Package: RCASPAR

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCASPAR_1.28.0.tar.gz

StartedAt: 2019-04-16 02:13:08 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:13:38 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 29.4 seconds

RetCode: 0

Status:  OK

CheckDir: RCASPAR.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:RCASPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCASPAR_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RCASPAR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCASPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCASPAR’ version ‘1.28.0’
* 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 ‘RCASPAR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kmplt: no visible global function definition for ‘plot’
kmplt_svrl: no visible global function definition for ‘plot’
kmplt_svrl: no visible global function definition for ‘lines’
kmplt_svrl: no visible global function definition for ‘legend’
logrnk: no visible global function definition for ‘pchisq’
pltgamma: no visible global function definition for ‘plot’
pltprior: no visible global function definition for ‘persp’
survivAURC: no visible global function definition for ‘plot’
weights_BLH: no visible global function definition for ‘optim’
Undefined global functions or variables:
  legend lines optim pchisq persp plot
Consider adding
  importFrom("graphics", "legend", "lines", "persp", "plot")
  importFrom("stats", "optim", "pchisq")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.8-bioc/meat/RCASPAR.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 RCASPAR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RCASPAR’ ...
** R
** data
** 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 (RCASPAR)

name	user	system	elapsed
Bergamaschi	0.015	0.003	0.018
RCASPAR-package	0.572	0.024	0.603
STpredictor_BLH	0.099	0.008	0.108
STpredictor_xvBLH	0.839	0.016	0.860
deriv_weight_estimator_BLH	0.003	0.001	0.004
deriv_weight_estimator_BLH_noprior	0.003	0.001	0.004
kmplt	0.005	0.000	0.005
kmplt_svrl	0.011	0.000	0.018
logrnk	0.005	0.000	0.005
pltgamma	0.002	0.001	0.003
pltprior	0.003	0.001	0.004
simpson	0	0	0
survData	0.002	0.001	0.002
survivAURC	0.160	0.010	0.171
survivROC	0.035	0.003	0.038
trapezoid	0.000	0.000	0.001
weight_estimator_BLH	0	0	0
weight_estimator_BLH_noprior	0.004	0.002	0.007
weights_BLH	0.009	0.003	0.011
weights_xvBLH	0.051	0.005	0.056