Package: pandaR

Version: 1.19.3

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_1.19.3.tar.gz

StartedAt: 2020-01-16 07:13:32 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:15:37 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 124.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pandaR.Rcheck

Warnings: 1

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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_1.19.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pandaR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.3’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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:
  summary.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 ... OK
* 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 'summary.panda':
  ‘summary.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 (user + system) or elapsed time > 5s
           user system elapsed
panda     9.910  1.111  11.058
testMotif 4.367  0.564   8.564
plotZbyTF 3.867  0.302   6.042
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/pandaR.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 pandaR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

name	user	system	elapsed
calcDegree	0.466	0.148	0.613
calcDegreeDifference	0.000	0.000	0.001
importPandaMatlab	0	0	0
panda	9.910	1.111	11.058
plotCommunityDetection	0.220	0.020	0.241
plotGraph	0.228	0.106	0.334
plotZ	1.963	0.234	2.198
plotZbyTF	3.867	0.302	6.042
print.panda	0.003	0.003	0.022
subnetwork	0.249	0.099	0.622
summary.panda	0.003	0.002	0.005
targetedGenes	0.261	0.048	0.550
testMotif	4.367	0.564	8.564
topedges	0.416	0.137	0.752