Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-09 12:04 -0400 (Thu, 09 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 1913/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scider 1.7.2 (landing page) Yunshun Chen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.7.2 |
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_1.7.2.tar.gz |
StartedAt: 2025-10-09 04:28:09 -0400 (Thu, 09 Oct 2025) |
EndedAt: 2025-10-09 04:34:40 -0400 (Thu, 09 Oct 2025) |
EllapsedTime: 391.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scider.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.7.2.tar.gz ### ############################################################################## ############################################################################## * 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 ‘1.7.2’ * 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 44.201 0.267 25.948 runUMAP 29.595 0.433 25.119 getClusters 15.207 0.611 14.294 findNbrsSNN 11.089 0.495 10.077 runPCA 6.635 0.125 6.761 localMoran 5.724 0.032 1.618 * 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 ‘1.7.2’ ** 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 34.769 1.184 35.949
scider.Rcheck/scider-Ex.timings
name | user | system | elapsed | |
allocateCells | 4.186 | 0.111 | 4.315 | |
corDensity | 1.377 | 0.140 | 1.517 | |
findNbrsGrid | 1.789 | 0.190 | 1.986 | |
findNbrsSNN | 11.089 | 0.495 | 10.077 | |
findNbrsSpatial | 0.271 | 0.017 | 0.219 | |
findROI | 0.851 | 0.033 | 0.884 | |
getClusters | 15.207 | 0.611 | 14.294 | |
getContour | 0.931 | 0.010 | 0.941 | |
getNiche | 0.438 | 0.008 | 0.361 | |
globalMoran | 1.500 | 0.007 | 0.877 | |
gridDensity | 0.759 | 0.002 | 0.761 | |
gridSPE | 3.601 | 0.266 | 3.867 | |
localMoran | 5.724 | 0.032 | 1.618 | |
mergeROI | 0.806 | 0.008 | 0.815 | |
normalizeAssay | 1.024 | 0.034 | 1.057 | |
plotCellCompo | 2.729 | 0.034 | 2.764 | |
plotContour | 1.458 | 0.027 | 1.485 | |
plotCorHeatmap | 1.453 | 0.010 | 1.463 | |
plotDR | 44.201 | 0.267 | 25.948 | |
plotDensCor | 3.999 | 0.035 | 4.033 | |
plotDensity | 2.313 | 0.030 | 2.343 | |
plotGrid | 1.284 | 0.056 | 1.341 | |
plotLISA | 2.571 | 0.048 | 1.467 | |
plotROI | 1.543 | 0.025 | 1.568 | |
plotSpatial | 0.660 | 0.016 | 0.677 | |
postSelRegion | 0.780 | 0.007 | 0.786 | |
runPCA | 6.635 | 0.125 | 6.761 | |
runUMAP | 29.595 | 0.433 | 25.119 | |
selectRegion | 0.157 | 0.010 | 0.167 | |
spe2PB | 1.612 | 0.070 | 1.682 | |
xenium_bc_spe | 0.116 | 0.007 | 0.123 | |