Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 2000/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialDE 1.13.0 (landing page) Gabriele Sales
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.13.0 |
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_1.13.0.tar.gz |
StartedAt: 2024-12-22 21:33:34 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:35:16 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 102.2 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/spatialDE.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spatialDE/DESCRIPTION’ ... OK * this is package ‘spatialDE’ version ‘1.13.0’ * 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 ‘spatialDE’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/Users/biocbuild/bbs-3.21-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 6.949 1.733 8.062 * 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘spatialDE’ ... ** 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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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: GenomeInfoDb 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 [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 20%|██ | 2/10 [00:00<00:00, 12.24it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A 98%|█████████▊| 98/100 [00:00<00:00, 971.67it/s][A [A Models: 40%|████ | 4/10 [00:00<00:00, 10.67it/s] 0%| | 0/100 [00:00<?, ?it/s][A 97%|█████████▋| 97/100 [00:00<00:00, 962.91it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A 98%|█████████▊| 98/100 [00:00<00:00, 974.60it/s][A [A Models: 60%|██████ | 6/10 [00:00<00:00, 10.12it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 80%|████████ | 8/10 [00:00<00:00, 10.11it/s] 0%| | 0/100 [00:00<?, ?it/s][A 85%|████████▌ | 85/100 [00:00<00:00, 846.29it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 100%|██████████| 10/10 [00:00<00:00, 9.95it/s] Models: 100%|██████████| 10/10 [00:00<00:00, 10.18it/s] Models: 0%| | 0/10 [00:00<?, ?it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 20%|██ | 2/10 [00:00<00:00, 12.44it/s] 0%| | 0/100 [00:00<?, ?it/s][A 93%|█████████▎| 93/100 [00:00<00:00, 926.33it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 40%|████ | 4/10 [00:00<00:00, 10.55it/s] 0%| | 0/100 [00:00<?, ?it/s][A 99%|█████████▉| 99/100 [00:00<00:00, 983.17it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 60%|██████ | 6/10 [00:00<00:00, 10.22it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 80%|████████ | 8/10 [00:00<00:00, 10.20it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 100%|██████████| 10/10 [00:00<00:00, 10.37it/s] Models: 100%|██████████| 10/10 [00:00<00:00, 10.45it/s] /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.0/spatialDE/1.13.0/env/lib/python3.10/site-packages/pandas/core/internals/blocks.py:351: RuntimeWarning: invalid value encountered in log result = func(self.values, **kwargs) Models: 0%| | 0/10 [00:00<?, ?it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 20%|██ | 2/10 [00:00<00:00, 12.71it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A 96%|█████████▌| 96/100 [00:00<00:00, 908.99it/s][A [A Models: 40%|████ | 4/10 [00:00<00:00, 10.66it/s] 0%| | 0/100 [00:00<?, ?it/s][A 95%|█████████▌| 95/100 [00:00<00:00, 948.97it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A 100%|██████████| 100/100 [00:00<00:00, 989.79it/s][A [A Models: 60%|██████ | 6/10 [00:00<00:00, 10.14it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 80%|████████ | 8/10 [00:00<00:00, 10.21it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 100%|██████████| 10/10 [00:00<00:00, 10.48it/s] Models: 100%|██████████| 10/10 [00:00<00:00, 10.52it/s] Models: 0%| | 0/10 [00:00<?, ?it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 20%|██ | 2/10 [00:00<00:00, 13.02it/s] 0%| | 0/100 [00:00<?, ?it/s][A 100%|██████████| 100/100 [00:00<00:00, 927.51it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 40%|████ | 4/10 [00:00<00:00, 10.75it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 60%|██████ | 6/10 [00:00<00:00, 10.40it/s] 0%| | 0/100 [00:00<?, ?it/s][A 97%|█████████▋| 97/100 [00:00<00:00, 963.91it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 80%|████████ | 8/10 [00:00<00:00, 10.21it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 100%|██████████| 10/10 [00:00<00:00, 10.26it/s] Models: 100%|██████████| 10/10 [00:00<00:00, 10.45it/s] Models: 0%| | 0/10 [00:00<?, ?it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 20%|██ | 2/10 [00:00<00:00, 12.97it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 40%|████ | 4/10 [00:00<00:00, 11.36it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 60%|██████ | 6/10 [00:00<00:00, 10.71it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 80%|████████ | 8/10 [00:00<00:00, 10.55it/s] 0%| | 0/100 [00:00<?, ?it/s][A [A 0%| | 0/100 [00:00<?, ?it/s][A [A Models: 100%|██████████| 10/10 [00:00<00:00, 10.72it/s] Models: 100%|██████████| 10/10 [00:00<00:00, 10.87it/s] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 15.460 0.813 16.512
spatialDE.Rcheck/spatialDE-Ex.timings
name | user | system | elapsed | |
FSV_sig | 2.042 | 0.668 | 4.489 | |
mockSVG | 0.064 | 0.025 | 0.088 | |
modelSearch | 0.609 | 0.173 | 0.727 | |
model_search | 0.542 | 0.163 | 0.670 | |
multiGenePlots | 0.570 | 0.108 | 0.675 | |
regress_out | 0.039 | 0.002 | 0.041 | |
run | 0.255 | 0.055 | 0.275 | |
spatialDE | 0.311 | 0.087 | 0.366 | |
spatialPatterns | 0.334 | 0.147 | 0.528 | |
spatial_patterns | 6.949 | 1.733 | 8.062 | |
stabilize | 0.020 | 0.001 | 0.020 | |