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CHECK report for BrowserViz on nebbiolo1

This page was generated on 2020-09-19 10:17:14 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BrowserViz PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 203/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrowserViz 2.11.0
Paul Shannon
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/BrowserViz
Branch: master
Last Commit: c965f73
Last Changed Date: 2020-04-27 14:47:02 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ TIMEOUT ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BrowserViz
Version: 2.11.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BrowserViz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BrowserViz_2.11.0.tar.gz
StartedAt: 2020-09-18 20:56:42 -0400 (Fri, 18 Sep 2020)
EndedAt: 2020-09-18 21:37:29 -0400 (Fri, 18 Sep 2020)
EllapsedTime: 2447.4 seconds
RetCode: None
Status:  TIMEOUT 
CheckDir: BrowserViz.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BrowserViz.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BrowserViz_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BrowserViz.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BrowserViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BrowserViz’ version ‘2.11.0’
* package encoding: UTF-8
* 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 ‘BrowserViz’ 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 ... 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

Installation output

BrowserViz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BrowserViz
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BrowserViz’ ...
** using staged installation
** R
** 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 (BrowserViz)

Tests output

BrowserViz.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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("BrowserViz")

Attaching package: 'BrowserViz'

The following objects are masked from 'package:jsonlite':

    fromJSON, toJSON

attempting to open websocket connection on port 10000
/usr/bin/xdg-open: 869: x-www-browser: not found
/usr/bin/xdg-open: 869: firefox: not found
/usr/bin/xdg-open: 869: iceweasel: not found
/usr/bin/xdg-open: 869: seamonkey: not found
/usr/bin/xdg-open: 869: mozilla: not found
/usr/bin/xdg-open: 869: epiphany: not found
/usr/bin/xdg-open: 869: konqueror: not found
/usr/bin/xdg-open: 869: chromium: not found
/usr/bin/xdg-open: 869: chromium-browser: not found
/usr/bin/xdg-open: 869: google-chrome: not found
/usr/bin/xdg-open: 869: www-browser: not found
/usr/bin/xdg-open: 869: links2: not found
/usr/bin/xdg-open: 869: elinks: not found
/usr/bin/xdg-open: 869: links: not found
/usr/bin/xdg-open: 869: lynx: not found
/usr/bin/xdg-open: 869: w3m: not found
xdg-open: no method available for opening 'http://localhost:10000'

Example timings

BrowserViz.Rcheck/BrowserViz-Ex.timings

nameusersystemelapsed
fromJSON0.0070.0000.007
toJSON0.050.000.05