Back to Multiple platform build/check report for BioC 3.8
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for erccdashboard on merida1

This page was generated on 2019-04-16 11:57:53 -0400 (Tue, 16 Apr 2019).

Package 485/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erccdashboard 1.16.1
Sarah Munro
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/erccdashboard
Branch: RELEASE_3_8
Last Commit: 503a11a
Last Changed Date: 2019-01-04 13:31:02 -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: erccdashboard
Version: 1.16.1
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_1.16.1.tar.gz
StartedAt: 2019-04-15 23:48:18 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:49:27 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 69.0 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/erccdashboard.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.1’
* 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 ‘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 or elapsed time > 5s
         user system elapsed
estLODR 8.554  0.062   8.724
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘erccdashboard’ ...
** 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
* DONE (erccdashboard)

Tests output


Example timings

erccdashboard.Rcheck/erccdashboard-Ex.timings

nameusersystemelapsed
ERCC0.0040.0010.005
SEQC.Example0.0010.0010.002
annotLODR1.7870.0961.920
dynRangePlot2.1050.0512.187
erccROC1.6540.0461.723
estLODR8.5540.0628.724
est_r_m1.1560.0201.188
geneExprTest1.1710.0311.210
initDat0.1480.0150.163
maSignal4.2430.0544.335
runDashboard000
saveERCCPlots000