Multiple platform build/check report for BioC 3.9 - CHECK report for RareVariantVis on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RareVariantVis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RareVariantVis_2.11.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RareVariantVis.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RareVariantVis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RareVariantVis' version '2.11.0'
* 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 'RareVariantVis' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RareVariantVis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chromosomeVis
> ### Title: Visualization of all genomic variants on the chromosome
> ### Aliases: chromosomeVis
> ### Keywords: ˜visualization ˜varaints
> 
> ### ** Examples
> 
> 
> # analyze chromosome 19 from example genome
> sample = system.file("extdata", "CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz",
+   package = "RareVariantVis")
> sv_sample = system.file("extdata", "CoriellIndex_S1.sv.vcf.gz",
+   package = "RareVariantVis")
> chromosomeVis(sample=sample, sv_sample=sv_sample, chromosomes=c("19"))
Error in validObject(.Object) : 
  invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: chromosomeVis ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RareVariantVis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chromosomeVis
> ### Title: Visualization of all genomic variants on the chromosome
> ### Aliases: chromosomeVis
> ### Keywords: ˜visualization ˜varaints
> 
> ### ** Examples
> 
> 
> # analyze chromosome 19 from example genome
> sample = system.file("extdata", "CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz",
+   package = "RareVariantVis")
> sv_sample = system.file("extdata", "CoriellIndex_S1.sv.vcf.gz",
+   package = "RareVariantVis")
> chromosomeVis(sample=sample, sv_sample=sv_sample, chromosomes=c("19"))
Error in validObject(.Object) : 
  invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: chromosomeVis ... VCFHeader -> new -> initialize -> initialize -> validObject
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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RareVariantVis.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RareVariantVis_2.11.0.tar.gz && rm -rf RareVariantVis.buildbin-libdir && mkdir RareVariantVis.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RareVariantVis.buildbin-libdir RareVariantVis_2.11.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RareVariantVis_2.11.0.zip && rm RareVariantVis_2.11.0.tar.gz RareVariantVis_2.11.0.zip
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100 2632k  100 2632k    0     0  9059k      0 --:--:-- --:--:-- --:--:-- 9268k

install for i386

* installing *source* package 'RareVariantVis' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** help
*** installing help indices
  converting help for package 'RareVariantVis'
    finding HTML links ... done
    callHomozygous                          html  
    chromosomeVis                           html  
    getCrisprGuides                         html  
    movingAverage                           html  
    multipleVis                             html  
    rareVariantVis                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package can be loaded from final location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RareVariantVis' ...
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
* MD5 sums
packaged installation of 'RareVariantVis' as RareVariantVis_2.11.0.zip
* DONE (RareVariantVis)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RareVariantVis' successfully unpacked and MD5 sums checked

CHECK report for RareVariantVis on tokay2

Summary

Command output

Installation output

Tests output

Example timings