4.158
attributes	0.067	0.004	0.070
boxplot-method	0.128	0.001	0.129
buildSsTypePwms	0.000	0.000	0.001
counts-method	0.150	0.003	0.154
deseqInterest	6.533	0.056	6.590
exactTestInterest	0.163	0.002	0.165
getRepeatTable	0	0	0
glmInterest	0.230	0.009	0.239
interest	2.129	0.025	2.158
interest.sequential	2.067	0.025	2.095
interestResult	0.027	0.002	0.029
interestResultIntEx	0.238	0.002	0.240
intexIndex	0.007	0.001	0.008
lfc	0.228	0.002	0.230
mergeInterestResult	0.483	0.002	0.486
plot-method	0.593	0.006	0.600
psi	1.803	0.009	1.813
qlfInterest	0.217	0.014	0.232
readInterestResults	0.033	0.003	0.036
referencePrepare	1.692	0.020	1.712
subInterestResult	0.048	0.002	0.050
treatInterest	0.213	0.009	0.221
u12Boxplot	0.196	0.002	0.198
u12BoxplotNb	0.193	0.001	0.194
u12DensityPlot	0.419	0.024	0.443
u12Index	0.009	0.001	0.009
u12NbIndex	0.123	0.002	0.126
unionRefTr	0.019	0.000	0.019
updateRowDataCol	0.063	0.001	0.064