Package: BubbleTree

Version: 2.8.0

Command: rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.8.0.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.8.0.tar.gz

StartedAt: 2018-04-11 22:37:37 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:45:52 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 495.5 seconds

RetCode: 0

Status:  OK

CheckDir: BubbleTree.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.8.0.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BubbleTree.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 'BubbleTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BubbleTree' version '2.8.0'
* 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 27.2Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
    doc    3.4Mb
* 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
** 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeRBD         17.42   0.02   17.44
heteroLociTrack  7.66   0.39    8.04
saveXLS          0.19   0.00    8.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeRBD         21.55   0.04   21.60
heteroLociTrack 10.42   0.27   10.69
* 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-3.6-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BubbleTree' ...
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'BubbleTree' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BubbleTree' as BubbleTree_2.8.0.zip
* DONE (BubbleTree)
In R CMD INSTALL
In R CMD INSTALL