Package: IntEREst

Version: 1.7.3

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_1.7.3.tar.gz

StartedAt: 2019-04-09 01:39:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:45:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 360.2 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_1.7.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IntEREst.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.7.3’
* 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 ... NOTE
annotateU12: no visible binding for global variable ‘query’
Undefined global functions or variables:
  query
* 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 42.533  0.440  43.218
deseqInterest   5.064  0.057   5.162
* 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: 2 NOTEs
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’ ...
** 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
* DONE (IntEREst)

name	user	system	elapsed
DEXSeqIntEREst	42.533	0.440	43.218
addAnnotation	0.044	0.001	0.045
annotateU12	3.088	0.050	3.150
attributes	0.043	0.002	0.045
boxplot-method	0.064	0.001	0.065
buildSsTypePwms	0	0	0
counts-method	0.070	0.002	0.071
deseqInterest	5.064	0.057	5.162
exactTestInterest	0.134	0.001	0.138
getRepeatTable	0	0	0
glmInterest	0.178	0.004	0.182
interest	1.774	0.018	1.796
interest.sequential	1.546	0.013	1.569
interestResult	0.019	0.001	0.021
interestResultIntEx	0.190	0.001	0.192
intexIndex	0.005	0.000	0.005
lfc	0.149	0.001	0.151
mergeInterestResult	0.319	0.001	0.325
plot-method	0.412	0.003	0.418
psi	1.136	0.004	1.144
qlfInterest	0.189	0.006	0.196
readInterestResults	0.040	0.002	0.042
referencePrepare	1.233	0.007	1.244
subInterestResult	0.035	0.001	0.036
treatInterest	0.186	0.008	0.194
u12Boxplot	0.092	0.001	0.094
u12BoxplotNb	0.139	0.001	0.140
u12DensityPlot	0.387	0.016	0.406
u12Index	0.011	0.000	0.013
u12NbIndex	0.115	0.001	0.116
unionRefTr	0.026	0.000	0.025
updateRowDataCol	0.043	0.000	0.045