Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:53 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the SubCellBarCode package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1969/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.15.0  (landing page)
Taner Arslan
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: master
git_last_commit: 68d1c97
git_last_commit_date: 2022-11-01 11:19:56 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: SubCellBarCode
Version: 1.15.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SubCellBarCode.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SubCellBarCode_1.15.0.tar.gz
StartedAt: 2022-12-29 04:01:23 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 04:05:09 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 226.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SubCellBarCode.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SubCellBarCode_1.15.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/SubCellBarCode.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SubCellBarCode/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SubCellBarCode' version '1.15.0'
* 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    17.55   0.34   17.89
applyThresholdNeighborhood   15.83   0.23   16.07
computeThresholdNeighborhood 15.06   0.02   15.07
computeThresholdCompartment  14.67   0.11   14.79
svmExternalData              13.25   0.03   13.28
svmClassification            11.75   0.05   11.80
candidateRelocatedProteins    5.87   0.83    6.70
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/SubCellBarCode.Rcheck/00check.log'
for details.



Installation output

SubCellBarCode.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SubCellBarCode
###
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* installing to library 'F:/biocbuild/bbs-3.17-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
** 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)

Tests output


Example timings

SubCellBarCode.Rcheck/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment17.55 0.3417.89
applyThresholdNeighborhood15.83 0.2316.07
calRowMean0.010.000.01
calculateCoveredProtein0.10.00.1
candidateRelocatedProteins5.870.836.70
compareCls0.020.000.01
computeThresholdCompartment14.67 0.1114.79
computeThresholdNeighborhood15.06 0.0215.07
convert2symbol000
hcc827Ctrl000
hcc827CtrlPSMCount000
hcc827GEF000
hcc827GEFClass000
hcc827GefPSMCount000
hcc827exon000
loadData000
markerQualityControl0.350.020.36
mergeCls0.010.000.01
mergeProbability000
plotBarcode0.550.010.57
plotMultipleProtein0.280.000.28
replacePrediction000
sankeyPlot0.030.000.03
sumProbability000
svmClassification11.75 0.0511.80
svmExternalData13.25 0.0313.28
tsneVisualization0.160.050.20