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CHECK report for GeneGA on merida2

This page was generated on 2018-10-17 08:48:53 -0400 (Wed, 17 Oct 2018).

Package 566/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGA 1.30.0
Zhenpeng Li
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GeneGA
Branch: RELEASE_3_7
Last Commit: 649e241
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneGA
Version: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2018-10-16 21:34:25 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:38:13 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 227.8 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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneGA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.30.0’
* 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             58.795 20.314  85.293
GeneFoldGA         17.735 16.487  38.851
GeneGA-package     17.636 16.285  38.459
plotGeneGA-methods 17.118 16.005  37.741
* 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-3.7-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/3.5/Resources/library’
* installing *source* package ‘GeneGA’ ...
** 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 (GeneGA)

Tests output


Example timings

GeneGA.Rcheck/GeneGA-Ex.timings

nameusersystemelapsed
GeneCodon0.1480.0060.157
GeneFoldGA17.73516.48738.851
GeneGA-package17.63616.28538.459
GeneGA58.79520.31485.293
plotGeneGA-methods17.11816.00537.741
wSet0.0040.0010.005