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CHECK report for erccdashboard on veracruz1

This page was generated on 2018-04-12 13:39:11 -0400 (Thu, 12 Apr 2018).

Package 435/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erccdashboard 1.12.1
Sarah Munro
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/erccdashboard
Branch: RELEASE_3_6
Last Commit: 4b5bdd5
Last Changed Date: 2018-03-22 21:24:15 -0400 (Thu, 22 Mar 2018)
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  OK  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: erccdashboard
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings erccdashboard_1.12.1.tar.gz
StartedAt: 2018-04-12 03:28:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:29:41 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 57.6 seconds
RetCode: 0
Status:  OK 
CheckDir: erccdashboard.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings erccdashboard_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/erccdashboard.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 ‘erccdashboard/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘erccdashboard’ version ‘1.12.1’
* 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 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
estLODR 7.929  0.045   8.105
* 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/erccdashboard.Rcheck/00check.log’
for details.



Installation output

erccdashboard.Rcheck/00install.out

* installing *source* package ‘erccdashboard’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
ERCC0.0020.0010.003
SEQC.Example0.0010.0010.002
annotLODR1.8710.0571.943
dynRangePlot2.4860.0282.545
erccROC2.3420.0282.392
estLODR7.9290.0458.105
est_r_m0.7210.0110.744
geneExprTest0.9400.0230.966
initDat0.1570.0060.166
maSignal2.3340.0362.384
runDashboard0.0010.0000.001
saveERCCPlots0.0010.0000.000