Package: gwascat

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gwascat_1.3.2.tar.gz

StartedAt: 2013-03-25 03:01:07 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:09:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 502.7 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gwascat.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '1.3.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'SNPlocs.Hsapiens.dbSNP.20111119'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'gwascat' can be installed ... [38s/39s] OK
* checking installed package size ... NOTE
  installed size is 23.7Mb
  sub-directories of 1Mb or more:
    data  20.4Mb
    obo    1.3Mb
    tab    1.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chklocs: no visible global function definition for 'getSNPlocs'
snpGenos: no visible global function definition for 'getSNPlocs'
traitsManh: no visible binding for global variable 'Pvalue_mlog'
traitsManh: no visible binding for global variable 'Trait'
* 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 examples ... [71s/72s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 20.882  0.783  21.731
gwcex2gviz       13.448  1.200  14.745
traitsManh        6.294  0.827   7.175
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/gwascat.Rcheck/00check.log'
for details.

* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'gwascat.Rnw' 
** testing if installed package can be loaded
NOTE: input data had non-ASCII characters replaced by '*'.
* DONE (gwascat)

name	user	system	elapsed
gwascat-package	0.010	0.007	0.016
gwaswloc-class	0.004	0.005	0.010
gwcex2gviz	13.448	1.200	14.745
gwdf_2012_02_02	0.014	0.006	0.020
locon6	0.056	0.010	0.065
makeCurrentGwascat	0.022	0.007	0.029
riskyAlleleCount	20.882	0.783	21.731
topTraits	2.938	0.646	3.613
traitsManh	6.294	0.827	7.175