Package: Clomial

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Clomial.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Clomial_1.18.1.tar.gz

StartedAt: 2019-04-15 23:02:46 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:06:52 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 246.6 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 --install=check:Clomial.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Clomial_1.18.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Clomial.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.1’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
choose.best        76.572  5.529  83.062
Clomial            28.230  2.007  30.524
Clomial-package    25.688  1.821  27.742
compute.bic        17.981  1.255  19.509
Clomial.likelihood 14.155  1.025  15.350
Clomial.iterate    13.655  0.983  14.804
compute.errors      8.308  0.540   8.967
* 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-3.8-bioc/meat/Clomial.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Clomial
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Clomial’ ...
** R
** data
** inst
** byte-compile and prepare 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	25.688	1.821	27.742
Clomial	28.230	2.007	30.524
Clomial.generate.data	0.052	0.002	0.054
Clomial.iterate	13.655	0.983	14.804
Clomial.likelihood	14.155	1.025	15.350
Clomial1000	0.471	0.014	0.491
breastCancer	0.003	0.002	0.005
choose.best	76.572	5.529	83.062
compute.bic	17.981	1.255	19.509
compute.errors	8.308	0.540	8.967