Package: interactiveDisplay

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:interactiveDisplay.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings interactiveDisplay_1.20.0.tar.gz

StartedAt: 2019-04-13 03:12:40 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:16:32 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 232.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: interactiveDisplay.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:interactiveDisplay.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings interactiveDisplay_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/interactiveDisplay.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'interactiveDisplay/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'interactiveDisplay' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Package which this enhances but not available for checking: 'rstudio'
* 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 'interactiveDisplay' 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 ... WARNING
'::' or ':::' import not declared from: '.interactiveDisplayBase'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.altgr : <anonymous>: no visible global function definition for
  'elementMetadata'
.altgr : <anonymous>: no visible global function definition for
  'seqlevels<-'
.bicgo : <anonymous>: no visible binding for global variable 'GO.db'
.bicgo : <anonymous>: no visible global function definition for 'exprs'
.bicgo : <anonymous>: no visible global function definition for
  'cutree'
.bicgo : <anonymous>: no visible global function definition for
  'hclust'
.bicgo : <anonymous>: no visible global function definition for 'dist'
.bicgo : <anonymous>: no visible global function definition for 'cim'
.choose_gen: no visible global function definition for 'ucscGenomes'
.simplenet : <anonymous>: no visible global function definition for
  'cutree'
.simplenet : <anonymous>: no visible global function definition for
  'rainbow'
.simplenet : <anonymous> : hc: no visible global function definition
  for 'hclust'
.simplenet : <anonymous> : hc: no visible global function definition
  for 'dist'
.simplenet : <anonymous> : dm: no visible global function definition
  for 'dist'
.usePackage: no visible global function definition for
  'installed.packages'
ggheat: no visible global function definition for 'colorRampPalette'
ggheat: no visible binding for global variable 'Var2'
ggheat: no visible binding for global variable 'Var1'
ggheat: no visible binding for global variable 'value'
ggheat: no visible global function definition for 'coord_flip'
grid2jssvg: no visible global function definition for 'png'
grid2jssvg: no visible global function definition for 'dev.off'
subgr: no visible global function definition for 'seqnames'
subgr: no visible global function definition for 'seqlevels<-'
subgr: no visible global function definition for 'ranges'
subgr2: no visible global function definition for 'seqnames'
subgr2: no visible global function definition for 'seqlevels<-'
subgr2: no visible global function definition for 'ranges'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'exprs'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'experimentData'
display,ExpressionSet : <anonymous>: no visible binding for global
  variable 'GO.db'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'cutree'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'rainbow'
display,ExpressionSet : <anonymous> : hc: no visible global function
  definition for 'hclust'
display,ExpressionSet : <anonymous> : hc: no visible global function
  definition for 'dist'
display,ExpressionSet : <anonymous> : dm: no visible global function
  definition for 'dist'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'as.dendrogram'
display,ExpressionSet : <anonymous> : <local> : <anonymous>: no visible
  global function definition for 'is.leaf'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'dendrapply'
display,ExpressionSet : <anonymous>: no visible global function
  definition for 'plot'
display,GRanges: no visible global function definition for 'mcols'
display,GRanges : <anonymous>: no visible global function definition
  for 'AnnotationTrack'
display,GRanges : <anonymous>: no visible global function definition
  for 'GenomeAxisTrack'
display,GRanges : <anonymous>: no visible global function definition
  for 'IdeogramTrack'
display,GRanges : <anonymous>: no visible global function definition
  for 'plotTracks'
display,GRanges : <anonymous>: no visible global function definition
  for 'layout_circle'
display,GRanges : <anonymous>: no visible binding for global variable
  'seqnames'
display,GRanges : <anonymous>: no visible global function definition
  for 'plot'
display,GRanges : <anonymous>: no visible global function definition
  for 'seqnames'
display,GRanges : <anonymous>: no visible global function definition
  for 'ranges'
display,GRanges : <anonymous>: no visible global function definition
  for 'ucscGenomes'
display,GRanges : <anonymous>: no visible global function definition
  for 'GRanges'
display,GRanges : <anonymous>: no visible global function definition
  for 'IRanges'
display,GRanges : <anonymous>: no visible global function definition
  for 'seqlengths<-'
display,GRanges : <anonymous>: no visible global function definition
  for 'seqlengths'
display,GRangesList : <anonymous>: no visible global function
  definition for 'mcols'
display,GRangesList : <anonymous>: no visible global function
  definition for 'AnnotationTrack'
display,GRangesList : <anonymous>: no visible global function
  definition for 'GenomeAxisTrack'
display,GRangesList : <anonymous>: no visible global function
  definition for 'IdeogramTrack'
display,GRangesList : <anonymous>: no visible global function
  definition for 'plotTracks'
display,GRangesList : <anonymous>: no visible global function
  definition for 'layout_circle'
display,GRangesList : <anonymous>: no visible binding for global
  variable 'seqnames'
display,GRangesList : <anonymous>: no visible global function
  definition for 'plot'
display,GRangesList : <anonymous>: no visible global function
  definition for 'seqnames'
display,GRangesList : <anonymous>: no visible global function
  definition for 'ranges'
display,GRangesList : <anonymous>: no visible global function
  definition for 'ucscGenomes'
display,GRangesList : <anonymous>: no visible global function
  definition for 'GRanges'
display,GRangesList : <anonymous>: no visible global function
  definition for 'IRanges'
display,GRangesList : <anonymous>: no visible global function
  definition for 'seqlengths<-'
display,GRangesList : <anonymous>: no visible global function
  definition for 'seqlengths'
display,GRangesList : <anonymous>: no visible global function
  definition for 'GRangesList'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'MRcounts'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'pData'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'colorRampPalette'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'legend'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'plotFeature'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'plotOrd'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'libSize'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'plot'
display,MRexperiment : <anonymous>: no visible global function
  definition for 'fData'
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for 'seqnames'
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for 'rowRanges'
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for 'assays'
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for 'colorRampPalette'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable 'Var1'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable 'Var2'
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable 'value'
Undefined global functions or variables:
  AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges
  IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim
  colorRampPalette coord_flip cutree dendrapply dev.off dist
  elementMetadata experimentData exprs fData hclust installed.packages
  is.leaf layout_circle legend libSize mcols pData plot plotFeature
  plotOrd plotTracks png rainbow ranges rowRanges seqlengths
  seqlengths<- seqlevels<- seqnames ucscGenomes value
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "rainbow")
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist",
             "hclust", "is.leaf")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/interactiveDisplay.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/interactiveDisplay_1.20.0.tar.gz && rm -rf interactiveDisplay.buildbin-libdir && mkdir interactiveDisplay.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=interactiveDisplay.buildbin-libdir interactiveDisplay_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL interactiveDisplay_1.20.0.zip && rm interactiveDisplay_1.20.0.tar.gz interactiveDisplay_1.20.0.zip
###
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install for i386

* installing *source* package 'interactiveDisplay' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'display' with signature 'object="GRanges"': no definition for class "GRanges"
in method for 'display' with signature 'object="GRangesList"': no definition for class "GRangesList"
in method for 'display' with signature 'object="RangedSummarizedExperiment"': no definition for class "RangedSummarizedExperiment"
in method for 'display' with signature 'object="MRexperiment"': no definition for class "MRexperiment"
** help
*** installing help indices
  converting help for package 'interactiveDisplay'
    finding HTML links ... done
    altgr                                   html  
    bicgo                                   html  
    expr                                    html  
    gridsvgjs                               html  
    gridtweak                               html  
    interactiveDisplay-methods              html  
    mmgr                                    html  
    mmgrl                                   html  
    se                                      html  
    simplenet                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'interactiveDisplay' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'interactiveDisplay' as interactiveDisplay_1.20.0.zip
* DONE (interactiveDisplay)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'interactiveDisplay' successfully unpacked and MD5 sums checked
In R CMD INSTALL