BioC 2.13: CHECK report for gwascat on zin1

Package: gwascat

Version: 1.6.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings gwascat_1.6.0.tar.gz

StartedAt: 2014-04-05 01:46:56 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:52:35 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 338.8 seconds

RetCode: 0

Status:  OK

CheckDir: gwascat.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/gwascat.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 ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘1.6.0’
* 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 ... [23s/23s] 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 ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘graph’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘graph’ ‘methods’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fixNonASCII’ ‘gwdf2GRanges’
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
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 files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
riskyAlleleCount 11.045  0.052  11.112
gwcex2gviz        7.881  0.128   8.021
* 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.004	0.000	0.006
gwaswloc-class	0.000	0.004	0.008
gwcex2gviz	7.881	0.128	8.021
gwdf_2012_02_02	0.012	0.000	0.011
locon6	0.044	0.000	0.042
makeCurrentGwascat	0.012	0.000	0.011
riskyAlleleCount	11.045	0.052	11.112
topTraits	1.488	0.032	1.521
traitsManh	3.432	0.040	3.484