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This page was generated on 2025-09-15 11:39 -0400 (Mon, 15 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
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

Package 2124/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.24.0  (landing page)
Taner Arslan
Snapshot Date: 2025-09-11 13:40 -0400 (Thu, 11 Sep 2025)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: RELEASE_3_21
git_last_commit: fd4fea3
git_last_commit_date: 2025-04-15 11:46:29 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for SubCellBarCode on merida1

To the developers/maintainers of the SubCellBarCode package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SubCellBarCode
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SubCellBarCode_1.24.0.tar.gz
StartedAt: 2025-09-12 11:14:22 -0400 (Fri, 12 Sep 2025)
EndedAt: 2025-09-12 11:22:17 -0400 (Fri, 12 Sep 2025)
EllapsedTime: 475.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SubCellBarCode.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SubCellBarCode_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SubCellBarCode.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SubCellBarCode’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/SubCellBarCode.Rcheck/00install.out’ for details.
* 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 code 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    29.172  0.357  31.673
computeThresholdCompartment  23.401  0.271  25.542
applyThresholdNeighborhood   20.806  0.238  22.489
computeThresholdNeighborhood 18.069  0.153  19.422
candidateRelocatedProteins   16.163  0.239  17.625
svmExternalData              15.973  0.111  16.838
svmClassification            14.708  0.099  15.650
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.


Installation output

SubCellBarCode.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SubCellBarCode
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SubCellBarCode’ ...
** this is package ‘SubCellBarCode’ version ‘1.24.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SubCellBarCode’
** testing if installed package keeps a record of temporary installation path
* DONE (SubCellBarCode)

Tests output


Example timings

SubCellBarCode.Rcheck/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment29.172 0.35731.673
applyThresholdNeighborhood20.806 0.23822.489
calRowMean0.0090.0010.011
calculateCoveredProtein0.5420.0090.570
candidateRelocatedProteins16.163 0.23917.625
compareCls0.0350.0030.047
computeThresholdCompartment23.401 0.27125.542
computeThresholdNeighborhood18.069 0.15319.422
convert2symbol0.0010.0010.002
hcc827Ctrl0.0060.0020.008
hcc827CtrlPSMCount0.0100.0010.011
hcc827GEF0.0050.0010.007
hcc827GEFClass0.0030.0010.003
hcc827GefPSMCount0.0020.0000.003
hcc827exon0.0060.0020.008
loadData0.0020.0000.002
markerQualityControl1.7910.0211.895
mergeCls0.0120.0010.014
mergeProbability0.0100.0010.013
plotBarcode1.7290.0081.814
plotMultipleProtein1.1740.0051.229
replacePrediction0.0090.0000.010
sankeyPlot0.0530.0030.056
sumProbability0.0100.0010.010
svmClassification14.708 0.09915.650
svmExternalData15.973 0.11116.838
tsneVisualization0.6130.0060.640