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CHECK report for pandaR on celaya2

This page was generated on 2019-04-09 13:13:59 -0400 (Tue, 09 Apr 2019).

Package 1140/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pandaR 1.15.0
Joseph N. Paulson , Dan Schlauch
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/pandaR
Branch: master
Last Commit: cada07d
Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: pandaR
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pandaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pandaR_1.15.0.tar.gz
StartedAt: 2019-04-09 04:11:35 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:13:19 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 103.7 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 --install=check:pandaR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pandaR_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pandaR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.0’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.panda
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
panda     10.108  0.681  10.789
testMotif  3.562  0.597   7.672
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/pandaR.Rcheck/00check.log’
for details.



Installation output

pandaR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pandaR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pandaR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pandaR)

Tests output


Example timings

pandaR.Rcheck/pandaR-Ex.timings

nameusersystemelapsed
calcDegree0.5260.1810.707
calcDegreeDifference000
importPandaMatlab000
panda10.108 0.68110.789
plot.panda0.1040.0350.139
plotCommunityDetection0.2650.0180.283
plotGraph0.2160.0550.271
plotZ1.7570.2121.970
plotZbyTF3.1510.2693.465
print.panda0.0990.0450.174
subnetwork0.3700.0700.556
summary.panda0.0990.0430.194
targetedGenes0.2120.0480.383
testMotif3.5620.5977.672
topedges0.1810.0860.484