Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1164/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MatrixQCvis 1.14.0 (landing page) Thomas Naake
| teran2 | Linux (Ubuntu 24.04.1 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 MatrixQCvis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MatrixQCvis.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: MatrixQCvis |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MatrixQCvis_1.14.0.tar.gz |
StartedAt: 2024-11-09 06:17:45 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 06:23:07 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 322.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MatrixQCvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MatrixQCvis_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MatrixQCvis.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MatrixQCvis’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘MatrixQCvis’ 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 ... 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 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: OK
MatrixQCvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MatrixQCvis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MatrixQCvis’ ... ** 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 (MatrixQCvis)
MatrixQCvis.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-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(MatrixQCvis) Loading required package: DT 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, saveRDS, 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: plotly Loading required package: ggplot2 Attaching package: 'plotly' The following object is masked from 'package:ggplot2': last_plot The following object is masked from 'package:IRanges': slice The following object is masked from 'package:S4Vectors': rename The following object is masked from 'package:stats': filter The following object is masked from 'package:graphics': layout Loading required package: shiny Attaching package: 'shiny' The following objects are masked from 'package:DT': dataTableOutput, renderDataTable > testthat::test_check("MatrixQCvis") initial value 0.091643 final value 0.091636 converged initial value 0.091643 final value 0.091636 converged [1] "Perform batch correction using 100 features." [1] 28.64894 [ FAIL 0 | WARN 3 | SKIP 0 | PASS 504 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 504 ] > > proc.time() user system elapsed 10.541 0.339 10.883
MatrixQCvis.Rcheck/MatrixQCvis-Ex.timings
name | user | system | elapsed | |
ECDF | 0.083 | 0.003 | 0.086 | |
MAplot | 0.659 | 0.018 | 0.678 | |
MAvalues | 0.024 | 0.001 | 0.024 | |
barplotSamplesMeasuredMissing | 0.108 | 0.012 | 0.121 | |
batchCorrectionAssay | 1.282 | 0.005 | 1.288 | |
createBoxplot | 0.094 | 0.000 | 0.094 | |
createDfFeature | 0.001 | 0.000 | 0.001 | |
cv | 0.001 | 0.000 | 0.000 | |
cvFeaturePlot | 0.075 | 0.007 | 0.082 | |
dimensionReduction | 0.300 | 0.046 | 0.347 | |
dimensionReductionPlot | 0.039 | 0.006 | 0.045 | |
distSample | 0.243 | 0.005 | 0.248 | |
distShiny | 0.001 | 0.000 | 0.001 | |
driftPlot | 0.146 | 0.006 | 0.151 | |
explVar | 0.002 | 0.000 | 0.002 | |
extractComb | 0.007 | 0.000 | 0.007 | |
featurePlot | 0.075 | 0.001 | 0.075 | |
histFeature | 0.033 | 0.005 | 0.039 | |
histFeatureCategory | 0.066 | 0.005 | 0.070 | |
hist_sample | 0.041 | 0.004 | 0.045 | |
hist_sample_num | 0.008 | 0.000 | 0.007 | |
hoeffDPlot | 0.219 | 0.014 | 0.234 | |
hoeffDValues | 0.052 | 0.001 | 0.052 | |
imputeAssay | 0.002 | 0.000 | 0.003 | |
measuredCategory | 0.005 | 0.000 | 0.005 | |
mosaic | 0.097 | 0.001 | 0.098 | |
normalizeAssay | 0.000 | 0.000 | 0.001 | |
permuteExplVar | 0.003 | 0.001 | 0.004 | |
plotCV | 0.048 | 0.000 | 0.048 | |
plotPCALoadings | 0.046 | 0.005 | 0.050 | |
plotPCAVar | 0.070 | 0.001 | 0.070 | |
plotPCAVarPvalue | 0.067 | 0.001 | 0.067 | |
samplesMeasuredMissing | 0.009 | 0.000 | 0.009 | |
shinyQC | 0.010 | 0.000 | 0.011 | |
sumDistSample | 0.036 | 0.005 | 0.041 | |
tblPCALoadings | 0.039 | 0.000 | 0.039 | |
transformAssay | 0.032 | 0.007 | 0.039 | |
upsetCategory | 0.140 | 0.001 | 0.141 | |
volcanoPlot | 0.043 | 0.005 | 0.047 | |