BioC 2.13: CHECK report for GeneGA on zin1

Package: GeneGA

Version: 1.12.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GeneGA_1.12.1.tar.gz

StartedAt: 2014-04-05 01:21:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:23:27 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 126.3 seconds

RetCode: 0

Status:  OK

CheckDir: GeneGA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GeneGA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.12.1’
* 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/1s] 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 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 binding for global variable ‘wSet’
GeneGA: no visible binding for global variable ‘wSet’
GeneGA_internal: no visible binding for global variable ‘wSet’
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GeneGA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [61s/110s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
GeneGA             41.442  7.840  63.846
plotGeneGA-methods  1.440  2.644  15.208
GeneGA-package      1.484  2.264  15.523
GeneFoldGA          1.284  2.204  15.088
* 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

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/GeneGA.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GeneCodon	0.124	0.000	0.159
GeneFoldGA	1.284	2.204	15.088
GeneGA-package	1.484	2.264	15.523
GeneGA	41.442	7.840	63.846
plotGeneGA-methods	1.440	2.644	15.208
wSet	0.004	0.004	0.006