BioC 3.5: CHECK report for Clomial on veracruz2

Package: Clomial

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clomial_1.12.0.tar.gz

StartedAt: 2017-10-18 01:48:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:51:12 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 189.4 seconds

RetCode: 0

Status:  OK

CheckDir: Clomial.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 Clomial_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Clomial.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 ‘Clomial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clomial’ version ‘1.12.0’
* 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 ‘Clomial’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Clomial: no visible global function definition for ‘runif’
Clomial.generate.data: no visible global function definition for
  ‘runif’
Clomial.generate.data: no visible global function definition for
  ‘rbinom’
Clomial.likelihood: no visible global function definition for ‘dbinom’
Phi: no visible global function definition for ‘dbinom’
choose.best: no visible global function definition for ‘tail’
compute.P.reparam : update.Wj: no visible global function definition
  for ‘optim’
compute.P.reparam : plot.obj: no visible global function definition for
  ‘plot’
compute.q: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom optim plot rbinom runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbinom", "optim", "rbinom", "runif")
  importFrom("utils", "tail")
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
Examples with CPU or elapsed time > 5s
                     user system elapsed
choose.best        55.526  3.850  61.547
Clomial-package    20.150  1.425  22.232
Clomial            18.983  1.310  20.892
compute.bic        12.576  0.863  13.958
Clomial.likelihood 10.121  0.689  11.291
Clomial.iterate     9.463  0.658  10.397
compute.errors      5.755  0.371   6.347
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Clomial.Rcheck/00check.log’
for details.

* installing *source* package ‘Clomial’ ...
** 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 (Clomial)

name	user	system	elapsed
Clomial-package	20.150	1.425	22.232
Clomial	18.983	1.310	20.892
Clomial.generate.data	0.456	0.004	0.468
Clomial.iterate	9.463	0.658	10.397
Clomial.likelihood	10.121	0.689	11.291
Clomial1000	0.286	0.006	0.303
breastCancer	0.002	0.002	0.005
choose.best	55.526	3.850	61.547
compute.bic	12.576	0.863	13.958
compute.errors	5.755	0.371	6.347