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CHECK report for pandaR on veracruz1

This page was generated on 2018-04-12 13:40:52 -0400 (Thu, 12 Apr 2018).

Package 993/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pandaR 1.10.0
Joseph N. Paulson , Dan Schlauch
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/pandaR
Branch: RELEASE_3_6
Last Commit: 2745534
Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pandaR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pandaR_1.10.0.tar.gz
StartedAt: 2018-04-12 07:23:59 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:25:21 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 82.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pandaR.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/pandaR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pandaR/DESCRIPTION’ ... OK
* this is package ‘pandaR’ 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 ‘pandaR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
* 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
dFunction: no visible global function definition for ‘cor’
importPandaMatlab: no visible global function definition for
  ‘read.delim’
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 title
Consider adding
  importFrom("graphics", "hist", "title")
  importFrom("stats", "aggregate", "cor", "pnorm")
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
panda     6.937  0.530   9.560
plotZbyTF 3.046  0.126   5.133
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/pandaR.Rcheck/00check.log’
for details.



Installation output

pandaR.Rcheck/00install.out

* 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)

Tests output


Example timings

pandaR.Rcheck/pandaR-Ex.timings

nameusersystemelapsed
calcDegree0.6590.0540.714
calcDegreeDifference000
importPandaMatlab0.0010.0000.001
panda6.9370.5309.560
plot.panda0.0790.0150.169
plotCommunityDetection1.2840.0232.280
plotGraph0.1400.0220.243
plotZ2.2250.1043.873
plotZbyTF3.0460.1265.133
print.panda0.0910.0140.138
subnetwork0.2160.0160.294
summary.panda0.1890.0080.229
targetedGenes0.1460.0160.193
testMotif2.7400.3033.200
topedges0.1470.0270.301