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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BubbleTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BubbleTree_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BubbleTree.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BubbleTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BubbleTree' version '2.22.0'
* 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 'BubbleTree' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
 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
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
Undefined global functions or variables:
  queryHits
* 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
makeRBD         13.28   0.01   13.30
heteroLociTrack  5.54   0.18    5.74
saveXLS          0.18   0.03    7.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
makeRBD         17.25   0.04   17.28
heteroLociTrack  6.57   0.20    6.76
* 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-3.13-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BubbleTree_2.22.0.tar.gz && rm -rf BubbleTree.buildbin-libdir && mkdir BubbleTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BubbleTree.buildbin-libdir BubbleTree_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BubbleTree_2.22.0.zip && rm BubbleTree_2.22.0.tar.gz BubbleTree_2.22.0.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
  8 23.7M    8 2075k    0     0  2523k      0  0:00:09 --:--:--  0:00:09 2521k
 22 23.7M   22 5504k    0     0  3020k      0  0:00:08  0:00:01  0:00:07 3020k
 42 23.7M   42 10.0M    0     0  3656k      0  0:00:06  0:00:02  0:00:04 3655k
 63 23.7M   63 15.1M    0     0  4070k      0  0:00:05  0:00:03  0:00:02 4069k
 89 23.7M   89 21.3M    0     0  4528k      0  0:00:05  0:00:04  0:00:01 4527k
100 23.7M  100 23.7M    0     0  4705k      0  0:00:05  0:00:05 --:--:-- 5119k

install for i386

* installing *source* package 'BubbleTree' ...
** using staged installation
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BubbleTree'
    finding HTML links ... done
    Annotate                                html  
    BTreePlotter                            html  
    BTreePredictor                          html  
    RBD                                     html  
    RscoreTrack                             html  
    TrackPlotter                            html  
    all.somatic.lst                         html  
    allCNV.lst                              html  
    allCall.lst                             html  
    allHetero.lst                           html  
    allRBD.lst                              html  
    annoByGenesAndCyto                      html  
    bafTrack                                html  
    btcompare                               html  
    btpredict                               html  
    cancer.genes.minus2                     html  
    centromere.dat                          html  
    cnv.gr                                  html  
    cyto.gr                                 html  
    drawBTree                               html  
    drawBubbles                             html  
    drawFeatures                            html  
    gene.uni.clean.gr                       html  
    getTracks                               html  
    heteroLociTrack                         html  
    hg19.seqinfo                            html  
    info                                    html  
    loadRBD                                 html  
    makeRBD                                 html  
    mergeSnpCnv                             html  
    saveXLS                                 html  
    snp.gr                                  html  
    trackBTree                              html  
    vol.genes                               html  
    xyTrack                                 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 'BubbleTree' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BubbleTree' as BubbleTree_2.22.0.zip
* DONE (BubbleTree)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BubbleTree' successfully unpacked and MD5 sums checked