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This page was generated on 2022-01-21 11:08:44 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SubCellBarCode on riesling1


To the developers/maintainers of the SubCellBarCode package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SubCellBarCode.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1891/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.11.0  (landing page)
Taner Arslan
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: master
git_last_commit: b34ded0
git_last_commit_date: 2021-10-26 12:52:05 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SubCellBarCode
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SubCellBarCode.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SubCellBarCode_1.11.0.tar.gz
StartedAt: 2022-01-20 20:12:54 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:16:30 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 216.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SubCellBarCode.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SubCellBarCode_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SubCellBarCode.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.11.0'
* 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
* 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
calculateCoveredProtein: no visible binding for global variable
  'Compartments'
calculateCoveredProtein: no visible binding for global variable
  'ProteinCoverage'
candidateRelocatedProteins: no visible binding for global variable
  'Pearson.Corr'
markerQualityControl: no visible binding for global variable
  'Correlation'
markerQualityControl: no visible binding for global variable 'Pearson'
markerQualityControl: no visible binding for global variable 'Spearman'
plotBarcode: no visible binding for global variable 'Level'
plotBarcode: no visible binding for global variable 'Probability'
plotBarcode: no visible binding for global variable 'Locs'
plotMultipleProtein: no visible binding for global variable
  'Neighborhood'
plotMultipleProtein: no visible binding for global variable 'Count'
plotMultipleProtein: no visible binding for global variable
  'Compartment'
Undefined global functions or variables:
  Compartment Compartments Correlation Count Level Locs Neighborhood
  Pearson Pearson.Corr Probability ProteinCoverage Spearman
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
applyThresholdCompartment    15.21   0.19   15.39
computeThresholdNeighborhood 15.19   0.05   15.23
computeThresholdCompartment  14.66   0.03   14.69
applyThresholdNeighborhood   13.65   0.06   13.71
svmExternalData              12.49   0.07   12.54
svmClassification            10.90   0.06   10.97
candidateRelocatedProteins    5.22   1.13    6.34
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SubCellBarCode.Rcheck/00check.log'
for details.



Installation output

SubCellBarCode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SubCellBarCode
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (SubCellBarCode)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SCnorm' is missing or broken
 done

Tests output


Example timings

SubCellBarCode.Rcheck/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment15.21 0.1915.39
applyThresholdNeighborhood13.65 0.0613.71
calRowMean000
calculateCoveredProtein0.140.000.14
candidateRelocatedProteins5.221.136.34
compareCls0.010.000.02
computeThresholdCompartment14.66 0.0314.69
computeThresholdNeighborhood15.19 0.0515.23
convert2symbol000
hcc827Ctrl0.010.000.02
hcc827CtrlPSMCount000
hcc827GEF0.020.000.01
hcc827GEFClass000
hcc827GefPSMCount000
hcc827exon000
loadData000
markerQualityControl0.480.000.49
mergeCls000
mergeProbability0.000.010.01
plotBarcode0.470.000.47
plotMultipleProtein0.200.000.21
replacePrediction000
sankeyPlot0.020.000.01
sumProbability0.020.000.02
svmClassification10.90 0.0610.97
svmExternalData12.49 0.0712.54
tsneVisualization0.140.000.14