Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 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" | 4373 |
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 1959/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SingleCellExperiment 1.29.1 (landing page) Davide Risso
| 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 SingleCellExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleCellExperiment.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: SingleCellExperiment |
Version: 1.29.1 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleCellExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.29.1.tar.gz |
StartedAt: 2024-12-24 05:05:35 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 05:09:29 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 234.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SingleCellExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleCellExperiment.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SingleCellExperiment_1.29.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SingleCellExperiment.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SingleCellExperiment/DESCRIPTION' ... OK * this is package 'SingleCellExperiment' version '1.29.1' * 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 whether package 'SingleCellExperiment' can be installed ... OK * 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'S4Vectors:::disableValidity' 'SummarizedExperiment:::.SummarizedExperiment.charbound' See the note in ?`:::` about the use of this operator. * 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: SingleCellExperiment.Rd: RangedSummarizedExperiment-class, SummarizedExperiment, SummarizedExperiment-class, SelfHits-class, assays, rowData, colData altExps.Rd: SummarizedExperiment-class, colData, List-class, assay<-, Annotated-class, metadata, Vector-class, mcols assays.Rd: assay, assay<- colLabels.Rd: SummarizedExperiment-class, colData colPairs.Rd: SelfHits-class, List-class, mcols combine.Rd: rbind,SummarizedExperiment-method, cbind,SummarizedExperiment-method, colData, combineCols,SummarizedExperiment-method, combineCols, [,SummarizedExperiment-method, SummarizedExperiment-class internals.Rd: DataFrame-class, rowData, colData, metadata, rowData,SummarizedExperiment-method, colData,SummarizedExperiment-method, rowData<-, colData<-, metadata<- reducedDims.Rd: List-class, assay<-, Annotated-class, metadata, Vector-class, mcols rowPairs.Rd: SelfHits-class, List-class, mcols rowSubset.Rd: rowData simplifyToSCE.Rd: SummarizedExperiment-class sizeFactors.Rd: colData unsplitAltExps.Rd: colData, ConstantMatrix-class, DelayedArray-class updateObject.Rd: sizeFactors<-, colData 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 files in 'vignettes' ... OK * checking examples ... OK * 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 'E:/biocbuild/bbs-3.21-bioc/meat/SingleCellExperiment.Rcheck/00check.log' for details.
SingleCellExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SingleCellExperiment ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'SingleCellExperiment' ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SingleCellExperiment)
SingleCellExperiment.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(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 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 > test_check("SingleCellExperiment") class: SingleCellExperiment dim: 200 100 metadata(0): assays(2): counts logcounts rownames: NULL rowData names(0): colnames: NULL colData names(1): sizeFactor reducedDimNames(2): PCA TSNE mainExpName: NULL altExpNames(2): Spike Protein [ FAIL 0 | WARN 7 | SKIP 0 | PASS 766 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 766 ] > > proc.time() user system elapsed 53.48 1.42 54.96
SingleCellExperiment.Rcheck/SingleCellExperiment-Ex.timings
name | user | system | elapsed | |
LEM-combine | 0.11 | 0.00 | 0.13 | |
LEM-getset | 0.06 | 0.14 | 0.21 | |
LEM-misc | 0.01 | 0.02 | 0.03 | |
LEM-subset | 0.05 | 0.01 | 0.07 | |
LinearEmbeddingMatrix | 0 | 0 | 0 | |
SingleCellExperiment | 0.55 | 0.02 | 0.56 | |
altExps | 0.58 | 0.00 | 0.57 | |
applySCE | 1.22 | 0.05 | 1.27 | |
assays | 0.36 | 0.04 | 0.41 | |
colLabels | 0.23 | 0.04 | 0.26 | |
colPairs | 0.36 | 0.00 | 0.42 | |
combine | 1.63 | 0.06 | 1.74 | |
internals | 0.15 | 0.00 | 0.15 | |
miscellaneous | 0.3 | 0.0 | 0.3 | |
reduced.dim.matrix | 0.02 | 0.00 | 0.02 | |
reducedDims | 0.43 | 0.00 | 0.43 | |
rowPairs | 0.32 | 0.00 | 0.32 | |
rowSubset | 0.20 | 0.01 | 0.21 | |
simplifyToSCE | 0.58 | 0.00 | 0.58 | |
sizeFactors | 0.28 | 0.02 | 0.30 | |
splitAltExps | 0.40 | 0.00 | 0.41 | |
swapAltExp | 0.71 | 0.00 | 0.71 | |
unsplitAltExps | 0.65 | 0.00 | 0.66 | |