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CHECK report for PANR on malbec1

This page was generated on 2021-05-06 12:28:29 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PANR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1297/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PANR 1.36.0  (landing page)
Xin Wang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PANR
Branch: RELEASE_3_12
Last Commit: 4badc77
Last Changed Date: 2020-10-27 10:42:44 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: PANR
Version: 1.36.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings PANR_1.36.0.tar.gz
StartedAt: 2021-05-06 04:18:16 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:19:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 76.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PANR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:PANR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings PANR_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/PANR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.36.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
fitNULL 24.636  0.028  35.085
* 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-3.12-bioc/meat/PANR.Rcheck/00check.log’
for details.



Installation output

PANR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL PANR
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘PANR’ ...
** using staged installation
** 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 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 (PANR)

Tests output


Example timings

PANR.Rcheck/PANR-Ex.timings

nameusersystemelapsed
BetaMixture-class000
PAN-class000
SNR2p000
assoScore0.0080.0000.023
buildPAN0.5800.0201.078
cosineSim0.0040.0000.004
data-Bakal20070.0200.0040.071
exportPAN000
fitBM000
fitNULL24.636 0.02835.085
infer0.4160.0040.420
p2SNR000
permNULL0.020.000.02
pvclustModule000
sigModules0.0040.0000.001
summarize0.0520.0000.053
view0.1760.0040.179
viewLegend000
viewNestedModules000
viewPAN000