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CHECK report for GeneGA on celaya2

This page was generated on 2019-10-16 12:48:25 -0400 (Wed, 16 Oct 2019).

Package 629/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGA 1.34.0
Zhenpeng Li
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GeneGA
Branch: RELEASE_3_9
Last Commit: 546eca4
Last Changed Date: 2019-05-02 11:53:19 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneGA
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneGA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneGA_1.34.0.tar.gz
StartedAt: 2019-10-16 03:03:20 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:08:58 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 338.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneGA.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:GeneGA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneGA_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneGA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneGA’ version ‘1.34.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GeneGA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2
Standardizable: TRUE
Standardized license specification:
  GPL-2
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘GeneGA’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘hash’ ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GeneCodon: no visible global function definition for ‘s2c’
GeneCodon: no visible global function definition for ‘data’
GeneCodon: no visible binding for global variable ‘wSet’
GeneCodon: no visible global function definition for ‘hash’
GeneCodon: no visible global function definition for ‘translate’
GeneCodon: no visible global function definition for ‘invert’
GeneFoldGA: no visible global function definition for ‘s2c’
GeneFoldGA: no visible global function definition for ‘hash’
GeneFoldGA: no visible global function definition for ‘translate’
GeneFoldGA: no visible global function definition for ‘invert’
GeneFoldGA: no visible global function definition for ‘runif’
GeneFoldGA: no visible global function definition for ‘new’
GeneGA: no visible global function definition for ‘s2c’
GeneGA: no visible global function definition for ‘data’
GeneGA: no visible binding for global variable ‘wSet’
GeneGA: no visible global function definition for ‘hash’
GeneGA: no visible global function definition for ‘translate’
GeneGA: no visible global function definition for ‘invert’
GeneGA: no visible global function definition for ‘runif’
GeneGA: no visible global function definition for ‘new’
GeneGA_internal: no visible global function definition for ‘s2c’
GeneGA_internal: no visible global function definition for ‘data’
GeneGA_internal: no visible binding for global variable ‘wSet’
GeneGA_internal: no visible global function definition for ‘hash’
GeneGA_internal: no visible global function definition for ‘translate’
GeneGA_internal: no visible global function definition for ‘invert’
GeneGA_internal: no visible global function definition for ‘runif’
GeneGA_internal: no visible global function definition for ‘new’
evaluationFoldFunction: no visible global function definition for ‘s2c’
evaluationFunction: no visible global function definition for ‘s2c’
evaluationFunction: no visible global function definition for ‘cai’
evaluationFunction_internal: no visible global function definition for
  ‘s2c’
evaluationFunction_internal: no visible global function definition for
  ‘cai’
fold: no visible global function definition for ‘s2c’
plotGeneGA,GeneFoldGA: no visible global function definition for ‘plot’
plotGeneGA,GeneFoldGA: no visible global function definition for ‘par’
plotGeneGA,GeneGA: no visible global function definition for ‘plot’
plotGeneGA,GeneGA: no visible global function definition for ‘par’
Undefined global functions or variables:
  cai data hash invert new par plot runif s2c translate wSet
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("methods", "new")
  importFrom("stats", "runif")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
GeneGA             72.152 37.608 117.655
GeneFoldGA         23.280 32.053  61.408
plotGeneGA-methods 23.054 31.286  60.304
GeneGA-package     23.038 30.859  59.879
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneGA.Rcheck/00check.log’
for details.



Installation output

GeneGA.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneGA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GeneGA’ ...
** 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 (GeneGA)

Tests output


Example timings

GeneGA.Rcheck/GeneGA-Ex.timings

nameusersystemelapsed
GeneCodon0.1910.0120.203
GeneFoldGA23.28032.05361.408
GeneGA-package23.03830.85959.879
GeneGA 72.152 37.608117.655
plotGeneGA-methods23.05431.28660.304
wSet0.0030.0010.005