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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1922/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scider 1.7.3  (landing page)
Yunshun Chen
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/scider
git_branch: devel
git_last_commit: d9229d0
git_last_commit_date: 2025-10-14 14:58:38 -0400 (Tue, 14 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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: 1.7.3
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_1.7.3.tar.gz
StartedAt: 2025-10-18 01:18:36 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 01:25:26 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 409.3 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_1.7.3.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 ‘1.7.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotDR        40.013  1.039  28.959
runUMAP       31.209  0.476  27.930
getClusters   15.382  0.367  14.189
findNbrsSNN   10.826  0.171   9.443
runPCA         6.812  0.140   7.000
allocateCells  4.549  0.292   5.042
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck/00check.log’
for details.


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 ‘1.7.3’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c C_findSNN.cpp -o C_findSNN.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c C_globalMoran.cpp -o C_globalMoran.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c C_localMoran.cpp -o C_localMoran.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scider.so C_findSNN.o C_globalMoran.o C_localMoran.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-scider/00new/scider/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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. Proceed without contour.
Using bins = 10 to draw contours with equal cell numbers.
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 with equal cell numbers.
cell_typess is not a column of the colData. Skipping cell_typess
Using bins = 10 to draw contours with equal cell numbers.
Assigning cells to ROIs defined by Breast cancer fibroblasts 

Assigning cells to contour levels of Breast cancer 

Using bins = 10 to draw contours with equal cell numbers.
Assigning cells to ROIs defined by Breast cancer 

No contour detected. Proceed without contour.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 71 ]
> 
> proc.time()
   user  system elapsed 
 37.375   2.280  40.123 

Example timings

scider.Rcheck/scider-Ex.timings

nameusersystemelapsed
allocateCells4.5490.2925.042
corDensity1.3560.1071.479
findNbrsGrid1.0540.1141.176
findNbrsSNN10.826 0.171 9.443
findNbrsSpatial0.2970.0040.218
findROI0.8460.0630.916
getClusters15.382 0.36714.189
getContour0.8860.0620.954
getNiche0.4620.0400.412
globalMoran1.4490.0960.888
gridDensity0.7710.1561.026
gridSPE2.7900.3363.159
localMoran3.9630.0681.343
mergeROI0.8050.0410.852
normalizeAssay1.0300.1541.199
plotCellCompo2.9190.1293.063
plotContour1.4800.0551.558
plotCorHeatmap1.3690.1001.477
plotDR40.013 1.03928.959
plotDensCor4.5250.1204.674
plotDensity1.8050.1301.988
plotGrid1.4200.1511.671
plotLISA2.2790.0951.574
plotROI1.6130.0881.734
plotSpatial0.7530.0450.813
postSelRegion0.8780.0850.976
runPCA6.8120.1407.000
runUMAP31.209 0.47627.930
selectRegion0.1350.0120.148
spe2PB1.6340.0611.706
xenium_bc_spe0.1020.0110.113