BioC 3.5: CHECK report for PPInfer on malbec2

Package: PPInfer

Version: 1.2.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PPInfer_1.2.4.tar.gz

StartedAt: 2017-10-18 01:33:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:43:02 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 572.9 seconds

RetCode: 0

Status:  OK

CheckDir: PPInfer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PPInfer_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.4’
* 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 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
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.dotplot: 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 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 58.232  0.564  69.257
ppi.infer.mouse 47.484  0.488  60.883
ORA.dotplot      2.724  0.052  17.214
ORA              1.512  0.052  15.987
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘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: 3 NOTEs
See
  ‘/home/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
GSEA.barplot	3.244	0.044	3.352
ORA	1.512	0.052	15.987
ORA.dotplot	2.724	0.052	17.214
enrich.net	2.416	0.012	2.430
net.infer	3.056	0.012	3.102
net.infer.ST	0.276	0.000	0.275
net.kernel	0.044	0.000	0.045
ppi.infer.human	58.232	0.564	69.257
ppi.infer.mouse	47.484	0.488	60.883
self.train.kernel	0.192	0.004	0.196