Package: igvR

Version: 1.3.6

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:igvR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings igvR_1.3.6.tar.gz

StartedAt: 2019-04-09 03:36:09 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:41:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 310.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: igvR.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:igvR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings igvR_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/igvR.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 'igvR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'igvR' version '1.3.6'
* 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 'igvR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    browserCode   5.2Mb
    lib           1.3Mb
* 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 include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'igvR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VariantTrack-class
> ### Title: Constructor for VariantTrack
> ### Aliases: VariantTrack-class VariantTrack
> 
> ### ** Examples
> 
> 
>     #----------------------------
>     #  first, from a local file
>     #----------------------------
> 
> f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541),
+                                               end=c(50312106, 51001328),
+                                               names=c("gene_79087", "gene_644186")))
> vcf.sub <- readVcf(f, "hg19", param=roi)
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: readVcf ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'igvR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VariantTrack-class
> ### Title: Constructor for VariantTrack
> ### Aliases: VariantTrack-class VariantTrack
> 
> ### ** Examples
> 
> 
>     #----------------------------
>     #  first, from a local file
>     #----------------------------
> 
> f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541),
+                                               end=c(50312106, 51001328),
+                                               names=c("gene_79087", "gene_644186")))
> vcf.sub <- readVcf(f, "hg19", param=roi)
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: readVcf ... 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/igvR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/igvR_1.3.6.tar.gz && rm -rf igvR.buildbin-libdir && mkdir igvR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=igvR.buildbin-libdir igvR_1.3.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL igvR_1.3.6.zip && rm igvR_1.3.6.tar.gz igvR_1.3.6.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 2674k  100 2674k    0     0  26.4M      0 --:--:-- --:--:-- --:--:-- 28.3M

install for i386

* installing *source* package 'igvR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'igvR'
    finding HTML links ... done
    DataFrameAnnotationTrack-class          html  
    DataFrameQuantitativeTrack-class        html  
    GRangesAnnotationTrack-class            html  
    GRangesQuantitativeTrack-class          html  
    QuantitativeTrack-class                 html  
    Track-class                             html  
    UCSCBedAnnotationTrack-class            html  
    UCSCBedGraphQuantitativeTrack-class     html  
    VariantTrack-class                      html  
    displayTrack                            html  
    getGenomicRegion                        html  
    getTrackNames                           html  
    igvAnnotationTrack-class                html  
    igvR-class                              html  
    ping                                    html  
    removeTracksByName                      html  
    setGenome                               html  
    showGenomicRegion                       html  
    trackInfo                               html  
    trackSize-DataFrameAnnotationTrack-method
                                            html  
    trackSize-DataFrameQuantitativeTrack-method
                                            html  
    trackSize-GRangesAnnotationTrack-method
                                            html  
    trackSize-GRangesQuantitativeTrack-method
                                            html  
    trackSize-UCSCBedAnnotationTrack-method
                                            html  
    trackSize-UCSCBedGraphQuantitativeTrack-method
                                            html  
    trackSize-VariantTrack-method           html  
    trackSize                               html  
** 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 'igvR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'igvR' as igvR_1.3.6.zip
* DONE (igvR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'igvR' successfully unpacked and MD5 sums checked