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CHECK report for Clomial on celaya2

This page was generated on 2020-01-16 13:38:28 -0500 (Thu, 16 Jan 2020).

Package 301/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clomial 1.23.0
Habil Zare
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/Clomial
Branch: master
Last Commit: 0491d56
Last Changed Date: 2019-10-29 13:37:18 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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.



Installation output

Clomial.Rcheck/00install.out

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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)

Tests output


Example timings

Clomial.Rcheck/Clomial-Ex.timings

nameusersystemelapsed
Clomial-package39.241 3.99945.419
Clomial36.494 3.63142.267
Clomial.generate.data0.0340.0040.038
Clomial.iterate18.095 1.80520.568
Clomial.likelihood19.133 1.87821.246
Clomial10000.6410.0340.678
breastCancer0.0040.0040.008
choose.best102.518 10.200115.992
compute.bic24.990 2.47428.396
compute.errors11.131 1.02312.443