Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:14 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 1897/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scider 1.2.0 (landing page) Yunshun Chen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.2.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scider_1.2.0.tar.gz |
StartedAt: 2024-05-31 07:56:02 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 08:03:00 -0400 (Fri, 31 May 2024) |
EllapsedTime: 418.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scider.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scider.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scider_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scider.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scider/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scider’ version ‘1.2.0’ * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCellCompo 12.990 0.140 13.131 allocateCells 10.975 0.444 11.429 spe2PB 9.305 0.064 9.369 plotROI 8.915 0.108 9.024 plotDensCor 5.558 0.040 5.598 plotCorHeatmap 5.307 0.072 5.379 * 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: OK
scider.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scider ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘scider’ ... ** 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)
scider.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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. 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 3.10.2, GDAL 3.4.1, PROJ 8.2.1; 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 104.896 1.839 106.729
scider.Rcheck/scider-Ex.timings
name | user | system | elapsed | |
allocateCells | 10.975 | 0.444 | 11.429 | |
corDensity | 4.596 | 0.080 | 4.676 | |
findROI | 4.015 | 0.064 | 4.078 | |
getContour | 1.032 | 0.004 | 1.035 | |
gridDensity | 0.943 | 0.016 | 0.959 | |
mergeROI | 4.597 | 0.144 | 4.741 | |
plotCellCompo | 12.990 | 0.140 | 13.131 | |
plotContour | 1.445 | 0.028 | 1.473 | |
plotCorHeatmap | 5.307 | 0.072 | 5.379 | |
plotDensCor | 5.558 | 0.040 | 5.598 | |
plotDensity | 1.292 | 0.004 | 1.296 | |
plotROI | 8.915 | 0.108 | 9.024 | |
plotSpatial | 0.469 | 0.016 | 0.486 | |
postSelRegion | 1.611 | 0.052 | 1.664 | |
selectRegion | 0.157 | 0.008 | 0.166 | |
spe2PB | 9.305 | 0.064 | 9.369 | |
xenium_bc_spe | 0.120 | 0.004 | 0.124 | |