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This page was generated on 2025-06-12 11:48 -0400 (Thu, 12 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4838
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4578
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4602
kjohnson1macOS 13.6.6 Venturaarm644.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" 4556
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4576
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: 2025-06-09 13:40 -0400 (Mon, 09 Jun 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SubCellBarCode on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SubCellBarCode
Version: 1.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SubCellBarCode_1.24.0.tar.gz
StartedAt: 2025-06-10 14:50:54 -0000 (Tue, 10 Jun 2025)
EndedAt: 2025-06-10 14:56:04 -0000 (Tue, 10 Jun 2025)
EllapsedTime: 310.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SubCellBarCode_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SubCellBarCode.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 ... 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 loading without being on the library search path ... 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    21.363  0.167  22.570
applyThresholdNeighborhood   16.142  0.155  16.501
computeThresholdCompartment  15.916  0.024  17.082
computeThresholdNeighborhood 14.599  0.016  14.901
candidateRelocatedProteins   12.964  0.011  14.068
svmExternalData              12.388  0.012  12.646
svmClassification            10.648  0.012  10.715
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.


Installation output

SubCellBarCode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SubCellBarCode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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
** 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
applyThresholdCompartment21.363 0.16722.570
applyThresholdNeighborhood16.142 0.15516.501
calRowMean0.0130.0000.012
calculateCoveredProtein0.1910.0000.191
candidateRelocatedProteins12.964 0.01114.068
compareCls0.0190.0000.020
computeThresholdCompartment15.916 0.02417.082
computeThresholdNeighborhood14.599 0.01614.901
convert2symbol000
hcc827Ctrl0.0030.0000.003
hcc827CtrlPSMCount0.0070.0000.008
hcc827GEF0.0030.0000.002
hcc827GEFClass0.0010.0000.001
hcc827GefPSMCount0.0010.0000.001
hcc827exon0.0030.0000.002
loadData0.0010.0000.001
markerQualityControl0.6070.0000.666
mergeCls0.0050.0000.005
mergeProbability0.0010.0030.005
plotBarcode0.7530.0040.760
plotMultipleProtein0.4040.0000.405
replacePrediction0.0050.0000.005
sankeyPlot0.0350.0000.036
sumProbability0.0050.0000.005
svmClassification10.648 0.01210.715
svmExternalData12.388 0.01212.646
tsneVisualization0.2780.0080.287