Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:05 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 2053/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialDE 1.15.1 (landing page) Gabriele Sales
| 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 spatialDE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.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: spatialDE |
Version: 1.15.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialDE_1.15.1.tar.gz |
StartedAt: 2025-09-23 00:15:35 -0400 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 00:20:34 -0400 (Tue, 23 Sep 2025) |
EllapsedTime: 299.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialDE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialDE_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialDE.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 ‘spatialDE/DESCRIPTION’ ... OK * this is package ‘spatialDE’ version ‘1.15.1’ * 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 ‘spatialDE’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00install.out’ for details. * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: mockSVG.Rd: SpatialExperiment-class modelSearch.Rd: SpatialExperiment-class multiGenePlots.Rd: SpatialExperiment-class spatialDE.Rd: SpatialExperiment-class spatialPatterns.Rd: SpatialExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed spatial_patterns 20.207 3.963 13.360 FSV_sig 5.226 1.683 6.765 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00check.log’ for details.
spatialDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialDE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘spatialDE’ ... ** this is package ‘spatialDE’ version ‘1.15.1’ ** using non-staged installation via StagedInstall field ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (spatialDE)
spatialDE.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. > library(testthat) > library(spatialDE) > > test_check("spatialDE") Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Models: 0%| | 0/10 [00:00<?, ?it/s] 0%| | 0/100 [00:00<?, ?it/s][A 32%|███▏ | 32/100 [00:00<00:00, 316.63it/s][A 68%|██████▊ | 68/100 [00:00<00:00, 335.76it/s][A [A Models: 10%|█ | 1/10 [00:00<00:02, 3.32it/s] 0%| | 0/100 [00:00<?, ?it/s][A 28%|██▊ | 28/100 [00:00<00:00, 272.63it/s][A 56%|█████▌ | 56/100 [00:00<00:00, 273.25it/s][A 84%|████████▍ | 84/100 [00:00<00:00, 263.53it/s][A [A Models: 20%|██ | 2/10 [00:00<00:02, 2.87it/s] 0%| | 0/100 [00:00<?, ?it/s][A 21%|██ | 21/100 [00:00<00:00, 201.68it/s][A 44%|████▍ | 44/100 [00:00<00:00, 217.53it/s][A 68%|██████▊ | 68/100 [00:00<00:00, 223.95it/s][A 91%|█████████ | 91/100 [00:00<00:00, 219.40it/s][A [A Models: 30%|███ | 3/10 [00:01<00:02, 2.50it/s] 0%| | 0/100 [00:00<?, ?it/s][A 22%|██▏ | 22/100 [00:00<00:00, 218.19it/s][A 45%|████▌ | 45/100 [00:00<00:00, 224.46it/s][A 68%|██████▊ | 68/100 [00:00<00:00, 226.39it/s][A 92%|█████████▏| 92/100 [00:00<00:00, 229.51it/s][A [A Models: 40%|████ | 4/10 [00:01<00:02, 2.39it/s] 0%| | 0/100 [00:00<?, ?it/s][A 23%|██▎ | 23/100 [00:00<00:00, 218.60it/s][A 45%|████▌ | 45/100 [00:00<00:00, 212.95it/s][A 68%|██████▊ | 68/100 [00:00<00:00, 219.46it/s][A 93%|█████████▎| 93/100 [00:00<00:00, 230.13it/s][A [A Models: 50%|█████ | 5/10 [00:02<00:02, 2.33it/s] 0%| | 0/100 [00:00<?, ?it/s][A 21%|██ | 21/100 [00:00<00:00, 203.13it/s][A 42%|████▏ | 42/100 [00:00<00:00, 203.96it/s][A 65%|██████▌ | 65/100 [00:00<00:00, 210.95it/s][A 91%|█████████ | 91/100 [00:00<00:00, 226.15it/s][A [A Models: 60%|██████ | 6/10 [00:02<00:01, 2.27it/s] 0%| | 0/100 [00:00<?, ?it/s][A 23%|██▎ | 23/100 [00:00<00:00, 220.32it/s][A 47%|████▋ | 47/100 [00:00<00:00, 228.88it/s][A 70%|███████ | 70/100 [00:00<00:00, 226.66it/s][A 93%|█████████▎| 93/100 [00:00<00:00, 226.75it/s][A [A Models: 70%|███████ | 7/10 [00:02<00:01, 2.26it/s] 0%| | 0/100 [00:00<?, ?it/s][A 23%|██▎ | 23/100 [00:00<00:00, 223.45it/s][A 46%|████▌ | 46/100 [00:00<00:00, 226.13it/s][A 69%|██████▉ | 69/100 [00:00<00:00, 227.62it/s][A 92%|█████████▏| 92/100 [00:00<00:00, 227.65it/s][A [A Models: 80%|████████ | 8/10 [00:03<00:00, 2.27it/s] 0%| | 0/100 [00:00<?, ?it/s][A 27%|██▋ | 27/100 [00:00<00:00, 268.21it/s][A 54%|█████▍ | 54/100 [00:00<00:00, 253.39it/s][A 80%|████████ | 80/100 [00:00<00:00, 238.29it/s][A [A Models: 90%|█████████ | 9/10 [00:03<00:00, 2.21it/s] 0%| | 0/100 [00:00<?, ?it/s][A 27%|██▋ | 27/100 [00:00<00:00, 269.27it/s][A 56%|█████▌ | 56/100 [00:00<00:00, 280.27it/s][A 85%|████████▌ | 85/100 [00:00<00:00, 261.46it/s][A [A Models: 100%|██████████| 10/10 [00:04<00:00, 2.33it/s] Models: 100%|██████████| 10/10 [00:04<00:00, 2.36it/s] Warning! 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[00:00<00:00, 226.59it/s][A 100%|██████████| 100/100 [00:00<00:00, 231.48it/s][A [A Models: 80%|████████ | 8/10 [00:03<00:00, 2.45it/s] 0%| | 0/100 [00:00<?, ?it/s][A 26%|██▌ | 26/100 [00:00<00:00, 256.91it/s][A 52%|█████▏ | 52/100 [00:00<00:00, 249.42it/s][A 78%|███████▊ | 78/100 [00:00<00:00, 250.29it/s][A [A Models: 90%|█████████ | 9/10 [00:03<00:00, 2.43it/s] 0%| | 0/100 [00:00<?, ?it/s][A 26%|██▌ | 26/100 [00:00<00:00, 256.14it/s][A 52%|█████▏ | 52/100 [00:00<00:00, 249.28it/s][A 79%|███████▉ | 79/100 [00:00<00:00, 255.30it/s][A [A Models: 100%|██████████| 10/10 [00:03<00:00, 2.48it/s] Models: 100%|██████████| 10/10 [00:03<00:00, 2.57it/s] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 66.336 5.400 60.689 /Users/biocbuild/.pyenv/versions/3.11.13/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '
spatialDE.Rcheck/spatialDE-Ex.timings
name | user | system | elapsed | |
FSV_sig | 5.226 | 1.683 | 6.765 | |
mockSVG | 0.985 | 0.135 | 1.131 | |
modelSearch | 2.006 | 0.437 | 1.505 | |
model_search | 1.747 | 0.432 | 1.261 | |
multiGenePlots | 2.351 | 0.271 | 2.106 | |
regress_out | 0.119 | 0.004 | 0.125 | |
run | 0.947 | 0.189 | 0.722 | |
spatialDE | 1.048 | 0.233 | 0.805 | |
spatialPatterns | 1.576 | 0.380 | 1.164 | |
spatial_patterns | 20.207 | 3.963 | 13.360 | |
stabilize | 0.081 | 0.020 | 0.055 | |