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CHECK report for BrowserVizDemo on malbec1

This page was generated on 2018-04-12 13:13:31 -0400 (Thu, 12 Apr 2018).

Package 161/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrowserVizDemo 1.10.0
Paul Shannon
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BrowserVizDemo
Branch: RELEASE_3_6
Last Commit: 33f46ff
Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz1 OS X 10.11.6 El Capitan / x86_64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...

Summary

Package: BrowserVizDemo
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BrowserVizDemo_1.10.0.tar.gz
StartedAt: 2018-04-11 21:55:00 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:55:33 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 33.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BrowserVizDemo.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BrowserVizDemo_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BrowserVizDemo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BrowserVizDemo’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BrowserVizDemo’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BrowserViz::toJSON’ by ‘jsonlite::toJSON’ when loading ‘BrowserVizDemo’
See ‘/home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/00check.log’
for details.

Installation output

BrowserVizDemo.Rcheck/00install.out

* installing *source* package ‘BrowserVizDemo’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BrowserViz::toJSON’ by ‘jsonlite::toJSON’ when loading ‘BrowserVizDemo’
Creating a new generic function for ‘plot’ in package ‘BrowserVizDemo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BrowserViz::toJSON’ by ‘jsonlite::toJSON’ when loading ‘BrowserVizDemo’
* DONE (BrowserVizDemo)

Tests output

BrowserVizDemo.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("BrowserVizDemo")

Attaching package: 'BrowserViz'

The following object is masked from 'package:jsonlite':

    toJSON


Attaching package: 'BrowserVizDemo'

The following object is masked from 'package:graphics':

    plot

[1] "--- testConstructor"
BrowserViz constructor starting with html file '/home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/BrowserVizDemo/scripts/browserVizDemo.html'
 html file exists? TRUE
summoning default browser to get http://localhost:8000
[1] --- entering BrowserViz .setupWebSocketHandlers
[1]     browserFile: /home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/BrowserVizDemo/scripts/browserVizDemo.html
starting daemonized server on port 8000
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
[1] "BrowserViz..setupWebSocketHandlers, wsCon$onWSOpen"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] "BrowserViz..setupWebSocketHandlers, onMessage "
[1] BrowserViz dispatching on msg$cmd: handleResponse
[1] BrowserViz.dispatchMessage calling function 'handleResponse'
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
BrowserViz getBrowserResponse: ready
BrowserViz websocket ready after   0.50 seconds
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] "BrowserViz..setupWebSocketHandlers, onMessage "
[1] BrowserViz dispatching on msg$cmd: handleResponse
[1] BrowserViz.dispatchMessage calling function 'handleResponse'
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
BrowserViz getBrowserResponse: ready
[1] "--- testWindowTitle"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] "--- testPlot"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] "--- testConstructor"
BrowserViz constructor starting with html file '/home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/BrowserVizDemo/scripts/browserVizDemo.html'
 html file exists? TRUE
summoning default browser to get http://localhost:8000
[1] --- entering BrowserViz .setupWebSocketHandlers
[1]     browserFile: /home/biocbuild/bbs-3.6-bioc/meat/BrowserVizDemo.Rcheck/BrowserVizDemo/scripts/browserVizDemo.html
starting daemonized server on port 8000
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
BrowserViz websocket not ready, waiting   0.10 seconds
[1] "BrowserViz..setupWebSocketHandlers, wsCon$onWSOpen"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] "BrowserViz..setupWebSocketHandlers, onMessage "
[1] BrowserViz dispatching on msg$cmd: handleResponse
[1] BrowserViz.dispatchMessage calling function 'handleResponse'
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
BrowserViz getBrowserResponse: ready
BrowserViz websocket ready after   0.30 seconds
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] "BrowserViz..setupWebSocketHandlers, onMessage "
[1] BrowserViz dispatching on msg$cmd: handleResponse
[1] BrowserViz.dispatchMessage calling function 'handleResponse'
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
BrowserViz getBrowserResponse: ready
[1] "--- testPlot"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] "--- testWindowTitle"
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000
[1] waiting in BrowserViz.ready, browserResponseReady not yet true
[1] browserResponseReady now true, after 1 sleepInterval/s of 0.100000


RUNIT TEST PROTOCOL -- Wed Apr 11 21:55:30 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BrowserVizDemo RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning message:
replacing previous import 'BrowserViz::toJSON' by 'jsonlite::toJSON' when loading 'BrowserVizDemo' 
> 
> proc.time()
   user  system elapsed 
  1.476   0.112   6.065

Example timings

BrowserVizDemo.Rcheck/BrowserVizDemo-Ex.timings

nameusersystemelapsed
BrowserVizDemo-class0.2920.0121.376