BioC 3.3: CHECK report for pathifier on oaxaca

Package: pathifier

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathifier_1.10.0.tar.gz

StartedAt: 2016-10-13 04:52:07 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:53:01 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 54.0 seconds

RetCode: 0

Status:  OK

CheckDir: pathifier.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 pathifier_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pathifier.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathifier’ version ‘1.10.0’
* 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 ‘pathifier’ 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
.getpathway: no visible global function definition for ‘var’
.samplings_stdev: no visible binding for global variable ‘sd’
.score_pathway: no visible binding for global variable ‘sd’
.score_pathway: no visible global function definition for ‘aggregate’
.score_pathway: no visible global function definition for ‘dist’
quantify_pathways_deregulation: no visible binding for global variable
  ‘sd’
quantify_pathways_deregulation: no visible global function definition
  for ‘prcomp’
Undefined global functions or variables:
  aggregate dist prcomp sd var
Consider adding
  importFrom("stats", "aggregate", "dist", "prcomp", "sd", "var")
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 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 ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
pathifier-package              17.179  0.114  17.333
quantify_pathways_deregulation 16.834  0.124  16.971
* 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-3.3-bioc/meat/pathifier.Rcheck/00check.log’
for details.

* installing *source* package ‘pathifier’ ...
** 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 (pathifier)

name	user	system	elapsed
KEGG	0.014	0.002	0.016
Sheffer	0.021	0.003	0.023
pathifier-package	17.179	0.114	17.333
quantify_pathways_deregulation	16.834	0.124	16.971