BioC 2.12: CHECK report for gwascat on petty

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: 2013-10-01 22:42:33 -0700 (Tue, 01 Oct 2013)

EndedAt: 2013-10-01 22:53:52 -0700 (Tue, 01 Oct 2013)

EllapsedTime: 678.4 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 3.0.1 (2013-05-16)
* 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 ... [46s/47s] 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 ... [87s/88s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 27.793  0.393  28.483
gwcex2gviz       15.249  0.696  16.096
traitsManh        5.781  0.378   6.213
* 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	0.013	0.007	0.020
gwaswloc-class	0.016	0.005	0.020
gwcex2gviz	15.249	0.696	16.096
gwdf_2012_02_02	0.002	0.003	0.006
locon6	0.053	0.010	0.062
makeCurrentGwascat	0.002	0.004	0.007
riskyAlleleCount	27.793	0.393	28.483
topTraits	3.558	0.406	4.019
traitsManh	5.781	0.378	6.213