Back to Multiple platform build/check report for BioC 3.11
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for epivizr on tokay2

This page was generated on 2020-10-17 11:56:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE epivizr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 556/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epivizr 2.18.0
Hector Corrada Bravo
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/epivizr
Branch: RELEASE_3_11
Last Commit: 79ed1fa
Last Changed Date: 2020-04-27 14:36:51 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: epivizr
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings epivizr_2.18.0.tar.gz
StartedAt: 2020-10-17 03:47:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:58:30 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 663.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: epivizr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings epivizr_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/epivizr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epivizr/DESCRIPTION' ... OK
* this is package 'epivizr' version '2.18.0'
* 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 whether package 'epivizr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:33: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:63: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:64: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:73: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:25: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:22: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/epivizr.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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespaces in Imports field not imported from:
  'GenomeInfoDb' 'bumphunter'
  All declared Imports should be used.
* 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/epivizr.Rcheck/00check.log'
for details.



Installation output

epivizr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/epivizr_2.18.0.tar.gz && rm -rf epivizr.buildbin-libdir && mkdir epivizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epivizr.buildbin-libdir epivizr_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL epivizr_2.18.0.zip && rm epivizr_2.18.0.tar.gz epivizr_2.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  932k  100  932k    0     0  14.4M      0 --:--:-- --:--:-- --:--:-- 15.9M

install for i386

* installing *source* package 'epivizr' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epivizr'
    finding HTML links ... done
    EpivizApp-class                         html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:33: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:63: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:64: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/EpivizApp-class.Rd:73: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
    EpivizChart-class                       html  
    EpivizChartMgr-class                    html  
    restartEpiviz                           html  
    show-EpivizChart-method                 html  
    startEpiviz                             html  
    tcga_colon_blocks                       html  
    tcga_colon_curves                       html  
    tcga_colon_expression                   html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:25: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6RXv4k/R.INSTALL2c4034514d19/epivizr/man/tcga_colon_expression.Rd:22: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
** 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

install for x64

* installing *source* package 'epivizr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epivizr' as epivizr_2.18.0.zip
* DONE (epivizr)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'epivizr' successfully unpacked and MD5 sums checked

Tests output

epivizr.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(testthat)
> library(epivizr)
> 
> test_check("epivizr")
== testthat results  ===========================================================
[ OK: 115 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.68    1.31   25.17 

epivizr.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(epivizr)
> 
> test_check("epivizr")
== testthat results  ===========================================================
[ OK: 115 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  23.62    0.68   27.53 

Example timings

epivizr.Rcheck/examples_i386/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz1.080.031.11
startEpiviz0.030.000.03

epivizr.Rcheck/examples_x64/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz1.110.001.11
startEpiviz0.040.000.05