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CHECK report for erccdashboard on malbec2

This page was generated on 2018-10-17 08:26:32 -0400 (Wed, 17 Oct 2018).

Package 460/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erccdashboard 1.14.0
Sarah Munro
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/erccdashboard
Branch: RELEASE_3_7
Last Commit: ed70d99
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: erccdashboard
Version: 1.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:erccdashboard.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings erccdashboard_1.14.0.tar.gz
StartedAt: 2018-10-16 00:15:13 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:15:56 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 43.6 seconds
RetCode: 0
Status:  OK 
CheckDir: erccdashboard.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:erccdashboard.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings erccdashboard_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/erccdashboard.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.7-bioc/meat/erccdashboard.Rcheck/00check.log’
for details.



Installation output

erccdashboard.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL erccdashboard
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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
ERCC0.0000.0000.002
SEQC.Example0.0000.0000.001
annotLODR0.9520.0280.982
dynRangePlot1.2400.0041.249
erccROC1.1160.0081.129
estLODR4.8840.0164.909
est_r_m0.6560.0080.662
geneExprTest0.6440.0040.650
initDat0.1080.0000.106
maSignal2.4680.0042.475
runDashboard0.0040.0000.000
saveERCCPlots0.0000.0000.001