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 11:05:09 -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 MatrixQCvis package: - Please 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 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 1105/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MatrixQCvis 1.6.1 (landing page) Thomas Naake
| 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: MatrixQCvis |
Version: 1.6.1 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MatrixQCvis_1.6.1.tar.gz |
StartedAt: 2023-04-10 21:43:33 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:47:45 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 251.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MatrixQCvis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MatrixQCvis_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MatrixQCvis.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MatrixQCvis’ version ‘1.6.1’ * 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 ... 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 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 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MatrixQCvis.Rmd’ using ‘UTF-8’... OK NONE * 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-3.16-bioc/R/bin/R CMD INSTALL MatrixQCvis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(MatrixQCvis) 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, 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: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 > testthat::test_check("MatrixQCvis") initial value 0.091643 final value 0.091636 converged initial value 0.091643 final value 0.091636 converged [1] 28.64894 [ FAIL 0 | WARN 8 | SKIP 0 | PASS 463 ] [ FAIL 0 | WARN 8 | SKIP 0 | PASS 463 ] > > proc.time() user system elapsed 23.999 1.079 25.032
MatrixQCvis.Rcheck/MatrixQCvis-Ex.timings
name | user | system | elapsed | |
ECDF | 0.365 | 0.028 | 0.392 | |
MAplot | 1.031 | 0.084 | 1.116 | |
MAvalues | 0.060 | 0.024 | 0.085 | |
barplotSamplesMeasuredMissing | 0.360 | 0.044 | 0.404 | |
batchCorrectionAssay | 0.024 | 0.008 | 0.033 | |
createBoxplot | 0.368 | 0.004 | 0.372 | |
createDfFeature | 0.002 | 0.000 | 0.003 | |
cv | 0 | 0 | 0 | |
cvFeaturePlot | 0.253 | 0.016 | 0.253 | |
dimensionReduction | 1.698 | 0.059 | 1.758 | |
dimensionReductionPlot | 0.119 | 0.004 | 0.123 | |
distSample | 0.698 | 0.000 | 0.698 | |
distShiny | 0.001 | 0.000 | 0.001 | |
driftPlot | 0.755 | 0.028 | 0.783 | |
explVar | 0.006 | 0.004 | 0.010 | |
extractComb | 0.019 | 0.004 | 0.023 | |
featurePlot | 0.241 | 0.004 | 0.245 | |
histFeature | 0.094 | 0.012 | 0.105 | |
histFeatureCategory | 0.212 | 0.008 | 0.220 | |
hist_sample | 0.104 | 0.004 | 0.108 | |
hist_sample_num | 0.020 | 0.004 | 0.024 | |
hoeffDPlot | 0.764 | 0.044 | 0.794 | |
hoeffDValues | 0.189 | 0.004 | 0.193 | |
imputeAssay | 0.007 | 0.000 | 0.007 | |
measuredCategory | 0.016 | 0.000 | 0.017 | |
mosaic | 0.340 | 0.003 | 0.344 | |
normalizeAssay | 0.001 | 0.000 | 0.001 | |
permuteExplVar | 0.012 | 0.000 | 0.012 | |
plotCV | 0.212 | 0.001 | 0.212 | |
plotPCALoadings | 0.141 | 0.003 | 0.145 | |
plotPCAVar | 0.269 | 0.000 | 0.269 | |
plotPCAVarPvalue | 0.227 | 0.001 | 0.226 | |
samplesMeasuredMissing | 0.029 | 0.000 | 0.029 | |
shinyQC | 0.029 | 0.000 | 0.030 | |
sumDistSample | 0.109 | 0.011 | 0.120 | |
tblPCALoadings | 0.125 | 0.003 | 0.129 | |
transformAssay | 0.039 | 0.012 | 0.051 | |
upsetCategory | 0.410 | 0.000 | 0.411 | |
volcanoPlot | 0.125 | 0.008 | 0.133 | |