Package: Clomial

Version: 1.23.0

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_1.23.0.tar.gz

StartedAt: 2020-01-16 02:56:55 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:02:50 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 354.9 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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Clomial.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.23.0’
* 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 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 (user + system) or elapsed time > 5s
                      user system elapsed
choose.best        102.518 10.200 115.992
Clomial-package     39.241  3.999  45.419
Clomial             36.494  3.631  42.267
compute.bic         24.990  2.474  28.396
Clomial.likelihood  19.133  1.878  21.246
Clomial.iterate     18.095  1.805  20.568
compute.errors      11.131  1.023  12.443
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘Clomial’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Clomial)

name	user	system	elapsed
Clomial-package	39.241	3.999	45.419
Clomial	36.494	3.631	42.267
Clomial.generate.data	0.034	0.004	0.038
Clomial.iterate	18.095	1.805	20.568
Clomial.likelihood	19.133	1.878	21.246
Clomial1000	0.641	0.034	0.678
breastCancer	0.004	0.004	0.008
choose.best	102.518	10.200	115.992
compute.bic	24.990	2.474	28.396
compute.errors	11.131	1.023	12.443