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CHECK report for epivizr on tokay2

This page was generated on 2018-10-17 08:37:48 -0400 (Wed, 17 Oct 2018).

Package 455/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epivizr 2.10.0
Hector Corrada Bravo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/epivizr
Branch: RELEASE_3_7
Last Commit: 9294b94
Last Changed Date: 2018-04-30 10:35:31 -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 [ WARNINGS ] 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: epivizr
Version: 2.10.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings epivizr_2.10.0.tar.gz
StartedAt: 2018-10-17 01:51:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:56:43 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 340.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: epivizr.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings epivizr_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/epivizr.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.10.0'
* 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 ... 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-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:14: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:16: file link 'EpivizDataMgr' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/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-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:57: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:58: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:67: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:33: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:55: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:56: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:60: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:121: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:126: file link 'EpivizMeasurement' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:128: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_blocks.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_blocks.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_curves.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_curves.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:23: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:7: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:20: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 ... NOTE
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'SummarizedExperiment'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* 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-3.7-bioc/meat/epivizr.Rcheck/00check.log'
for details.



Installation output

epivizr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/epivizr_2.10.0.tar.gz && rm -rf epivizr.buildbin-libdir && mkdir epivizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epivizr.buildbin-libdir epivizr_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL epivizr_2.10.0.zip && rm epivizr_2.10.0.tar.gz epivizr_2.10.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  932k  100  932k    0     0  14.9M      0 --:--:-- --:--:-- --:--:-- 16.5M

install for i386

* installing *source* package 'epivizr' ...
** 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-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:14: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:16: file link 'EpivizDataMgr' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/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-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:57: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:58: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizApp-class.Rd:67: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
    EpivizChart-class                       html  
    EpivizChartMgr-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:33: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:55: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:56: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:60: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:121: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:126: file link 'EpivizMeasurement' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/EpivizChartMgr-class.Rd:128: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
    restartEpiviz                           html  
    show-EpivizChart-method                 html  
    startEpiviz                             html  
    tcga_colon_blocks                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_blocks.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_blocks.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    tcga_colon_curves                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_curves.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_curves.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    tcga_colon_expression                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:23: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:7: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpgxMQuD/R.INSTALLf80a04654/epivizr/man/tcga_colon_expression.Rd:20: 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
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_2.10.0.zip
* DONE (epivizr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'epivizr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

epivizr.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  16.59    1.54   19.79 

epivizr.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
  16.54    0.59   17.31 

Example timings

epivizr.Rcheck/examples_i386/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz0.690.120.81
startEpiviz0.030.020.04

epivizr.Rcheck/examples_x64/epivizr-Ex.timings

nameusersystemelapsed
restartEpiviz0.440.000.44
startEpiviz0.050.000.05