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

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneGA
###
##############################################################################
##############################################################################


* 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)

name	user	system	elapsed
GeneCodon	0.191	0.012	0.203
GeneFoldGA	23.280	32.053	61.408
GeneGA-package	23.038	30.859	59.879
GeneGA	72.152	37.608	117.655
plotGeneGA-methods	23.054	31.286	60.304
wSet	0.003	0.001	0.005