Package: igvR

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 04:31:50 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:37:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 323.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: igvR.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/igvR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.4.0'
* 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 ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    browserCode   5.2Mb
    extdata       1.6Mb
    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 ... WARNING
Undocumented S4 classes:
  'GenomicAlignmentTrack'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'getSupportedGenomes,igvR-method'
  'genomeName'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 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_1.4.0.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_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL igvR_1.4.0.zip && rm igvR_1.4.0.tar.gz igvR_1.4.0.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 3639k  100 3639k    0     0  39.4M      0 --:--:-- --:--:-- --:--:-- 42.3M

install for i386

* installing *source* package 'igvR' ...
** using staged installation
** 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  
    GenomicAlignmentsTrack-class            html  
    QuantitativeTrack-class                 html  
    Track-class                             html  
    UCSCBedAnnotationTrack-class            html  
    UCSCBedGraphQuantitativeTrack-class     html  
    VariantTrack-class                      html  
    displayTrack                            html  
    getGenomicRegion                        html  
    getSupportedGenomes                     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-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
** 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_1.4.0.zip
* DONE (igvR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'igvR' successfully unpacked and MD5 sums checked