BioC 3.4: CHECK report for RCASPAR on malbec1

Package: RCASPAR

Version: 1.20.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCASPAR_1.20.0.tar.gz

StartedAt: 2017-04-15 00:45:25 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:45:43 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 18.3 seconds

RetCode: 0

Status:  OK

CheckDir: RCASPAR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RCASPAR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RCASPAR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.0’
* 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 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
  ‘/home/biocbuild/bbs-3.4-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	0.020	0.000	0.022
RCASPAR-package	0.608	0.016	0.625
STpredictor_BLH	0.084	0.000	0.085
STpredictor_xvBLH	0.876	0.000	0.873
deriv_weight_estimator_BLH	0.000	0.000	0.003
deriv_weight_estimator_BLH_noprior	0.000	0.000	0.003
kmplt	0.000	0.000	0.003
kmplt_svrl	0.008	0.000	0.010
logrnk	0.004	0.000	0.003
pltgamma	0.004	0.000	0.002
pltprior	0.000	0.000	0.002
simpson	0	0	0
survData	0.000	0.000	0.002
survivAURC	0.180	0.000	0.181
survivROC	0.024	0.008	0.033
trapezoid	0.000	0.000	0.001
weight_estimator_BLH	0	0	0
weight_estimator_BLH_noprior	0.004	0.000	0.006
weights_BLH	0.012	0.000	0.009
weights_xvBLH	0.060	0.004	0.065