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CHECK report for PANR on malbec1

This page was generated on 2019-04-16 11:49:21 -0400 (Tue, 16 Apr 2019).

Package 1115/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.28.1
Xin Wang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/PANR
Branch: RELEASE_3_8
Last Commit: 81b5a65
Last Changed Date: 2019-01-04 13:42:47 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.28.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PANR_1.28.1.tar.gz
StartedAt: 2019-04-16 01:56:57 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:57:52 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 55.2 seconds
RetCode: 0
Status:  OK 
CheckDir: PANR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PANR_1.28.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PANR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.28.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
fitNULL 22.724  0.024  23.322
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/PANR.Rcheck/00check.log’
for details.



Installation output

PANR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PANR
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


Example timings

PANR.Rcheck/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore0.0040.0000.007
buildPAN0.5080.0320.574
cosineSim0.0080.0040.011
data-Bakal20070.0200.0000.027
exportPAN000
fitBM000
fitNULL22.724 0.02423.322
infer0.3960.0000.591
p2SNR000
permNULL0.0200.0000.044
pvclustModule000
sigModules0.0000.0000.001
summarize0.0480.0000.097
view0.1840.0000.368
viewLegend000
viewNestedModules000
viewPAN000