Package: IntEREst

Version: 1.10.2

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_1.10.2.tar.gz

StartedAt: 2020-04-15 03:13:21 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:19:48 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 386.3 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_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/IntEREst.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.2’
* 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 36.897  0.376  37.518
deseqInterest   8.864  0.054   8.966
* 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-3.10-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	36.897	0.376	37.518
addAnnotation	0.032	0.001	0.033
annotateU12	4.095	0.071	4.186
applyOverlap	0.275	0.001	0.277
attributes	0.042	0.001	0.044
boxplot-method	0.102	0.000	0.103
buildSsTypePwms	0.000	0.000	0.001
counts-method	0.045	0.002	0.047
deseqInterest	8.864	0.054	8.966
exactTestInterest	0.160	0.002	0.162
getRepeatTable	0.000	0.000	0.001
glmInterest	0.234	0.002	0.237
interest	2.192	0.019	2.220
interest.sequential	1.986	0.017	2.011
interestResult	0.027	0.001	0.029
interestResultIntEx	0.220	0.002	0.224
intexIndex	0.008	0.000	0.007
lfc	0.350	0.009	0.359
mergeInterestResult	0.362	0.001	0.367
plot-method	0.397	0.003	0.402
psi	1.473	0.006	1.486
qlfInterest	0.292	0.007	0.301
readInterestResults	0.047	0.003	0.050
referencePrepare	1.464	0.012	1.490
subInterestResult	0.045	0.001	0.047
treatInterest	0.186	0.003	0.190
u12Boxplot	0.084	0.000	0.085
u12BoxplotNb	0.142	0.001	0.146
u12DensityPlot	0.347	0.013	0.361
u12Index	0.01	0.00	0.01
u12NbIndex	0.130	0.003	0.133
unionRefTr	0.027	0.000	0.028
updateRowDataCol	0.066	0.001	0.069