Package: RCASPAR

Version: 1.32.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RCASPAR_1.32.0.tar.gz

StartedAt: 2020-04-15 01:02:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:02:20 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 18.7 seconds

RetCode: 0

Status:  OK

CheckDir: RCASPAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RCASPAR_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/RCASPAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.32.0’
* 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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/RCASPAR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL RCASPAR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘RCASPAR’ ...
** using staged installation
** 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 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 (RCASPAR)

name	user	system	elapsed
Bergamaschi	0.008	0.004	0.014
RCASPAR-package	0.340	0.004	0.346
STpredictor_BLH	0.044	0.008	0.053
STpredictor_xvBLH	0.560	0.004	0.574
deriv_weight_estimator_BLH	0.004	0.000	0.003
deriv_weight_estimator_BLH_noprior	0.004	0.000	0.003
kmplt	0.004	0.000	0.003
kmplt_svrl	0.008	0.000	0.008
logrnk	0.000	0.000	0.003
pltgamma	0.000	0.000	0.002
pltprior	0.000	0.004	0.003
simpson	0	0	0
survData	0.000	0.000	0.002
survivAURC	0.156	0.004	0.158
survivROC	0.040	0.008	0.049
trapezoid	0.000	0.004	0.001
weight_estimator_BLH	0	0	0
weight_estimator_BLH_noprior	0.004	0.000	0.004
weights_BLH	0.004	0.000	0.005
weights_xvBLH	0.040	0.000	0.041