BioC 3.3: CHECK report for RCASPAR on zin2

Package: RCASPAR

Version: 1.18.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCASPAR_1.18.0.tar.gz

StartedAt: 2016-10-13 05:47:44 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:48:01 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 17.0 seconds

RetCode: 0

Status:  OK

CheckDir: RCASPAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RCASPAR_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RCASPAR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.18.0’
* 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
  ‘/home/biocbuild/bbs-3.3-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	0.013	0.004	0.018
RCASPAR-package	0.626	0.004	0.630
STpredictor_BLH	0.098	0.000	0.098
STpredictor_xvBLH	0.917	0.008	0.925
deriv_weight_estimator_BLH	0.003	0.004	0.003
deriv_weight_estimator_BLH_noprior	0.001	0.000	0.003
kmplt	0.004	0.000	0.004
kmplt_svrl	0.009	0.000	0.010
logrnk	0.004	0.000	0.004
pltgamma	0.002	0.000	0.002
pltprior	0.002	0.000	0.002
simpson	0.001	0.000	0.001
survData	0.000	0.000	0.002
survivAURC	0.147	0.001	0.147
survivROC	0.062	0.004	0.065
trapezoid	0.000	0.000	0.001
weight_estimator_BLH	0.001	0.000	0.000
weight_estimator_BLH_noprior	0.000	0.000	0.004
weights_BLH	0.009	0.000	0.009
weights_xvBLH	0.063	0.000	0.063