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CHECK report for CellScore on riesling1

This page was generated on 2020-10-18 12:33:25 -0400 (Sun, 18 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CellScore PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 248/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.9.0
Nancy Mah
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/CellScore
Branch: master
Last Commit: c066da8
Last Changed Date: 2020-04-27 15:13:55 -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
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellScore
Version: 1.9.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellScore.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellScore_1.9.0.tar.gz
StartedAt: 2020-10-17 20:02:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 20:09:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 396.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CellScore.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellScore.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellScore_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/CellScore.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellScore/DESCRIPTION' ... OK
* this is package 'CellScore' version '1.9.0'
* package encoding: UTF-8
* 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 'CellScore' 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 ... OK
* 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 installed files from 'inst/doc' ... 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
CellScoreReport                22.48   1.12   23.72
heatmapOnOffMarkers            14.64   0.26   15.13
ScatterplotCellScoreComponents 13.36   0.39   13.77
extractTransitions             13.38   0.19   13.60
RugplotCellScore               13.39   0.07   13.48
PlotCosineSimHeatmap           10.59   0.26   10.89
CellScore                       8.86   0.30    9.15
BoxplotCellScore                8.70   0.36    9.08
PcaStandards                    7.72   0.22    7.94
CosineSimScore                  7.33   0.19    7.51
BarplotOnOff                    5.64   0.60    6.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
CellScoreReport                20.47   0.66   21.22
heatmapOnOffMarkers            14.91   0.15   15.63
RugplotCellScore               13.00   0.14   13.15
ScatterplotCellScoreComponents 12.97   0.06   13.05
extractTransitions             12.97   0.05   13.01
PlotCosineSimHeatmap           10.58   0.05   10.64
BoxplotCellScore                8.70   0.31    9.04
CellScore                       8.70   0.13    8.83
PcaStandards                    7.63   0.15    7.79
CosineSimScore                  7.26   0.25    7.52
BarplotOnOff                    5.40   0.45    5.86
* 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: OK


Installation output

CellScore.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CellScore_1.9.0.tar.gz && rm -rf CellScore.buildbin-libdir && mkdir CellScore.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellScore.buildbin-libdir CellScore_1.9.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CellScore_1.9.0.zip && rm CellScore_1.9.0.tar.gz CellScore_1.9.0.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
 10 4209k   10  461k    0     0  4617k      0 --:--:-- --:--:-- --:--:-- 4571k
100 4209k  100 4209k    0     0  20.5M      0 --:--:-- --:--:-- --:--:-- 20.5M

install for i386

* installing *source* package 'CellScore' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellScore'
    finding HTML links ... done
    BarplotOnOff                            html  
    BoxplotCellScore                        html  
    CellScore                               html  
    CellScoreReport                         html  
    CosineSimScore                          html  
    OnOff                                   html  
    PcaStandards                            html  
    PlotCosineSimHeatmap                    html  
    RugplotCellScore                        html  
    ScatterplotCellScoreComponents          html  
    extractTransitions                      html  
    heatmapOnOffMarkers                     html  
    rugplotDonorTargetTest                  html  
    scatterplotDonorTargetTest              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 'CellScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellScore' as CellScore_1.9.0.zip
* DONE (CellScore)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'CellScore' successfully unpacked and MD5 sums checked

Tests output


Example timings

CellScore.Rcheck/examples_i386/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff5.640.606.26
BoxplotCellScore8.700.369.08
CellScore8.860.309.15
CellScoreReport22.48 1.1223.72
CosineSimScore7.330.197.51
OnOff4.690.254.94
PcaStandards7.720.227.94
PlotCosineSimHeatmap10.59 0.2610.89
RugplotCellScore13.39 0.0713.48
ScatterplotCellScoreComponents13.36 0.3913.77
extractTransitions13.38 0.1913.60
heatmapOnOffMarkers14.64 0.2615.13
rugplotDonorTargetTest000
scatterplotDonorTargetTest000

CellScore.Rcheck/examples_x64/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff5.400.455.86
BoxplotCellScore8.700.319.04
CellScore8.700.138.83
CellScoreReport20.47 0.6621.22
CosineSimScore7.260.257.52
OnOff4.360.114.47
PcaStandards7.630.157.79
PlotCosineSimHeatmap10.58 0.0510.64
RugplotCellScore13.00 0.1413.15
ScatterplotCellScoreComponents12.97 0.0613.05
extractTransitions12.97 0.0513.01
heatmapOnOffMarkers14.91 0.1515.63
rugplotDonorTargetTest000
scatterplotDonorTargetTest000