Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-26 12:07 -0400 (Fri, 26 Sep 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" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: spatialDE |
Version: 1.15.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spatialDE_1.15.1.tar.gz |
StartedAt: 2025-09-26 12:29:44 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 12:37:04 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 439.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialDE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spatialDE_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 ‘/home/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 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 ... 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 43.776 0.006 28.690 multiGenePlots 11.692 0.095 11.971 FSV_sig 8.215 0.249 14.669 modelSearch 5.152 0.016 3.971 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00check.log’ for details.
spatialDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL spatialDE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > 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 17%|█▋ | 17/100 [00:00<00:00, 161.90it/s][A 34%|███▍ | 34/100 [00:00<00:00, 155.43it/s][A 51%|█████ | 51/100 [00:00<00:00, 159.47it/s][A 68%|██████▊ | 68/100 [00:00<00:00, 161.79it/s][A 85%|████████▌ | 85/100 [00:00<00:00, 155.53it/s][A [A Models: 10%|█ | 1/10 [00:00<00:05, 1.55it/s] 0%| | 0/100 [00:00<?, ?it/s][A 12%|█▏ | 12/100 [00:00<00:00, 110.26it/s][A 25%|██▌ | 25/100 [00:00<00:00, 109.36it/s][A 36%|███▌ | 36/100 [00:00<00:00, 106.40it/s][A 47%|████▋ | 47/100 [00:00<00:00, 104.39it/s][A 60%|██████ | 60/100 [00:00<00:00, 110.64it/s][A 72%|███████▏ | 72/100 [00:00<00:00, 110.13it/s][A 84%|████████▍ | 84/100 [00:00<00:00, 111.19it/s][A [A Models: 20%|██ | 2/10 [00:01<00:06, 1.30it/s] 0%| | 0/100 [00:00<?, ?it/s][A 24%|██▍ | 24/100 [00:00<00:00, 229.68it/s][A 47%|████▋ | 47/100 [00:00<00:00, 224.07it/s][A 70%|███████ | 70/100 [00:00<00:00, 223.95it/s][A 93%|█████████▎| 93/100 [00:00<00:00, 225.19it/s][A [A Models: 30%|███ | 3/10 [00:01<00:04, 1.61it/s] 0%| | 0/100 [00:00<?, ?it/s][A 20%|██ | 20/100 [00:00<00:00, 192.39it/s][A 40%|████ | 40/100 [00:00<00:00, 129.28it/s][A 62%|██████▏ | 62/100 [00:00<00:00, 159.03it/s][A 83%|████████▎ | 83/100 [00:00<00:00, 175.75it/s][A [A Models: 40%|████ | 4/10 [00:02<00:03, 1.66it/s] 0%| | 0/100 [00:00<?, ?it/s][A 22%|██▏ | 22/100 [00:00<00:00, 218.26it/s][A 44%|████▍ | 44/100 [00:00<00:00, 217.21it/s][A 66%|██████▌ | 66/100 [00:00<00:00, 213.66it/s][A 88%|████████▊ | 88/100 [00:00<00:00, 212.06it/s][A [A Models: 50%|█████ | 5/10 [00:02<00:02, 1.79it/s] 0%| | 0/100 [00:00<?, ?it/s][A 21%|██ | 21/100 [00:00<00:00, 204.96it/s][A 43%|████▎ | 43/100 [00:00<00:00, 209.59it/s][A 65%|██████▌ | 65/100 [00:00<00:00, 211.47it/s][A 87%|████████▋ | 87/100 [00:00<00:00, 208.66it/s][A [A Models: 60%|██████ | 6/10 [00:03<00:02, 1.88it/s] 0%| | 0/100 [00:00<?, ?it/s][A 19%|█▉ | 19/100 [00:00<00:00, 180.88it/s][A 38%|███▊ | 38/100 [00:00<00:00, 114.13it/s][A 57%|█████▋ | 57/100 [00:00<00:00, 137.64it/s][A 77%|███████▋ | 77/100 [00:00<00:00, 157.36it/s][A 98%|█████████▊| 98/100 [00:00<00:00, 172.28it/s][A [A Models: 70%|███████ | 7/10 [00:04<00:01, 1.77it/s] 0%| | 0/100 [00:00<?, ?it/s][A 21%|██ | 21/100 [00:00<00:00, 205.77it/s][A 42%|████▏ | 42/100 [00:00<00:00, 208.14it/s][A 64%|██████▍ | 64/100 [00:00<00:00, 210.19it/s][A 86%|████████▌ | 86/100 [00:00<00:00, 209.06it/s][A [A Models: 80%|████████ | 8/10 [00:04<00:01, 1.85it/s] 0%| | 0/100 [00:00<?, ?it/s][A 23%|██▎ | 23/100 [00:00<00:00, 228.63it/s][A 46%|████▌ | 46/100 [00:00<00:00, 222.09it/s][A 69%|██████▉ | 69/100 [00:00<00:00, 185.50it/s][A 90%|█████████ | 90/100 [00:00<00:00, 189.60it/s][A [A Models: 90%|█████████ | 9/10 [00:05<00:00, 1.89it/s] 0%| | 0/100 [00:00<?, ?it/s][A 26%|██▌ | 26/100 [00:00<00:00, 253.09it/s][A 52%|█████▏ | 52/100 [00:00<00:00, 240.32it/s][A 77%|███████▋ | 77/100 [00:00<00:00, 235.26it/s][A [A Models: 100%|██████████| 10/10 [00:05<00:00, 2.01it/s] Models: 100%|██████████| 10/10 [00:05<00:00, 1.81it/s] Warning! 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spatialDE.Rcheck/spatialDE-Ex.timings
name | user | system | elapsed | |
FSV_sig | 8.215 | 0.249 | 14.669 | |
mockSVG | 0.202 | 0.000 | 0.202 | |
modelSearch | 5.152 | 0.016 | 3.971 | |
model_search | 4.073 | 0.062 | 3.043 | |
multiGenePlots | 11.692 | 0.095 | 11.971 | |
regress_out | 0.130 | 0.004 | 0.133 | |
run | 1.809 | 0.019 | 1.628 | |
spatialDE | 1.738 | 0.010 | 1.284 | |
spatialPatterns | 3.965 | 0.000 | 3.464 | |
spatial_patterns | 43.776 | 0.006 | 28.690 | |
stabilize | 0.114 | 0.000 | 0.151 | |