Multiple platform build/check report for BioC 3.6 - CHECK report for hiAnnotator on tokay1

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### Running command:
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###   rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.12.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/hiAnnotator.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hiAnnotator/DESCRIPTION' ... OK
* this is package 'hiAnnotator' version '1.12.0'
* 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 'hiAnnotator' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getLowestDists.Rd:32: missing file link 'nearest'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getLowestDists.Rd:19: missing file link 'nearest'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getSitesInFeature.Rd:38: missing file link 'findOverlaps'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/hiAnnotator.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
get2NearestFeature: no visible global function definition for 'IRanges'
get2NearestFeature: no visible global function definition for 'mid'
get2NearestFeature: no visible binding for global variable 'dist'
get2NearestFeature: no visible binding for global variable 'qStrand'
get2NearestFeature: no visible binding for global variable
  'subjectHits'
get2NearestFeature : <anonymous>: no visible binding for global
  variable 'queryHits'
get2NearestFeature : <anonymous>: no visible binding for global
  variable 'dist'
get2NearestFeature : <anonymous>: no visible binding for global
  variable 'featureName'
getFeatureCounts : <anonymous>: no visible global function definition
  for 'countQueryHits'
getFeatureCountsBig: no visible global function definition for 'mid'
getLowestDists: no visible binding for global variable 'queryHits'
getLowestDists: no visible binding for global variable 'dist'
getNearestFeature: no visible global function definition for 'IRanges'
getNearestFeature: no visible global function definition for 'mid'
getNearestFeature: no visible binding for global variable 'queryHits'
getNearestFeature: no visible binding for global variable 'n'
getNearestFeature: no visible binding for global variable 'featureName'
getNearestFeature: no visible binding for global variable 'dist'
getSitesInFeature: no visible global function definition for
  'overlapsAny'
getSitesInFeature: no visible binding for global variable 'queryHits'
getSitesInFeature: no visible global function definition for 'n'
getSitesInFeature: no visible binding for global variable 'featureName'
makeChunks: no visible global function definition for 'breakInChunks'
makeChunks: no visible global function definition for 'detectCores'
makeChunks : <anonymous>: no visible global function definition for
  'keepSeqlevels'
makeChunks : <anonymous>: no visible global function definition for
  'seqlevelsInUse'
makeGRanges: no visible global function definition for 'IRanges'
makeGRanges: no visible global function definition for 'seqlengths'
makeGRanges: no visible global function definition for 'seqlevels<-'
makeGRanges: no visible global function definition for 'sortSeqlevels'
makeGRanges: no visible global function definition for 'seqlevelsInUse'
makeGRanges: no visible global function definition for 'seqlengths<-'
makeGRanges: no visible global function definition for 'seqlevels'
Undefined global functions or variables:
  IRanges breakInChunks countQueryHits detectCores dist featureName
  keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
  seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
  subjectHits
Consider adding
  importFrom("stats", "dist")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* 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-3.6-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'hiAnnotator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'hiAnnotator'
    finding HTML links ... done
    cleanColname                            html  
    doAnnotation                            html  
    genes                                   html  
    get2NearestFeature                      html  
    getFeatureCounts                        html  
    getFeatureCountsBig                     html  
    getLowestDists                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getLowestDists.Rd:32: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getLowestDists.Rd:19: missing file link 'nearest'
    getNearestFeature                       html  
    getRelevantCol                          html  
    getSitesInFeature                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgjazm/R.INSTALLe982e515ee9/hiAnnotator/man/getSitesInFeature.Rd:38: missing file link 'findOverlaps'
    getUCSCtable                            html  
    finding level-2 HTML links ... done

    getWindowLabel                          html  
    hiAnnotator                             html  
    makeChunks                              html  
    makeGRanges                             html  
    makeUCSCsession                         html  
    plotdisFeature                          html  
    sites                                   html  
    sites.ctrl                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'hiAnnotator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.12.0.zip
* DONE (hiAnnotator)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for hiAnnotator on tokay1

Summary

Command output

Installation output

Tests output

Example timings