Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:59 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1990/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialDE 1.9.1 (landing page) Gabriele Sales
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | 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: 1.9.1 |
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_1.9.1.tar.gz |
StartedAt: 2024-03-02 10:59:51 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 11:14:52 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 900.5 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_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/spatialDE.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spatialDE/DESCRIPTION’ ... OK * this is package ‘spatialDE’ version ‘1.9.1’ * 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-3.19-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 R 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 ... 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 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 37.870 6.408 206.355 FSV_sig 12.601 3.191 31.553 modelSearch 4.012 0.532 12.831 multiGenePlots 3.798 0.325 9.407 model_search 3.197 0.468 12.450 spatialPatterns 3.073 0.400 17.023 spatialDE 2.075 0.225 6.837 run 1.727 0.232 5.348 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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")'. 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18/100 [00:00<00:01, 79.09it/s][A 26%|██▌ | 26/100 [00:00<00:00, 78.13it/s][A 35%|███▌ | 35/100 [00:00<00:00, 77.71it/s][A 44%|████▍ | 44/100 [00:00<00:00, 79.46it/s][A 52%|█████▏ | 52/100 [00:00<00:00, 78.66it/s][A 60%|██████ | 60/100 [00:00<00:00, 78.49it/s][A 69%|██████▉ | 69/100 [00:00<00:00, 79.48it/s][A 77%|███████▋ | 77/100 [00:00<00:00, 76.04it/s][A 85%|████████▌ | 85/100 [00:01<00:00, 76.38it/s][A 94%|█████████▍| 94/100 [00:01<00:00, 78.96it/s][A [A Models: 100%|██████████| 10/10 [00:13<00:00, 1.37s/it] Models: 100%|██████████| 10/10 [00:13<00:00, 1.36s/it] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 158.028 5.525 204.981 /private/var/cache/basilisk/1.15.5/spatialDE/1.9.1/env/lib/python3.9/multiprocessing/resource_tracker.py:216: 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 | 12.601 | 3.191 | 31.553 | |
mockSVG | 0.697 | 0.102 | 0.916 | |
modelSearch | 4.012 | 0.532 | 12.831 | |
model_search | 3.197 | 0.468 | 12.450 | |
multiGenePlots | 3.798 | 0.325 | 9.407 | |
regress_out | 0.341 | 0.015 | 0.406 | |
run | 1.727 | 0.232 | 5.348 | |
spatialDE | 2.075 | 0.225 | 6.837 | |
spatialPatterns | 3.073 | 0.400 | 17.023 | |
spatial_patterns | 37.870 | 6.408 | 206.355 | |
stabilize | 0.163 | 0.005 | 0.168 | |