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CHECK report for epivizr on tokay1

This page was generated on 2018-04-12 13:23:25 -0400 (Thu, 12 Apr 2018).

Package 430/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epivizr 2.8.0
Hector Corrada Bravo
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/epivizr
Branch: RELEASE_3_6
Last Commit: 6535bb0
Last Changed Date: 2017-10-30 12:40:08 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: epivizr
Version: 2.8.0
Command: rm -rf epivizr.buildbin-libdir epivizr.Rcheck && mkdir epivizr.buildbin-libdir epivizr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epivizr.buildbin-libdir epivizr_2.8.0.tar.gz >epivizr.Rcheck\00install.out 2>&1 && cp epivizr.Rcheck\00install.out epivizr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=epivizr.buildbin-libdir --install="check:epivizr-install.out" --force-multiarch --no-vignettes --timings epivizr_2.8.0.tar.gz
StartedAt: 2018-04-11 23:48:16 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:53:28 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 311.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: epivizr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf epivizr.buildbin-libdir epivizr.Rcheck && mkdir epivizr.buildbin-libdir epivizr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epivizr.buildbin-libdir epivizr_2.8.0.tar.gz >epivizr.Rcheck\00install.out 2>&1 && cp epivizr.Rcheck\00install.out epivizr-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=epivizr.buildbin-libdir --install="check:epivizr-install.out" --force-multiarch --no-vignettes --timings epivizr_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/epivizr.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '2.8.0'
* 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-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:14: missing file link 'EpivizServer'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:16: missing file link 'EpivizDataMgr'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:33: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:57: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:58: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:67: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:33: missing file link 'EpivizServer'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:55: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:56: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:60: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:121: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:126: missing file link 'EpivizMeasurement'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:128: missing file link 'EpivizData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_blocks.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_blocks.Rd:29: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_curves.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_curves.Rd:25: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:23: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:7: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:20: missing file link 'RangedSummarizedExperiment'
See 'C:/Users/biocbuild/bbs-3.6-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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... 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
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/epivizr.Rcheck/00check.log'
for details.



Installation output

epivizr.Rcheck/00install.out


install for i386

* installing *source* package 'epivizr' ...
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:14: missing file link 'EpivizServer'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:16: missing file link 'EpivizDataMgr'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:33: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:57: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:58: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizApp-class.Rd:67: missing file link 'EpivizData'
    EpivizChart-class                       html  
    EpivizChartMgr-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:33: missing file link 'EpivizServer'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:55: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:56: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:60: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:121: missing file link 'EpivizData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:126: missing file link 'EpivizMeasurement'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/EpivizChartMgr-class.Rd:128: missing file link 'EpivizData'
    restartEpiviz                           html  
    show-EpivizChart-method                 html  
    startEpiviz                             html  
    tcga_colon_blocks                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_blocks.Rd:7: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_blocks.Rd:29: missing file link 'GRanges'
    tcga_colon_curves                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_curves.Rd:7: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_curves.Rd:25: missing file link 'GRanges'
    tcga_colon_expression                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:23: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:7: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMtlUkB/R.INSTALLcfc22197790/epivizr/man/tcga_colon_expression.Rd:20: missing file link 'RangedSummarizedExperiment'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'epivizr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epivizr' as epivizr_2.8.0.zip
* DONE (epivizr)
In R CMD INSTALL
In R CMD INSTALL

Tests output

epivizr.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  15.40    0.42   16.61 

epivizr.Rcheck/tests_x64/testthat.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-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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.40    0.35   17.86 

Example timings

epivizr.Rcheck/examples_i386/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz0.20.00.2
startEpiviz0.390.000.40

epivizr.Rcheck/examples_x64/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz0.180.010.21
startEpiviz0.490.000.50