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CHECK report for PANR on veracruz1

This page was generated on 2018-04-12 13:34:56 -0400 (Thu, 12 Apr 2018).

Package 997/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.24.0
Xin Wang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PANR
Branch: RELEASE_3_6
Last Commit: 6b27f5b
Last Changed Date: 2017-10-30 12:39:35 -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  WARNINGS  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: PANR
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PANR_1.24.0.tar.gz
StartedAt: 2018-04-12 07:25:24 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 07:26:20 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 55.6 seconds
RetCode: 0
Status:  OK 
CheckDir: PANR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PANR_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PANR.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 ‘PANR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PANR’ version ‘1.24.0’
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 16.574  0.129  17.162
* 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-3.6-bioc/meat/PANR.Rcheck/00check.log’
for details.



Installation output

PANR.Rcheck/00install.out

* installing *source* package ‘PANR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PANR)

Tests output


Example timings

PANR.Rcheck/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class0.0010.0010.001
PAN-class0.0010.0000.002
SNR2p0.0010.0000.001
assoScore0.0070.0010.009
buildPAN0.8030.0280.864
cosineSim0.0030.0000.003
data-Bakal20070.0170.0030.019
exportPAN0.0010.0000.001
fitBM0.0000.0010.001
fitNULL16.574 0.12917.162
infer0.3460.0060.358
p2SNR0.0010.0010.001
permNULL0.0160.0020.018
pvclustModule0.0000.0000.001
sigModules0.0010.0000.001
summarize0.0320.0020.035
view0.3020.0110.314
viewLegend0.0010.0000.001
viewNestedModules0.0010.0000.001
viewPAN0.0010.0010.001