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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hiAnnotator.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hiAnnotator_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/hiAnnotator.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.28.0'
* 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 ... 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 ... 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 '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 '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'
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'
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 featureName
  keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
  seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
  subjectHits
* 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' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hiAnnotator_1.28.0.tar.gz && rm -rf hiAnnotator.buildbin-libdir && mkdir hiAnnotator.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hiAnnotator.buildbin-libdir hiAnnotator_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hiAnnotator_1.28.0.zip && rm hiAnnotator_1.28.0.tar.gz hiAnnotator_1.28.0.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
 49  798k   49  394k    0     0   530k      0  0:00:01 --:--:--  0:00:01  530k
100  798k  100  798k    0     0   551k      0  0:00:01  0:00:01 --:--:--  551k

install for i386

* installing *source* package 'hiAnnotator' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hiAnnotator'
    finding HTML links ... done
    cleanColname                            html  
    doAnnotation                            html  
    dot-checkArgsSetDefaults                html  
    dot-mergeAndReturn                      html  
    genes                                   html  
    get2NearestFeature                      html  
    getFeatureCounts                        html  
    getFeatureCountsBig                     html  
    getLowestDists                          html  
    getNearestFeature                       html  
    getRelevantCol                          html  
    getSitesInFeature                       html  
    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 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 'hiAnnotator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.28.0.zip
* DONE (hiAnnotator)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'hiAnnotator' successfully unpacked and MD5 sums checked