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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:igvR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings igvR_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/igvR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.0'
* package encoding: UTF-8
* 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 ... 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
  Found 'inst/doc/makefile': should be 'Makefile' and will be ignored
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/igvR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/igvR_1.10.0.tar.gz && rm -rf igvR.buildbin-libdir && mkdir igvR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=igvR.buildbin-libdir igvR_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL igvR_1.10.0.zip && rm igvR_1.10.0.tar.gz igvR_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 53 7888k   53 4254k    0     0  70.2M      0 --:--:-- --:--:-- --:--:-- 70.4M
100 7888k  100 7888k    0     0  84.9M      0 --:--:-- --:--:-- --:--:-- 84.6M

install for i386

* installing *source* package 'igvR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
  converting help for package 'igvR'
    finding HTML links ... done
    BedpeInteractionsTrack-class            html  
    DataFrameAnnotationTrack-class          html  
    DataFrameQuantitativeTrack-class        html  
    GRangesAnnotationTrack-class            html  
    GRangesQuantitativeTrack-class          html  
    GenomicAlignmentTrack-class             html  
    QuantitativeTrack-class                 html  
    Track-class                             html  
    UCSCBedAnnotationTrack-class            html  
    UCSCBedGraphQuantitativeTrack-class     html  
    VariantTrack-class                      html  
    displayTrack                            html  
    enableMotifLogoPopups                   html  
    getGenomicRegion                        html  
    getSupportedGenomes                     html  
    getTrackNames                           html  
    igvAnnotationTrack-class                html  
    igvR-class                              html  
    ping                                    html  
    removeTracksByName                      html  
    saveToSVG                               html  
    setGenome                               html  
    setTrackClickFunction                   html  
    showGenomicRegion                       html  
    trackInfo                               html  
    trackSize-BedpeInteractionsTrack-method
                                            html  
    trackSize-DataFrameAnnotationTrack-method
                                            html  
    trackSize-DataFrameQuantitativeTrack-method
                                            html  
    trackSize-GRangesAnnotationTrack-method
                                            html  
    trackSize-GRangesQuantitativeTrack-method
                                            html  
    trackSize-GenomicAlignmentTrack-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
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** 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
See system.file("LICENSE", package="MotifDb") for use restrictions.
* MD5 sums
packaged installation of 'igvR' as igvR_1.10.0.zip
* DONE (igvR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'igvR' successfully unpacked and MD5 sums checked