Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 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" | 4372 |
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 1281/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.31.0 (landing page) Eva Hamrud
| 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 mixOmics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mixOmics.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: mixOmics |
Version: 6.31.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mixOmics_6.31.0.tar.gz |
StartedAt: 2024-12-23 09:42:13 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 09:53:21 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 667.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mixOmics_6.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mixOmics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mixOmics’ version ‘6.31.0’ * 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 ‘mixOmics’ can be installed ... OK * checking installed package size ... INFO installed size is 6.3Mb sub-directories of 1Mb or more: R 1.4Mb data 3.3Mb * checking package 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 ...Warning: program compiled against libxml 212 using older 211 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gsignal’ All declared Imports should be used. * 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: rcc.Rd: estimate.lambda tune.Rd: BiocParallelParam-class tune.block.splsda.Rd: BiocParallelParam-class tune.spca.Rd: BiocParallelParam-class tune.spls.Rd: BiocParallelParam-class 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot 18.157 0.143 18.338 background.predict 12.938 0.128 13.092 tune.rcc 12.561 0.080 12.663 image.tune.rcc 12.587 0.028 12.636 block.splsda 9.626 0.048 9.695 circosPlot 8.845 0.036 8.934 block.spls 7.886 0.084 7.988 tune 6.531 0.014 6.558 tune.splsda 6.139 0.040 6.190 pca 5.794 0.020 5.826 perf 5.367 0.020 5.398 plotArrow 5.178 0.008 5.198 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘mixOmics’ ... ** using staged installation ** R ** data ** 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 (mixOmics)
mixOmics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(mixOmics) Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.31.0 Thank you for using mixOmics! Tutorials: http://mixomics.org Bookdown vignette: https://mixomicsteam.github.io/Bookdown Questions, issues: Follow the prompts at http://mixomics.org/contact-us Cite us: citation('mixOmics') > > test_check("mixOmics") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ] Warning messages: 1: In for (a in args) { : closing unused connection 6 (<-localhost:11188) 2: In for (a in args) { : closing unused connection 5 (<-localhost:11188) > > proc.time() user system elapsed 329.654 4.099 357.670
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.062 | 0.004 | 0.066 | |
auroc | 1.370 | 0.040 | 1.412 | |
background.predict | 12.938 | 0.128 | 13.092 | |
biplot | 18.157 | 0.143 | 18.338 | |
block.pls | 0.721 | 0.028 | 0.752 | |
block.plsda | 0.959 | 0.004 | 0.965 | |
block.spls | 7.886 | 0.084 | 7.988 | |
block.splsda | 9.626 | 0.048 | 9.695 | |
cim | 0.049 | 0.000 | 0.049 | |
cimDiablo | 0.383 | 0.004 | 0.388 | |
circosPlot | 8.845 | 0.036 | 8.934 | |
colors | 0.033 | 0.000 | 0.033 | |
explained_variance | 0.219 | 0.000 | 0.219 | |
get.confusion_matrix | 0.298 | 0.004 | 0.302 | |
image.tune.rcc | 12.587 | 0.028 | 12.636 | |
imgCor | 0.165 | 0.000 | 0.165 | |
impute.nipals | 0.013 | 0.000 | 0.013 | |
ipca | 1.215 | 0.036 | 1.254 | |
logratio-transformations | 0.095 | 0.000 | 0.096 | |
map | 0.004 | 0.000 | 0.004 | |
mat.rank | 0.003 | 0.000 | 0.002 | |
mint.block.pls | 0.211 | 0.000 | 0.211 | |
mint.block.plsda | 0.162 | 0.004 | 0.166 | |
mint.block.spls | 0.535 | 0.016 | 0.552 | |
mint.block.splsda | 0.168 | 0.000 | 0.168 | |
mint.pca | 0.506 | 0.000 | 0.506 | |
mint.pls | 0.734 | 0.000 | 0.736 | |
mint.plsda | 0.855 | 0.000 | 0.857 | |
mint.spls | 0.736 | 0.000 | 0.738 | |
mint.splsda | 0.879 | 0.000 | 0.881 | |
mixOmics | 0.758 | 0.000 | 0.760 | |
nearZeroVar | 1.179 | 0.004 | 1.185 | |
network | 0.059 | 0.000 | 0.060 | |
pca | 5.794 | 0.020 | 5.826 | |
perf | 5.367 | 0.020 | 5.398 | |
plot.rcc | 0.361 | 0.004 | 0.366 | |
plot.tune | 0 | 0 | 0 | |
plotArrow | 5.178 | 0.008 | 5.198 | |
plotDiablo | 0.245 | 0.000 | 0.246 | |
plotIndiv | 0.468 | 0.000 | 0.469 | |
plotLoadings | 0.212 | 0.000 | 0.212 | |
plotMarkers | 0.001 | 0.000 | 0.000 | |
plotVar | 0.843 | 0.000 | 0.845 | |
pls | 0.008 | 0.000 | 0.008 | |
plsda | 0.480 | 0.000 | 0.481 | |
predict | 0.3 | 0.0 | 0.3 | |
rcc | 0.003 | 0.000 | 0.003 | |
selectVar | 0.583 | 0.004 | 0.588 | |
sipca | 0.731 | 0.000 | 0.734 | |
spca | 4.013 | 0.008 | 4.030 | |
spls | 0.511 | 0.004 | 0.516 | |
splsda | 0.519 | 0.000 | 0.521 | |
study_split | 0.005 | 0.000 | 0.006 | |
summary | 0.078 | 0.000 | 0.078 | |
tune | 6.531 | 0.014 | 6.558 | |
tune.block.splsda | 0 | 0 | 0 | |
tune.mint.splsda | 4.713 | 0.004 | 4.728 | |
tune.pca | 0.253 | 0.000 | 0.253 | |
tune.rcc | 12.561 | 0.080 | 12.663 | |
tune.spca | 0.918 | 0.027 | 0.948 | |
tune.spls | 0 | 0 | 0 | |
tune.splsda | 6.139 | 0.040 | 6.190 | |
tune.splslevel | 2.179 | 0.040 | 2.223 | |
unmap | 0.004 | 0.000 | 0.004 | |
vip | 0.012 | 0.000 | 0.012 | |
withinVariation | 1.243 | 0.008 | 1.253 | |
wrapper.rgcca | 0.093 | 0.008 | 0.101 | |
wrapper.sgcca | 0.221 | 0.004 | 0.226 | |