Package: PANR

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PANR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PANR_1.26.0.tar.gz

StartedAt: 2018-10-16 23:06:41 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:07:46 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 64.6 seconds

RetCode: 0

Status:  OK

CheckDir: PANR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PANR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PANR_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PANR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PANR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PANR’ version ‘1.26.0’
* 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 ‘PANR’ 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 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
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘runif’
SNR2p,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘pbeta’
p2SNR,BetaMixture-numeric_Or_integer: no visible global function
  definition for ‘qbeta’
Undefined global functions or variables:
  pbeta qbeta runif
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 22.482  0.323  23.008
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/PANR.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 PANR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PANR’ ...
** R
** data
** 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
* DONE (PANR)

name	user	system	elapsed
BetaMixture-class	0.002	0.000	0.003
PAN-class	0.003	0.000	0.004
SNR2p	0.003	0.000	0.002
assoScore	0.014	0.002	0.016
buildPAN	0.566	0.046	0.622
cosineSim	0.015	0.002	0.017
data-Bakal2007	0.019	0.003	0.022
exportPAN	0.002	0.000	0.003
fitBM	0.003	0.000	0.003
fitNULL	22.482	0.323	23.008
infer	0.371	0.016	0.389
p2SNR	0.001	0.000	0.001
permNULL	0.016	0.003	0.018
pvclustModule	0.002	0.000	0.003
sigModules	0.003	0.000	0.003
summarize	0.037	0.004	0.041
view	0.192	0.046	0.240
viewLegend	0.002	0.000	0.002
viewNestedModules	0.003	0.000	0.003
viewPAN	0.002	0.000	0.002