BioC 3.3: CHECK report for pandaR on oaxaca

Package: pandaR

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pandaR_1.4.2.tar.gz

StartedAt: 2016-10-13 04:49:13 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:50:26 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 73.2 seconds

RetCode: 0

Status:  OK

CheckDir: pandaR.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 pandaR_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pandaR.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 ‘pandaR/DESCRIPTION’ ... OK
* this is package ‘pandaR’ version ‘1.4.2’
* 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 ‘pandaR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
* checking package 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
dFunction: no visible global function definition for ‘cor’
importPandaMatlab: no visible global function definition for
  ‘read.delim’
normalizeNetwork: no visible global function definition for ‘sd’
panda: no visible global function definition for ‘cor’
panda: no visible global function definition for ‘aggregate’
plot.panda: no visible global function definition for ‘hist’
plotCommunityDetection: no visible global function definition for
  ‘title’
plotZbyTF: no visible global function definition for ‘aggregate’
prepResult: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  aggregate cor hist pnorm read.delim sd title
Consider adding
  importFrom("graphics", "hist", "title")
  importFrom("stats", "aggregate", "cor", "pnorm", "sd")
  importFrom("utils", "read.delim")
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 ... NOTE
S3 methods shown with full name in documentation object 'plot.panda':
  ‘plot.panda’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
panda     7.321  0.617   7.941
plotZbyTF 2.844  0.133   6.013
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/pandaR.Rcheck/00check.log’
for details.

* installing *source* package ‘pandaR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pandaR)

name	user	system	elapsed
calcDegree	0.718	0.075	0.794
calcDegreeDifference	0.001	0.000	0.000
importPandaMatlab	0.001	0.000	0.000
panda	7.321	0.617	7.941
plot.panda	0.079	0.021	0.100
plotCommunityDetection	0.145	0.004	0.168
plotGraph	0.203	0.026	0.258
plotZ	1.057	0.088	2.189
plotZbyTF	2.844	0.133	6.013
print.panda	0.077	0.018	0.150
subnetwork	0.158	0.035	0.306
summary.panda	0.080	0.008	0.088
targetedGenes	0.279	0.026	0.466
testMotif	2.958	0.357	4.336
topedges	0.157	0.041	0.198