Back to Multiple platform build/check report for BioC 3.12
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for erccdashboard on merida1

This page was generated on 2021-05-06 12:34:55 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the erccdashboard package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 565/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erccdashboard 1.24.0  (landing page)
Sarah Munro
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/erccdashboard
Branch: RELEASE_3_12
Last Commit: b13c8b8
Last Changed Date: 2020-10-27 10:58:20 -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    OK    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: erccdashboard
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:erccdashboard.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings erccdashboard_1.24.0.tar.gz
StartedAt: 2021-05-06 01:35:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:36:54 -0400 (Thu, 06 May 2021)
EllapsedTime: 83.5 seconds
RetCode: 0
Status:   OK  
CheckDir: erccdashboard.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:erccdashboard.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings erccdashboard_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/erccdashboard.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘erccdashboard/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘erccdashboard’ 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 ‘erccdashboard’ 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
dynRangePlot: no visible binding for global variable ‘value’
dynRangePlot: no visible binding for global variable ‘Rep’
saveERCCPlots: no visible global function definition for ‘par’
testDECount: no visible binding for global variable ‘Atrend’
testDECount: no visible binding for global variable ‘Dispersion’
testDECount: no visible binding for global variable ‘Ratio’
Undefined global functions or variables:
  Atrend Dispersion Ratio Rep par value
Consider adding
  importFrom("graphics", "par")
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 (user + system) or elapsed time > 5s
         user system elapsed
estLODR 7.125   0.06   7.198
* 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-3.12-bioc/meat/erccdashboard.Rcheck/00check.log’
for details.



Installation output

erccdashboard.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL erccdashboard
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘erccdashboard’ ...
** 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 (erccdashboard)

Tests output


Example timings

erccdashboard.Rcheck/erccdashboard-Ex.timings

nameusersystemelapsed
ERCC0.0020.0010.003
SEQC.Example0.0020.0020.004
annotLODR1.4730.0731.550
dynRangePlot1.3640.0311.402
erccROC1.2840.0331.319
estLODR7.1250.0607.198
est_r_m0.8840.0140.900
geneExprTest0.8830.0180.901
initDat0.1620.0080.170
maSignal2.3770.0322.412
runDashboard0.0000.0010.000
saveERCCPlots000