BioC 3.5: CHECK report for RCASPAR on veracruz2

Package: RCASPAR

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RCASPAR_1.22.0.tar.gz

StartedAt: 2017-10-18 07:57:06 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:57:29 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 23.5 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 --no-vignettes --timings RCASPAR_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RCASPAR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.22.0’
* 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 loading without being on the library search path ... 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 installed files from ‘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-3.5-bioc/meat/RCASPAR.Rcheck/00check.log’
for details.

* installing *source* package ‘RCASPAR’ ...
** R
** data
** inst
** preparing 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	0.050	0.002	0.053
RCASPAR-package	1.298	0.030	1.367
STpredictor_BLH	0.216	0.006	0.233
STpredictor_xvBLH	0.831	0.016	0.864
deriv_weight_estimator_BLH	0.004	0.001	0.005
deriv_weight_estimator_BLH_noprior	0.004	0.002	0.006
kmplt	0.004	0.000	0.005
kmplt_svrl	0.010	0.002	0.012
logrnk	0.006	0.000	0.006
pltgamma	0.002	0.001	0.006
pltprior	0.003	0.001	0.003
simpson	0.001	0.000	0.002
survData	0.002	0.000	0.003
survivAURC	0.129	0.009	0.142
survivROC	0.036	0.004	0.041
trapezoid	0.001	0.000	0.001
weight_estimator_BLH	0.001	0.000	0.001
weight_estimator_BLH_noprior	0.004	0.001	0.005
weights_BLH	0.006	0.001	0.008
weights_xvBLH	0.051	0.002	0.055