Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -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 1158/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MatrixQCvis 1.15.0 (landing page) Thomas Naake
| 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 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: 1.15.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MatrixQCvis_1.15.0.tar.gz |
StartedAt: 2024-12-23 23:28:54 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:35:20 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 386.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MatrixQCvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MatrixQCvis_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MatrixQCvis.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MatrixQCvis’ version ‘1.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 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 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
MatrixQCvis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MatrixQCvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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(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 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 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 31.807 1.203 32.974
MatrixQCvis.Rcheck/MatrixQCvis-Ex.timings
name | user | system | elapsed | |
ECDF | 0.490 | 0.004 | 0.494 | |
MAplot | 2.150 | 0.163 | 2.313 | |
MAvalues | 0.091 | 0.004 | 0.094 | |
barplotSamplesMeasuredMissing | 0.354 | 0.044 | 0.400 | |
batchCorrectionAssay | 4.452 | 0.111 | 4.567 | |
createBoxplot | 0.331 | 0.001 | 0.332 | |
createDfFeature | 0.002 | 0.001 | 0.002 | |
cv | 0.000 | 0.000 | 0.001 | |
cvFeaturePlot | 0.240 | 0.022 | 0.248 | |
dimensionReduction | 0.870 | 0.168 | 1.039 | |
dimensionReductionPlot | 0.138 | 0.006 | 0.144 | |
distSample | 0.735 | 0.008 | 0.743 | |
distShiny | 0.000 | 0.001 | 0.002 | |
driftPlot | 0.501 | 0.004 | 0.505 | |
explVar | 0.004 | 0.001 | 0.005 | |
extractComb | 0.020 | 0.001 | 0.020 | |
featurePlot | 0.262 | 0.009 | 0.270 | |
histFeature | 0.106 | 0.005 | 0.112 | |
histFeatureCategory | 0.208 | 0.008 | 0.216 | |
hist_sample | 0.136 | 0.008 | 0.145 | |
hist_sample_num | 0.026 | 0.000 | 0.025 | |
hoeffDPlot | 0.781 | 0.021 | 0.784 | |
hoeffDValues | 0.179 | 0.004 | 0.184 | |
imputeAssay | 0.007 | 0.002 | 0.010 | |
measuredCategory | 0.016 | 0.001 | 0.017 | |
mosaic | 0.318 | 0.001 | 0.318 | |
normalizeAssay | 0.000 | 0.001 | 0.002 | |
permuteExplVar | 0.012 | 0.001 | 0.013 | |
plotCV | 0.162 | 0.000 | 0.161 | |
plotPCALoadings | 0.126 | 0.005 | 0.131 | |
plotPCAVar | 0.274 | 0.002 | 0.276 | |
plotPCAVarPvalue | 0.212 | 0.002 | 0.214 | |
samplesMeasuredMissing | 0.028 | 0.000 | 0.027 | |
shinyQC | 0.027 | 0.002 | 0.030 | |
sumDistSample | 0.113 | 0.005 | 0.117 | |
tblPCALoadings | 0.101 | 0.002 | 0.103 | |
transformAssay | 0.045 | 0.028 | 0.074 | |
upsetCategory | 0.475 | 0.003 | 0.477 | |
volcanoPlot | 0.127 | 0.017 | 0.144 | |