BioC 3.5: CHECK report for PPInfer on veracruz2

Package: PPInfer

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PPInfer_1.2.3.tar.gz

StartedAt: 2017-08-16 06:37:44 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:46:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 528.3 seconds

RetCode: 0

Status:  OK

CheckDir: PPInfer.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 PPInfer_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PPInfer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PPInfer’ version ‘1.2.3’
* 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 ‘PPInfer’ 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
net.infer: no visible global function definition for ‘na.omit’
net.infer.ST: no visible global function definition for ‘na.omit’
ppi.infer.human: no visible global function definition for ‘na.omit’
ppi.infer.mouse: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
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
Examples with CPU or elapsed time > 5s
                  user system elapsed
ppi.infer.human 67.217  2.289  87.967
ppi.infer.mouse 61.186  2.223  78.469
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘ggplot2’ ‘httr’
* 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-3.5-bioc/meat/PPInfer.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
net.infer	4.191	0.106	4.441
net.infer.ST	0.195	0.003	0.208
net.kernel	0.035	0.002	0.036
ppi.infer.human	67.217	2.289	87.967
ppi.infer.mouse	61.186	2.223	78.469
self.train.kernel	0.247	0.002	0.252