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CHECK report for BubbleTree on tokay1

This page was generated on 2020-08-12 11:42:54 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BubbleTree PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 204/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.19.0
Todd Creasy , Wei Zhu
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/BubbleTree
Branch: master
Last Commit: 50dd6a4
Last Changed Date: 2020-04-27 14:46:47 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.19.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BubbleTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BubbleTree_2.19.0.tar.gz
StartedAt: 2020-08-12 02:10:11 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 02:18:46 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 514.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BubbleTree.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BubbleTree_2.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BubbleTree.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '2.19.0'
* 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         16.75   0.04   16.78
heteroLociTrack  6.32   0.20    6.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
makeRBD         16.77   0.00   16.76
heteroLociTrack  6.69   0.17    6.85
* 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-3.12-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.



Installation output

BubbleTree.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BubbleTree_2.19.0.tar.gz && rm -rf BubbleTree.buildbin-libdir && mkdir BubbleTree.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BubbleTree.buildbin-libdir BubbleTree_2.19.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BubbleTree_2.19.0.zip && rm BubbleTree_2.19.0.tar.gz BubbleTree_2.19.0.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
100 23.7M  100 23.7M    0     0  45.1M      0 --:--:-- --:--:-- --:--:-- 45.4M

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_2.19.0.zip
* DONE (BubbleTree)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BubbleTree' successfully unpacked and MD5 sums checked

Tests output


Example timings

BubbleTree.Rcheck/examples_i386/BubbleTree-Ex.timings

nameusersystemelapsed
Annotate000
BTreePlotter0.090.010.11
BTreePredictor0.020.000.02
RBD000
RscoreTrack1.370.051.42
TrackPlotter000
annoByGenesAndCyto0.570.300.86
bafTrack0.420.120.54
btcompare000
btpredict3.160.033.19
drawBTree0.300.050.34
drawBubbles0.310.050.36
drawFeatures1.120.091.22
getTracks1.470.001.47
heteroLociTrack6.320.206.51
info3.450.033.49
loadRBD0.030.000.03
makeRBD16.75 0.0416.78
saveXLS0.220.004.03
trackBTree0.390.010.41
xyTrack0.330.040.38

BubbleTree.Rcheck/examples_x64/BubbleTree-Ex.timings

nameusersystemelapsed
Annotate000
BTreePlotter0.110.000.11
BTreePredictor000
RBD000
RscoreTrack1.430.031.45
TrackPlotter000
annoByGenesAndCyto0.780.060.85
bafTrack0.360.020.37
btcompare000
btpredict2.920.113.03
drawBTree0.260.000.27
drawBubbles0.270.000.26
drawFeatures1.030.021.05
getTracks0.650.010.68
heteroLociTrack6.690.176.85
info3.950.074.02
loadRBD0.020.000.02
makeRBD16.77 0.0016.76
saveXLS0.170.010.47
trackBTree0.390.020.41
xyTrack0.380.030.41