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CHECK report for SubCellBarCode on tokay2

This page was generated on 2020-10-17 11:57:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SubCellBarCode PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1755/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.4.0
Taner Arslan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SubCellBarCode
Branch: RELEASE_3_11
Last Commit: fb924c3
Last Changed Date: 2020-04-27 15:27:14 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SubCellBarCode
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SubCellBarCode.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SubCellBarCode_1.4.0.tar.gz
StartedAt: 2020-10-17 08:41:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:49:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 447.1 seconds
RetCode: 0
Status:  OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SubCellBarCode.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SubCellBarCode_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SubCellBarCode.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 'SubCellBarCode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SubCellBarCode' version '1.4.0'
* 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 'SubCellBarCode' 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 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
applyThresholdCompartment    26.10   0.27   26.36
computeThresholdCompartment  23.62   0.00   23.62
computeThresholdNeighborhood 23.50   0.02   23.52
applyThresholdNeighborhood   22.82   0.03   22.85
svmClassification            18.60   0.04   18.64
svmExternalData              18.45   0.01   18.47
candidateRelocatedProteins    6.70   0.03    6.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
applyThresholdCompartment    23.17   0.28   23.47
applyThresholdNeighborhood   22.62   0.03   22.66
computeThresholdCompartment  19.66   0.00   19.66
computeThresholdNeighborhood 18.33   0.02   18.34
svmExternalData              17.20   0.02   17.22
svmClassification            13.19   0.00   13.23
candidateRelocatedProteins   10.11   0.26   10.38
* 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

SubCellBarCode.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SubCellBarCode_1.4.0.tar.gz && rm -rf SubCellBarCode.buildbin-libdir && mkdir SubCellBarCode.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SubCellBarCode.buildbin-libdir SubCellBarCode_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SubCellBarCode_1.4.0.zip && rm SubCellBarCode_1.4.0.tar.gz SubCellBarCode_1.4.0.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  807k  100  807k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 13.5M

install for i386

* installing *source* package 'SubCellBarCode' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SubCellBarCode'
    finding HTML links ... done
    applyThresholdCompartment               html  
    applyThresholdNeighborhood              html  
    calRowMean                              html  
    calculateCoveredProtein                 html  
    candidateRelocatedProteins              html  
    compareCls                              html  
    computeThresholdCompartment             html  
    computeThresholdNeighborhood            html  
    convert2symbol                          html  
    hcc827Ctrl                              html  
    hcc827CtrlPSMCount                      html  
    hcc827GEF                               html  
    hcc827GEFClass                          html  
    hcc827GefPSMCount                       html  
    hcc827exon                              html  
    loadData                                html  
    markerProteins                          html  
    markerQualityControl                    html  
    mergeCls                                html  
    mergeProbability                        html  
    plotBarcode                             html  
    plotMultipleProtein                     html  
    replacePrediction                       html  
    sankeyPlot                              html  
    sumProbability                          html  
    svmClassification                       html  
    svmExternalData                         html  
    tsneVisualization                       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 'SubCellBarCode' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SubCellBarCode' as SubCellBarCode_1.4.0.zip
* DONE (SubCellBarCode)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SubCellBarCode' successfully unpacked and MD5 sums checked

Tests output


Example timings

SubCellBarCode.Rcheck/examples_i386/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment26.10 0.2726.36
applyThresholdNeighborhood22.82 0.0322.85
calRowMean0.020.000.02
calculateCoveredProtein0.20.00.2
candidateRelocatedProteins6.700.036.75
compareCls0.020.000.02
computeThresholdCompartment23.62 0.0023.62
computeThresholdNeighborhood23.50 0.0223.52
convert2symbol000
hcc827Ctrl000
hcc827CtrlPSMCount0.020.000.01
hcc827GEF000
hcc827GEFClass000
hcc827GefPSMCount000
hcc827exon0.020.000.02
loadData000
markerQualityControl0.540.010.56
mergeCls000
mergeProbability0.020.000.02
plotBarcode0.510.000.51
plotMultipleProtein0.350.000.35
replacePrediction000
sankeyPlot0.030.000.03
sumProbability0.010.000.01
svmClassification18.60 0.0418.64
svmExternalData18.45 0.0118.47
tsneVisualization0.220.000.22

SubCellBarCode.Rcheck/examples_x64/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment23.17 0.2823.47
applyThresholdNeighborhood22.62 0.0322.66
calRowMean0.010.000.02
calculateCoveredProtein0.130.000.12
candidateRelocatedProteins10.11 0.2610.38
compareCls0.010.000.01
computeThresholdCompartment19.66 0.0019.66
computeThresholdNeighborhood18.33 0.0218.34
convert2symbol000
hcc827Ctrl000
hcc827CtrlPSMCount000
hcc827GEF000
hcc827GEFClass000
hcc827GefPSMCount000
hcc827exon000
loadData000
markerQualityControl0.360.010.37
mergeCls0.020.000.02
mergeProbability000
plotBarcode0.450.000.45
plotMultipleProtein0.240.000.23
replacePrediction000
sankeyPlot0.030.000.03
sumProbability0.010.000.02
svmClassification13.19 0.0013.23
svmExternalData17.20 0.0217.22
tsneVisualization0.250.000.25