Package: PPInfer

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PPInfer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PPInfer_1.8.1.tar.gz

StartedAt: 2019-04-16 01:58:57 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:05:32 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 395.5 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 --install=check:PPInfer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PPInfer_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/PPInfer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘biomaRt’ ‘fgsea’ ‘kernlab’ ‘ggplot2’ ‘igraph’ ‘STRINGdb’
  ‘yeastExpData’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 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
ORA: no visible global function definition for ‘txtProgressBar’
ORA: no visible global function definition for ‘fisher.test’
ORA: no visible global function definition for ‘setTxtProgressBar’
ORA: no visible global function definition for ‘p.adjust’
ORA.barplot: no visible global function definition for ‘p.adjust’
enrich.net: no visible global function definition for ‘stack’
enrich.net: no visible global function definition for ‘adjustcolor’
enrich.net : <anonymous>: no visible global function definition for
  ‘adjustcolor’
enrich.net: no visible binding for global variable ‘legend’
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:
  adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar
  stack txtProgressBar
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "legend")
  importFrom("stats", "fisher.test", "na.omit", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar")
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 66.548  2.985 115.136
ppi.infer.mouse 56.523  2.620  90.450
ORA.barplot      1.915  0.039  20.303
ORA              1.604  0.178  19.999
* 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-3.8-bioc/meat/PPInfer.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PPInfer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PPInfer’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PPInfer.Rnw’ 
** testing if installed package can be loaded
* DONE (PPInfer)

name	user	system	elapsed
GSEA.barplot	3.812	0.807	3.451
ORA	1.604	0.178	19.999
ORA.barplot	1.915	0.039	20.303
enrich.net	3.246	0.954	2.866
net.infer	3.190	0.028	3.249
net.infer.ST	0.131	0.008	0.140
net.kernel	0.041	0.002	0.044
ppi.infer.human	66.548	2.985	115.136
ppi.infer.mouse	56.523	2.620	90.450
self.train.kernel	0.104	0.003	0.106