Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:52 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the SimBu package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1878/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SimBu 1.0.2 (landing page) Alexander Dietrich
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: SimBu |
Version: 1.0.2 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SimBu.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SimBu_1.0.2.tar.gz |
StartedAt: 2023-04-11 06:04:34 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 06:07:10 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 155.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SimBu.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SimBu.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SimBu_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SimBu.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SimBu/DESCRIPTION' ... OK * this is package 'SimBu' version '1.0.2' * 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 whether package 'SimBu' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'F:/biocbuild/bbs-3.16-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 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 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 simulate_bulk 16.45 1.14 17.59 setup_sfaira 1.42 1.21 28.25 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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 'F:/biocbuild/bbs-3.16-bioc/meat/SimBu.Rcheck/00check.log' for details.
SimBu.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SimBu ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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, sort, 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 objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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. 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 37 | SKIP 0 | PASS 28 ] [ FAIL 0 | WARN 37 | SKIP 0 | PASS 28 ] > > proc.time() user system elapsed 52.32 1.26 53.62
SimBu.Rcheck/SimBu-Ex.timings
name | user | system | elapsed | |
census | 1.62 | 0.15 | 1.76 | |
dataset | 4.46 | 0.19 | 4.66 | |
dataset_h5ad | 0 | 0 | 0 | |
dataset_merge | 1.54 | 0.03 | 1.58 | |
dataset_seurat | 3.44 | 0.25 | 3.69 | |
dataset_sfaira | 0 | 0 | 0 | |
dataset_sfaira_multiple | 0 | 0 | 0 | |
merge_simulations | 2.61 | 0.03 | 2.64 | |
plot_simulation | 2.08 | 0.05 | 2.13 | |
save_simulation | 1.17 | 0.01 | 1.19 | |
setup_sfaira | 1.42 | 1.21 | 28.25 | |
sfaira_overview | 0 | 0 | 0 | |
simulate_bulk | 16.45 | 1.14 | 17.59 | |