BioC 3.5: CHECK report for npGSEA on veracruz2

Package: npGSEA

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings npGSEA_1.12.0.tar.gz

StartedAt: 2017-10-18 06:49:22 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:51:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 98.5 seconds

RetCode: 0

Status:  OK

CheckDir: npGSEA.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 npGSEA_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/npGSEA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘npGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘npGSEA’ version ‘1.12.0’
* 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 ‘npGSEA’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.prepXYZ: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/npGSEA.Rcheck/00check.log’
for details.

* installing *source* package ‘npGSEA’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: unlist
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist
* DONE (npGSEA)

name	user	system	elapsed
DF-methods	0.018	0.000	0.018
alphaValue-methods	0.276	0.002	0.291
betaHats-methods	0.005	0.001	0.011
betaStat-methods	0.064	0.009	0.074
betaValue-methods	0.004	0.001	0.005
chiSqStat-methods	0.110	0.004	0.116
geneSetName-methods	0.015	0.000	0.016
getIncidence	0.002	0.000	0.002
npGSEA	0.003	0.000	0.003
npGSEAPlot-methods	0.004	0.000	0.004
npGSEAResultBeta-class	0.002	0.000	0.002
npGSEAResultBetaCollection-class	0.001	0.001	0.002
npGSEAResultChiSq-class	0.001	0.000	0.002
npGSEAResultChiSqCollection-class	0.001	0.000	0.001
npGSEAResultNorm-class	0.001	0.001	0.001
npGSEAResultNormCollection-class	0.001	0.000	0.002
pLeft-methods	0.003	0.001	0.003
pRight-methods	0.004	0.000	0.004
pTwoSided-methods	0.004	0.000	0.004
pValues-methods	0.004	0.000	0.004
show-methods	0.004	0.000	0.004
sigmaSq-methods	0.003	0.001	0.003
stat-methods	0.003	0.000	0.004
xSet-methods	0.005	0.001	0.007
zStat-methods	0.003	0.000	0.004