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CHECK report for CellScore on tokay2

This page was generated on 2018-10-17 08:45:18 -0400 (Wed, 17 Oct 2018).

Package 207/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.0.0
Nancy Mah
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CellScore
Branch: RELEASE_3_7
Last Commit: 6f5e1d7
Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellScore
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CellScore_1.0.0.tar.gz
StartedAt: 2018-10-17 00:59:17 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:09:12 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 594.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CellScore.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CellScore_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CellScore.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.0.0'
* 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 or elapsed time > 5s
                                user system elapsed
CellScoreReport                48.69   1.22   49.90
heatmapOnOffMarkers            23.78   0.15   24.23
extractTransitions             20.11   0.09   20.22
ScatterplotCellScoreComponents 19.69   0.08   19.78
BoxplotCellScore               18.55   0.77   19.36
RugplotCellScore               19.07   0.11   19.18
CosineSimScore                 18.25   0.88   19.13
PcaStandards                   17.75   1.11   43.00
PlotCosineSimHeatmap           17.28   0.81   18.11
CellScore                      14.56   0.48   15.05
BarplotOnOff                   10.61   0.72   13.21
OnOff                           9.97   0.50   10.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
CellScoreReport                36.34   0.57   37.16
heatmapOnOffMarkers            33.89   0.22   34.11
ScatterplotCellScoreComponents 32.14   0.29   32.44
extractTransitions             31.17   0.24   31.41
RugplotCellScore               28.34   0.58   28.92
PlotCosineSimHeatmap           21.16   0.42   21.58
BoxplotCellScore               18.51   0.37   18.89
PcaStandards                   16.97   0.24   17.20
CosineSimScore                 15.98   0.54   16.53
CellScore                      15.03   0.20   15.24
BarplotOnOff                    8.35   0.79    9.13
OnOff                           8.77   0.33    9.10
* 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 https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CellScore_1.0.0.tar.gz && rm -rf CellScore.buildbin-libdir && mkdir CellScore.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellScore.buildbin-libdir CellScore_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CellScore_1.0.0.zip && rm CellScore_1.0.0.tar.gz CellScore_1.0.0.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
 24 4211k   24 1024k    0     0  16.9M      0 --:--:-- --:--:-- --:--:-- 18.8M
100 4211k  100 4211k    0     0  44.5M      0 --:--:-- --:--:-- --:--:-- 47.2M

install for i386

* installing *source* package 'CellScore' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'CellScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellScore' as CellScore_1.0.0.zip
* DONE (CellScore)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CellScore' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

CellScore.Rcheck/examples_i386/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff10.61 0.7213.21
BoxplotCellScore18.55 0.7719.36
CellScore14.56 0.4815.05
CellScoreReport48.69 1.2249.90
CosineSimScore18.25 0.8819.13
OnOff 9.97 0.5010.47
PcaStandards17.75 1.1143.00
PlotCosineSimHeatmap17.28 0.8118.11
RugplotCellScore19.07 0.1119.18
ScatterplotCellScoreComponents19.69 0.0819.78
extractTransitions20.11 0.0920.22
heatmapOnOffMarkers23.78 0.1524.23
rugplotDonorTargetTest000
scatterplotDonorTargetTest000

CellScore.Rcheck/examples_x64/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff8.350.799.13
BoxplotCellScore18.51 0.3718.89
CellScore15.03 0.2015.24
CellScoreReport36.34 0.5737.16
CosineSimScore15.98 0.5416.53
OnOff8.770.339.10
PcaStandards16.97 0.2417.20
PlotCosineSimHeatmap21.16 0.4221.58
RugplotCellScore28.34 0.5828.92
ScatterplotCellScoreComponents32.14 0.2932.44
extractTransitions31.17 0.2431.41
heatmapOnOffMarkers33.89 0.2234.11
rugplotDonorTargetTest000
scatterplotDonorTargetTest000