| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-29 12:05 -0400 (Wed, 29 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1930/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scider 1.7.3 (landing page) Yunshun Chen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
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. |
| Package: scider |
| Version: 1.7.3 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scider_1.7.3.tar.gz |
| StartedAt: 2025-10-29 03:38:48 -0400 (Wed, 29 Oct 2025) |
| EndedAt: 2025-10-29 03:45:01 -0400 (Wed, 29 Oct 2025) |
| EllapsedTime: 373.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scider.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scider_1.7.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... 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 43.691 0.239 25.594
runUMAP 29.049 0.366 24.661
getClusters 15.979 0.456 14.890
findNbrsSNN 10.724 0.283 9.468
runPCA 6.451 0.123 6.575
localMoran 5.784 0.012 1.593
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/scider.Rcheck/00check.log’
for details.
scider.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scider ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scider’ ... ** this is package ‘scider’ version ‘1.7.3’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c C_findSNN.cpp -o C_findSNN.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c C_globalMoran.cpp -o C_globalMoran.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c C_localMoran.cpp -o C_localMoran.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scider.so C_findSNN.o C_globalMoran.o C_localMoran.o utils.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-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)
scider.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 3.12.1, GDAL 3.8.4, PROJ 9.4.0; 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
32.393 1.136 33.593
scider.Rcheck/scider-Ex.timings
| name | user | system | elapsed | |
| allocateCells | 3.407 | 0.077 | 3.489 | |
| corDensity | 1.309 | 0.058 | 1.368 | |
| findNbrsGrid | 1.534 | 0.046 | 1.580 | |
| findNbrsSNN | 10.724 | 0.283 | 9.468 | |
| findNbrsSpatial | 0.269 | 0.005 | 0.206 | |
| findROI | 0.810 | 0.012 | 0.821 | |
| getClusters | 15.979 | 0.456 | 14.890 | |
| getContour | 0.886 | 0.003 | 0.890 | |
| getNiche | 0.420 | 0.000 | 0.339 | |
| globalMoran | 1.482 | 0.002 | 0.858 | |
| gridDensity | 0.769 | 0.001 | 0.770 | |
| gridSPE | 3.070 | 0.171 | 3.242 | |
| localMoran | 5.784 | 0.012 | 1.593 | |
| mergeROI | 0.791 | 0.006 | 0.797 | |
| normalizeAssay | 0.920 | 0.031 | 0.951 | |
| plotCellCompo | 2.681 | 0.031 | 2.713 | |
| plotContour | 1.408 | 0.002 | 1.411 | |
| plotCorHeatmap | 1.468 | 0.004 | 1.472 | |
| plotDR | 43.691 | 0.239 | 25.594 | |
| plotDensCor | 3.812 | 0.049 | 3.862 | |
| plotDensity | 1.612 | 0.031 | 1.642 | |
| plotGrid | 1.259 | 0.010 | 1.269 | |
| plotLISA | 2.588 | 0.026 | 1.454 | |
| plotROI | 1.497 | 0.031 | 1.529 | |
| plotSpatial | 0.675 | 0.011 | 0.687 | |
| postSelRegion | 0.765 | 0.006 | 0.771 | |
| runPCA | 6.451 | 0.123 | 6.575 | |
| runUMAP | 29.049 | 0.366 | 24.661 | |
| selectRegion | 0.140 | 0.004 | 0.144 | |
| spe2PB | 1.509 | 0.045 | 1.558 | |
| xenium_bc_spe | 0.112 | 0.010 | 0.122 | |