Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:29:08 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1259/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.29.0 (landing page) Max Bladen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: mixOmics |
Version: 6.29.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mixOmics_6.29.0.tar.gz |
StartedAt: 2024-05-31 05:44:51 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:57:54 -0400 (Fri, 31 May 2024) |
EllapsedTime: 782.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mixOmics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mixOmics_6.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘mixOmics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mixOmics’ version ‘6.29.0’ * 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 ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: R 1.4Mb data 3.3Mb doc 1.9Mb * 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 ... 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot 14.136 0.228 14.365 background.predict 7.390 0.436 7.826 block.splsda 5.976 0.063 6.040 circosPlot 5.629 0.076 5.706 block.spls 4.977 0.056 5.032 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 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(mixOmics) Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.29.0 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 4 | SKIP 0 | PASS 236 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 236 ] Warning messages: 1: In for (m in 1:nlevels(study)) mean_centered.rownames.study[[m]] = mean_centered[[1]]$rownames.study[[m]] : closing unused connection 6 (<-localhost:11351) 2: In for (m in 1:nlevels(study)) mean_centered.rownames.study[[m]] = mean_centered[[1]]$rownames.study[[m]] : closing unused connection 5 (<-localhost:11351) > > proc.time() user system elapsed 98.436 3.341 116.028
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.014 | 0.003 | 0.018 | |
auroc | 1.072 | 0.044 | 1.117 | |
background.predict | 7.390 | 0.436 | 7.826 | |
biplot | 14.136 | 0.228 | 14.365 | |
block.pls | 0.476 | 0.008 | 0.485 | |
block.plsda | 0.610 | 0.048 | 0.659 | |
block.spls | 4.977 | 0.056 | 5.032 | |
block.splsda | 5.976 | 0.063 | 6.040 | |
cim | 0.054 | 0.004 | 0.058 | |
cimDiablo | 0.247 | 0.000 | 0.247 | |
circosPlot | 5.629 | 0.076 | 5.706 | |
colors | 0.028 | 0.000 | 0.027 | |
explained_variance | 0.088 | 0.012 | 0.101 | |
get.confusion_matrix | 0.134 | 0.004 | 0.138 | |
image.tune.rcc | 2.033 | 0.011 | 2.045 | |
imgCor | 0.077 | 0.000 | 0.077 | |
impute.nipals | 0.010 | 0.000 | 0.011 | |
ipca | 0.760 | 0.004 | 0.764 | |
logratio-transformations | 0.084 | 0.000 | 0.084 | |
map | 0.005 | 0.000 | 0.005 | |
mat.rank | 0.002 | 0.000 | 0.001 | |
mint.block.pls | 0.136 | 0.000 | 0.135 | |
mint.block.plsda | 0.12 | 0.00 | 0.12 | |
mint.block.spls | 0.154 | 0.000 | 0.153 | |
mint.block.splsda | 0.130 | 0.000 | 0.129 | |
mint.pca | 0.34 | 0.00 | 0.34 | |
mint.pls | 0.48 | 0.00 | 0.48 | |
mint.plsda | 0.576 | 0.016 | 0.592 | |
mint.spls | 0.487 | 0.000 | 0.488 | |
mint.splsda | 0.564 | 0.004 | 0.568 | |
mixOmics | 0.301 | 0.008 | 0.309 | |
nearZeroVar | 0.938 | 0.032 | 0.969 | |
network | 0.013 | 0.000 | 0.012 | |
pca | 4.092 | 0.072 | 4.164 | |
perf | 2.774 | 0.052 | 2.826 | |
plot.rcc | 0.013 | 0.000 | 0.013 | |
plot.tune | 0 | 0 | 0 | |
plotArrow | 3.379 | 0.011 | 3.391 | |
plotDiablo | 0.174 | 0.004 | 0.178 | |
plotIndiv | 0.283 | 0.008 | 0.291 | |
plotLoadings | 0.101 | 0.016 | 0.117 | |
plotMarkers | 0 | 0 | 0 | |
plotVar | 0.799 | 0.004 | 0.803 | |
pls | 0.006 | 0.000 | 0.006 | |
plsda | 0.319 | 0.004 | 0.323 | |
predict | 0.145 | 0.000 | 0.145 | |
rcc | 0.002 | 0.000 | 0.002 | |
selectVar | 0.328 | 0.009 | 0.337 | |
sipca | 0.460 | 0.002 | 0.462 | |
spca | 2.747 | 0.024 | 2.771 | |
spls | 0.211 | 0.000 | 0.210 | |
splsda | 0.576 | 0.000 | 0.576 | |
study_split | 0.001 | 0.004 | 0.005 | |
summary | 0.016 | 0.000 | 0.016 | |
tune | 4.048 | 0.042 | 4.106 | |
tune.block.splsda | 0 | 0 | 0 | |
tune.mint.splsda | 2.239 | 0.000 | 2.239 | |
tune.pca | 0.505 | 0.008 | 0.513 | |
tune.rcc | 1.981 | 0.008 | 1.989 | |
tune.spca | 0.614 | 0.008 | 0.623 | |
tune.spls | 0 | 0 | 0 | |
tune.splsda | 4.052 | 0.021 | 4.092 | |
tune.splslevel | 0.778 | 0.012 | 0.790 | |
unmap | 0.004 | 0.000 | 0.004 | |
vip | 0.009 | 0.000 | 0.009 | |
withinVariation | 0.813 | 0.004 | 0.817 | |
wrapper.rgcca | 0.076 | 0.000 | 0.076 | |
wrapper.sgcca | 0.114 | 0.000 | 0.113 | |