BioC 3.2: CHECK report for cpvSNP on perceval

Package: cpvSNP

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cpvSNP_1.2.0.tar.gz

StartedAt: 2015-11-10 03:48:07 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:52:57 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 289.9 seconds

RetCode: 0

Status:  OK

CheckDir: cpvSNP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cpvSNP_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cpvSNP.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cpvSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cpvSNP’ version ‘1.2.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cpvSNP’ can be installed ... [23s/24s] OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GSEABase’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createArrayData: no visible global function definition for ‘GRanges’
createArrayData: no visible global function definition for ‘Rle’
createArrayData: no visible global function definition for ‘IRanges’
createArrayData: no visible global function definition for
  ‘elementMetadata<-’
geneToSNPList: no visible global function definition for ‘findOverlaps’
plotPvals: no visible binding for global variable ‘pval’
vegasPrep: no visible global function definition for ‘elementMetadata’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [57s/22s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
geneToSNPList 9.911  4.704   9.174
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [62s/27s]
 [63s/27s] OK
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/cpvSNP.Rcheck/00check.log’
for details.

* installing *source* package ‘cpvSNP’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cpvSNP)

name	user	system	elapsed
GLOSSIResult-class	0.002	0.000	0.002
GLOSSIResultCollection-class	0.001	0.000	0.001
GeneSetResult-class	0.002	0.000	0.001
GeneSetResultCollection-class	0.001	0.000	0.002
VEGASResult-class	0.001	0.000	0.002
VEGASResultCollection-class	0.001	0.001	0.002
createArrayData	0.277	0.022	0.298
degreesOfFreedom-method	0.000	0.000	0.001
geneSetAnalysis	0.194	0.009	0.203
geneSetName-methods	0.001	0.000	0.000
geneToSNPList	9.911	4.704	9.174
glossi	0.020	0.013	0.033
glossiMarginal	0.009	0.002	0.011
pValue-method	0.001	0.001	0.001
simulatedStats-method	0.001	0.000	0.000
statistic-methods	0.001	0.001	0.001