Package: gwascat

Version: 1.2.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_1.2.1.tar.gz

StartedAt: 2013-03-25 02:02:46 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:11:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 539.9 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/gwascat.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.2.1’
* 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 whether package ‘gwascat’ can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 15.353  0.120  16.120
gwcex2gviz       10.341  0.208  11.537
* 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 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-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	0	0
gwaswloc-class	0.004	0.000	0.002
gwcex2gviz	10.341	0.208	11.537
gwdf_2012_02_02	0	0	0
locon6	0.032	0.000	0.031
makeCurrentGwascat	0	0	0
riskyAlleleCount	15.353	0.120	16.120
topTraits	2.320	0.088	2.722
traitsManh	4.676	0.056	4.904