Back to the "Multiple platform build/check report" A [B] C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for BrowserViz on windows1.bioconductor.org

This page was generated on 2015-10-27 17:32:01 -0400 (Tue, 27 Oct 2015).

Package 122/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BrowserViz 1.2.0
Paul Shannon
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BrowserViz
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ ERROR ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: BrowserViz
Version: 1.2.0
Command: rm -rf BrowserViz.buildbin-libdir BrowserViz.Rcheck && mkdir BrowserViz.buildbin-libdir BrowserViz.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BrowserViz.buildbin-libdir BrowserViz_1.2.0.tar.gz >BrowserViz.Rcheck\00install.out 2>&1 && cp BrowserViz.Rcheck\00install.out BrowserViz-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BrowserViz.buildbin-libdir --install="check:BrowserViz-install.out" --force-multiarch --no-vignettes --timings BrowserViz_1.2.0.tar.gz
StartedAt: 2015-10-27 00:12:05 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:12:34 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 29.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: BrowserViz.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BrowserViz.buildbin-libdir BrowserViz.Rcheck && mkdir BrowserViz.buildbin-libdir BrowserViz.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BrowserViz.buildbin-libdir BrowserViz_1.2.0.tar.gz >BrowserViz.Rcheck\00install.out 2>&1 && cp BrowserViz.Rcheck\00install.out BrowserViz-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BrowserViz.buildbin-libdir --install="check:BrowserViz-install.out" --force-multiarch --no-vignettes --timings BrowserViz_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BrowserViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BrowserViz' version '1.2.0'
* 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 '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
* 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
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'BrowserViz-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BrowserVizClass
> ### Title: BrowserViz: a base class (for extension) and standalone example
> ###   of R/Javascript interactive web browser visualization
> ### Aliases: BrowserViz class:BrowserVizClass BrowserVizClass-class
> ###   show,BrowserVizClass-method setBrowserWindowTitle
> ###   setBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{setBrowserWindowTitle}{BrowserVizClass}
> ###   getBrowserWindowSize getBrowserWindowSize,BrowserVizClass-method
> ###   \S4method{getBrowserWindowSize}{BrowserVizClass}
> ###   getBrowserWindowTitle getBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{getBrowserWindowTitle}{BrowserVizClass}
> ###   browserResponseReady browserResponseReady,BrowserVizClass-method
> ###   \S4method{browserResponseReady}{BrowserVizClass} getBrowserResponse
> ###   getBrowserResponse,BrowserVizClass-method
> ###   \S4method{getBrowserResponse}{BrowserVizClass} port
> ###   port,BrowserVizClass-method \S4method{port}{BrowserVizClass}
> ###   closeWebSocket closeWebSocket,BrowserVizClass-method
> ###   \S4method{closeWebSocket}{BrowserVizClass} getBrowserInfo
> ###   getBrowserInfo,BrowserVizClass-method
> ###   \S4method{getBrowserInfo}{BrowserVizClass} send
> ###   send,BrowserVizClass-method \S4method{send}{BrowserVizClass} ready
> ###   ready,BrowserVizClass-method \S4method{ready}{BrowserVizClass} toJSON
> ###   addRMessageHandler
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   library(BrowserViz)
>     
>   bv <- BrowserViz(4000:4024)
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
Calls: BrowserViz -> browseURL -> .getBrowser
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'BrowserViz-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BrowserVizClass
> ### Title: BrowserViz: a base class (for extension) and standalone example
> ###   of R/Javascript interactive web browser visualization
> ### Aliases: BrowserViz class:BrowserVizClass BrowserVizClass-class
> ###   show,BrowserVizClass-method setBrowserWindowTitle
> ###   setBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{setBrowserWindowTitle}{BrowserVizClass}
> ###   getBrowserWindowSize getBrowserWindowSize,BrowserVizClass-method
> ###   \S4method{getBrowserWindowSize}{BrowserVizClass}
> ###   getBrowserWindowTitle getBrowserWindowTitle,BrowserVizClass-method
> ###   \S4method{getBrowserWindowTitle}{BrowserVizClass}
> ###   browserResponseReady browserResponseReady,BrowserVizClass-method
> ###   \S4method{browserResponseReady}{BrowserVizClass} getBrowserResponse
> ###   getBrowserResponse,BrowserVizClass-method
> ###   \S4method{getBrowserResponse}{BrowserVizClass} port
> ###   port,BrowserVizClass-method \S4method{port}{BrowserVizClass}
> ###   closeWebSocket closeWebSocket,BrowserVizClass-method
> ###   \S4method{closeWebSocket}{BrowserVizClass} getBrowserInfo
> ###   getBrowserInfo,BrowserVizClass-method
> ###   \S4method{getBrowserInfo}{BrowserVizClass} send
> ###   send,BrowserVizClass-method \S4method{send}{BrowserVizClass} ready
> ###   ready,BrowserVizClass-method \S4method{ready}{BrowserVizClass} toJSON
> ###   addRMessageHandler
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   library(BrowserViz)
>     
>   bv <- BrowserViz(4000:4024)
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
Calls: BrowserViz -> browseURL -> .getBrowser
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [1s]
Warning message:
running command '"C:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 3 
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  Timing stopped at: 0 0 0 
  Error in BrowserViz(PORT_RANGE[1]) : 
    no available ports in range 7200:7200
  [1] "--- testRunOutOfPorts"
  
  This application has requested the Runtime to terminate it in an unusual way.
  Please contact the application's support team for more information.
  Assertion failed!
  
  Program: C:\biocbld\BBS-3˜1.2-B\R\bin\i386\Rterm.exe
  File: src/win/timer.c, Line 115
  
  Expression: old == NULL
** running tests for arch 'x64' ...
  Running 'runTests.R' [1s]
Warning message:
running command '"C:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_BrowserViz.R 
       testConstructor 
       testGetBrowserInfo 
       testGetWindowSize 
       testMultipleOpenCloseOnSamePort 
       testWindowTitle 
  
  
  Error in BiocGenerics:::testPackage("BrowserViz") : 
    unit tests failed for package BrowserViz
  Execution halted
* 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: 4 ERRORs, 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.Rcheck/00check.log'
for details.

BrowserViz.Rcheck/tests_i386/runTests.Rout.fail:


R version 3.2.2 Patched (2015-08-16 r69094) -- "Fire Safety"
Copyright (C) 2015 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.

> BiocGenerics:::testPackage("BrowserViz")

Attaching package: 'jsonlite'

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

    View


Attaching package: 'BrowserViz'

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

    toJSON

[1] "--- testConstructor"
BrowserViz constructor starting with html file 'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.buildbin-libdir/BrowserViz/scripts/viz.html'
 html file exists? TRUE
summoning default browser to get http://localhost:7200
Timing stopped at: 0 0 0 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testGetBrowserInfo"
BrowserViz constructor starting with html file 'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.buildbin-libdir/BrowserViz/scripts/viz.html'
 html file exists? TRUE
summoning default browser to get http://localhost:7201
Timing stopped at: 0 0 0 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testGetWindowSize"
Timing stopped at: 0.02 0 0.02 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testMultipleOpenCloseOnSamePort"
Timing stopped at: 0 0 0 
Error in BrowserViz(PORT_RANGE[1]) : 
  no available ports in range 7200:7200
[1] "--- testRunOutOfPorts"

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Assertion failed!

Program: C:\biocbld\BBS-3˜1.2-B\R\bin\i386\Rterm.exe
File: src/win/timer.c, Line 115

Expression: old == NULL

BrowserViz.Rcheck/tests_x64/runTests.Rout.fail:


R version 3.2.2 Patched (2015-08-16 r69094) -- "Fire Safety"
Copyright (C) 2015 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.

> BiocGenerics:::testPackage("BrowserViz")

Attaching package: 'jsonlite'

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

    View


Attaching package: 'BrowserViz'

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

    toJSON

[1] "--- testConstructor"
BrowserViz constructor starting with html file 'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.buildbin-libdir/BrowserViz/scripts/viz.html'
 html file exists? TRUE
summoning default browser to get http://localhost:7200
Timing stopped at: 0.01 0 0.01 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testGetBrowserInfo"
BrowserViz constructor starting with html file 'C:/biocbld/bbs-3.2-bioc/meat/BrowserViz.buildbin-libdir/BrowserViz/scripts/viz.html'
 html file exists? TRUE
summoning default browser to get http://localhost:7201
Timing stopped at: 0 0 0 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testGetWindowSize"
Timing stopped at: 0 0 0 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
[1] "--- testMultipleOpenCloseOnSamePort"
Timing stopped at: 0 0 0 
Error in BrowserViz(PORT_RANGE[1]) : 
  no available ports in range 7200:7200
[1] "--- testRunOutOfPorts"
[1] "--- testWindowTitle"
Timing stopped at: 0.02 0 0.02 
Error in .getBrowser() : BrowserViz not (yet) supported on Windows.


RUNIT TEST PROTOCOL -- Tue Oct 27 00:12:31 2015 
*********************************************** 
Number of test functions: 6 
Number of errors: 5 
Number of failures: 0 

 
1 Test Suite : 
BrowserViz RUnit Tests - 6 test functions, 5 errors, 0 failures
ERROR in testConstructor: Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
ERROR in testGetBrowserInfo: Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
ERROR in testGetWindowSize: Error in .getBrowser() : BrowserViz not (yet) supported on Windows.
ERROR in testMultipleOpenCloseOnSamePort: Error in BrowserViz(PORT_RANGE[1]) : 
  no available ports in range 7200:7200
ERROR in testWindowTitle: Error in .getBrowser() : BrowserViz not (yet) supported on Windows.

Test files with failing tests

   test_BrowserViz.R 
     testConstructor 
     testGetBrowserInfo 
     testGetWindowSize 
     testMultipleOpenCloseOnSamePort 
     testWindowTitle 


Error in BiocGenerics:::testPackage("BrowserViz") : 
  unit tests failed for package BrowserViz
Execution halted

BrowserViz.Rcheck/00install.out:


install for i386

* installing *source* package 'BrowserViz' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'jsonlite': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'jsonlite': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'BrowserViz' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'jsonlite': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'BrowserViz' as BrowserViz_1.2.0.zip
* DONE (BrowserViz)

BrowserViz.Rcheck/examples_i386/BrowserViz-Ex.timings:

nameusersystemelapsed

BrowserViz.Rcheck/examples_x64/BrowserViz-Ex.timings:

nameusersystemelapsed