Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1937/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SimBu 1.7.0 (landing page) Alexander Dietrich
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SimBu package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SimBu.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: SimBu |
Version: 1.7.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SimBu.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SimBu_1.7.0.tar.gz |
StartedAt: 2024-08-27 09:11:20 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 09:15:53 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 273.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SimBu.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SimBu.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SimBu_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SimBu.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SimBu/DESCRIPTION’ ... OK * this is package ‘SimBu’ version ‘1.7.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions .pre-commit-config.yaml .prettierignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SimBu’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/home/biocbuild/bbs-3.20-bioc/meat/SimBu.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 ... 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 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 setup_sfaira 48.837 2.822 72.746 simulate_bulk 18.817 0.308 19.167 dataset 7.559 0.140 7.713 dataset_seurat 5.561 0.176 5.747 * 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-3.20-bioc/meat/SimBu.Rcheck/00check.log’ for details.
SimBu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SimBu ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘SimBu’ ... ** using non-staged installation via StagedInstall field ** R ** 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 (SimBu)
SimBu.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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(SimBu) > > test_check("SimBu") 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 objects are masked from 'package:Matrix': expand, unname 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 Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Filtering genes... Created dataset. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'spam' You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... Finished simulation. You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... You set `rngseed` to FALSE. Make sure you've set & recorded the random seed of your session for reproducibility. See `?set.seed` ... Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Using EPIC scaling factors. Finished simulation. Using EPIC scaling factors. Finished simulation. Using ABIS scaling factors. Finished simulation. Using quanTIseq scaling factors. Finished simulation. Using quanTIseq scaling factors. Finished simulation. Using custom scaling factors. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. Finished simulation. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ] > > proc.time() user system elapsed 115.135 3.323 118.689
SimBu.Rcheck/SimBu-Ex.timings
name | user | system | elapsed | |
census | 2.227 | 0.067 | 2.297 | |
dataset | 7.559 | 0.140 | 7.713 | |
dataset_h5ad | 0 | 0 | 0 | |
dataset_merge | 1.890 | 0.012 | 1.906 | |
dataset_seurat | 5.561 | 0.176 | 5.747 | |
dataset_sfaira | 0 | 0 | 0 | |
dataset_sfaira_multiple | 0 | 0 | 0 | |
merge_simulations | 4.731 | 0.060 | 4.800 | |
plot_simulation | 2.706 | 0.048 | 2.760 | |
save_simulation | 2.380 | 0.063 | 2.448 | |
setup_sfaira | 48.837 | 2.822 | 72.746 | |
sfaira_overview | 0 | 0 | 0 | |
simulate_bulk | 18.817 | 0.308 | 19.167 | |