Package: gwascat

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gwascat_1.4.0.tar.gz

StartedAt: 2013-05-01 06:40:52 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:51:29 -0700 (Wed, 01 May 2013)

EllapsedTime: 636.3 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gwascat.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '1.4.0'
* 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 ... [41s/42s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [81s/84s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 25.489  0.418  26.623
gwcex2gviz       15.332  0.689  16.816
traitsManh        5.311  0.369   5.746
* 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
** testing if installed package can be loaded
NOTE: input data had non-ASCII characters replaced by '*'.
* DONE (gwascat)

name	user	system	elapsed
gwascat-package	0.016	0.009	0.026
gwaswloc-class	0.018	0.006	0.025
gwcex2gviz	15.332	0.689	16.816
gwdf_2012_02_02	0.003	0.004	0.006
locon6	0.080	0.020	0.103
makeCurrentGwascat	0.025	0.005	0.031
riskyAlleleCount	25.489	0.418	26.623
topTraits	3.218	0.348	3.694
traitsManh	5.311	0.369	5.746