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This page was generated on 2025-09-26 12:05 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1908/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scider 1.7.0  (landing page)
Yunshun Chen
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/scider
git_branch: devel
git_last_commit: f29810f
git_last_commit_date: 2025-04-15 13:23:55 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for scider on lconway

To the developers/maintainers of the scider package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scider.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: scider
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scider.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scider_1.7.0.tar.gz
StartedAt: 2025-09-26 00:00:13 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 00:07:44 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 451.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scider.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scider.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scider_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘scider/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scider’ version ‘1.7.0’
* 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 ‘scider’ 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 ... OK
* 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 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
plotCellCompo  15.813  0.233  16.165
allocateCells  13.772  0.443  14.387
spe2PB         11.477  0.225  11.769
plotROI        11.258  0.183  11.517
plotDensCor     7.227  0.069   7.339
plotCorHeatmap  6.030  0.094   6.154
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

scider.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scider’ ...
** this is package ‘scider’ version ‘1.7.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (scider)

Tests output

scider.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(scider)
> 
> test_check("scider")
Assigning cells to ROIs defined by Breast cancer 

No contour detected.
Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer 

Assigning cells to contour levels of Breast cancer 

Linking to GEOS 3.13.0, GDAL 3.8.5, PROJ 9.5.1; sf_use_s2() is TRUE
Using bins = 10 to draw contours.
Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer, Fibroblasts 

Assigning cells to contour levels of Breast cancer 

Using bins = 10 to draw contours.
Assigning cells to ROIs defined by Breast cancer 

No contour detected.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 78 ]
> 
> proc.time()
   user  system elapsed 
129.238   2.788 133.141 

Example timings

scider.Rcheck/scider-Ex.timings

nameusersystemelapsed
allocateCells13.772 0.44314.387
corDensity4.7930.0644.872
findROI4.2430.0474.312
getContour1.1280.0771.212
gridDensity0.8790.0390.921
mergeROI4.1240.0604.195
plotCellCompo15.813 0.23316.165
plotContour2.4810.0692.563
plotCorHeatmap6.0300.0946.154
plotDensCor7.2270.0697.339
plotDensity1.7440.0501.809
plotROI11.258 0.18311.517
plotSpatial0.6530.0150.676
postSelRegion1.0820.0351.125
selectRegion0.1740.0050.180
spe2PB11.477 0.22511.769
xenium_bc_spe0.1090.0030.113