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This page was generated on 2025-07-22 12:12 -0400 (Tue, 22 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4791
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4527
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4572
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4513
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4510
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 2099/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.25.0  (landing page)
Taner Arslan
Snapshot Date: 2025-07-21 13:25 -0400 (Mon, 21 Jul 2025)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: devel
git_last_commit: 4ef7e8f
git_last_commit_date: 2025-04-15 11:46:29 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SubCellBarCode on kjohnson3

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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2025-07-21 21:47:59 -0400 (Mon, 21 Jul 2025)
EndedAt: 2025-07-21 21:49:23 -0400 (Mon, 21 Jul 2025)
EllapsedTime: 84.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

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_1.25.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SubCellBarCode.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.25.0’
* 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 ... 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 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 4.833  0.103   5.012
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.


Installation output

SubCellBarCode.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SubCellBarCode’ ...
** this is package ‘SubCellBarCode’ version ‘1.25.0’
** 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
applyThresholdCompartment4.8330.1035.012
applyThresholdNeighborhood4.0260.1094.233
calRowMean0.0010.0010.002
calculateCoveredProtein0.0460.0000.047
candidateRelocatedProteins2.1340.3002.501
compareCls0.0060.0000.007
computeThresholdCompartment3.9230.0974.122
computeThresholdNeighborhood3.3640.1183.643
convert2symbol000
hcc827Ctrl0.0010.0010.001
hcc827CtrlPSMCount0.0030.0000.003
hcc827GEF0.0000.0000.001
hcc827GEFClass000
hcc827GefPSMCount0.0000.0010.000
hcc827exon0.0010.0000.001
loadData0.0000.0000.001
markerQualityControl0.1290.0040.133
mergeCls0.0020.0000.002
mergeProbability0.0010.0000.002
plotBarcode0.1780.0120.191
plotMultipleProtein0.0800.0020.081
replacePrediction0.0010.0000.001
sankeyPlot0.0080.0020.011
sumProbability0.0010.0000.002
svmClassification2.6350.0892.793
svmExternalData3.1470.1293.302
tsneVisualization0.0680.0030.071