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BioC 3.1: CHECK report for GeneGA on zin2

This page was generated on 2015-10-09 09:24:08 -0700 (Fri, 09 Oct 2015).

Package 376/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneGA 1.18.0
Zhenpeng Li
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GeneGA
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneGA
Version: 1.18.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GeneGA_1.18.0.tar.gz
StartedAt: 2015-10-09 01:33:06 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:38:39 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 333.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneGA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GeneGA_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GeneGA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 ... [1s/2s] 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ‘hash’
GeneCodon: no visible global function definition for ‘translate’
GeneCodon: no visible global function definition for ‘invert’
GeneCodon: no visible binding for global variable ‘wSet’
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’
GeneGA: no visible global function definition for ‘s2c’
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_internal: no visible global function definition for ‘s2c’
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’
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’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/308s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
GeneGA             33.345 16.925 124.852
plotGeneGA-methods  2.690  8.681  63.274
GeneGA-package      2.054  8.718  58.942
GeneFoldGA          2.131  8.528  59.713
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/GeneGA.Rcheck/00check.log’
for details.


GeneGA.Rcheck/00install.out:

* installing *source* package ‘GeneGA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneGA)

GeneGA.Rcheck/GeneGA-Ex.timings:

nameusersystemelapsed
GeneCodon0.1060.0000.107
GeneFoldGA 2.131 8.52859.713
GeneGA-package 2.054 8.71858.942
GeneGA 33.345 16.925124.852
plotGeneGA-methods 2.690 8.68163.274
wSet0.0040.0000.005