Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:08 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1284/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mixOmics 6.26.0 (landing page) Max Bladen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 6.26.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings mixOmics_6.26.0.tar.gz |
StartedAt: 2024-04-16 01:01:34 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 01:18:48 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 1033.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: mixOmics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings mixOmics_6.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mixOmics.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘6.26.0’ * 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 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 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 14.225 0.164 14.389 background.predict 6.655 0.123 6.779 block.splsda 6.232 0.095 6.329 circosPlot 5.279 0.051 5.333 block.spls 5.017 0.059 5.077 * 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 ... ‘vignette.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘vignette.Rmd’ ... > plotIndiv(final.plsda.srbct, ind.names = FALSE, legend = TRUE, + comp = c(2, 3), ellipse = TRUE, title = "PLS-DA on SRBCT comp 2-3", + X.l .... [TRUNCATED] > knitr::include_graphics(c("Figures/PLSDA/05-plsda-sample-plot-nc12-1.png", + "Figures/PLSDA/05-plsda-sample-plot-nc13-1.png")) When sourcing ‘vignette.R’: Error: Cannot find the file(s): "Figures/PLSDA/05-plsda-sample-plot-nc12-1.png"; "Figures/PLSDA/05-plsda-sample-plot-nc13-1.png" Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/mixOmics.Rcheck/00check.log’ for details.
mixOmics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL mixOmics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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(mixOmics) Loading required package: MASS Loading required package: lattice Loading required package: ggplot2 Loaded mixOmics 6.26.0 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 ] > > proc.time() user system elapsed 98.393 2.206 116.236
mixOmics.Rcheck/mixOmics-Ex.timings
name | user | system | elapsed | |
S3methods-print | 0.017 | 0.000 | 0.018 | |
auroc | 1.101 | 0.024 | 1.126 | |
background.predict | 6.655 | 0.123 | 6.779 | |
biplot | 14.225 | 0.164 | 14.389 | |
block.pls | 0.469 | 0.045 | 0.512 | |
block.plsda | 0.625 | 0.000 | 0.625 | |
block.spls | 5.017 | 0.059 | 5.077 | |
block.splsda | 6.232 | 0.095 | 6.329 | |
cim | 0.037 | 0.000 | 0.037 | |
cimDiablo | 0.233 | 0.000 | 0.233 | |
circosPlot | 5.279 | 0.051 | 5.333 | |
colors | 0.022 | 0.003 | 0.026 | |
explained_variance | 0.087 | 0.009 | 0.095 | |
get.confusion_matrix | 0.138 | 0.000 | 0.137 | |
image.tune.rcc | 1.940 | 0.032 | 1.972 | |
imgCor | 0.076 | 0.000 | 0.076 | |
impute.nipals | 0.004 | 0.007 | 0.011 | |
ipca | 0.700 | 0.024 | 0.725 | |
logratio-transformations | 0.068 | 0.004 | 0.072 | |
map | 0.004 | 0.000 | 0.005 | |
mat.rank | 0.002 | 0.000 | 0.002 | |
mint.block.pls | 0.13 | 0.00 | 0.13 | |
mint.block.plsda | 0.115 | 0.004 | 0.120 | |
mint.block.spls | 0.151 | 0.000 | 0.151 | |
mint.block.splsda | 0.128 | 0.000 | 0.127 | |
mint.pca | 0.332 | 0.000 | 0.332 | |
mint.pls | 0.459 | 0.000 | 0.460 | |
mint.plsda | 0.575 | 0.008 | 0.584 | |
mint.spls | 0.476 | 0.000 | 0.476 | |
mint.splsda | 0.586 | 0.004 | 0.589 | |
mixOmics | 0.572 | 0.028 | 0.601 | |
nearZeroVar | 0.653 | 0.000 | 0.653 | |
network | 0.008 | 0.004 | 0.012 | |
pca | 4.081 | 0.032 | 4.113 | |
perf | 2.527 | 0.004 | 2.530 | |
plot.rcc | 0.013 | 0.000 | 0.013 | |
plot.tune | 0.000 | 0.000 | 0.001 | |
plotArrow | 3.334 | 0.056 | 3.391 | |
plotDiablo | 0.170 | 0.004 | 0.174 | |
plotIndiv | 0.282 | 0.000 | 0.282 | |
plotLoadings | 0.094 | 0.000 | 0.094 | |
plotMarkers | 0 | 0 | 0 | |
plotVar | 0.549 | 0.000 | 0.549 | |
pls | 0.006 | 0.000 | 0.007 | |
plsda | 0.446 | 0.000 | 0.446 | |
predict | 0.148 | 0.001 | 0.148 | |
rcc | 0.000 | 0.003 | 0.002 | |
selectVar | 0.382 | 0.000 | 0.382 | |
sipca | 0.710 | 0.016 | 0.726 | |
spca | 2.937 | 0.023 | 2.961 | |
spls | 0.455 | 0.000 | 0.456 | |
splsda | 0.401 | 0.004 | 0.405 | |
study_split | 0.005 | 0.000 | 0.005 | |
summary | 0.014 | 0.000 | 0.015 | |
tune | 4.135 | 0.244 | 4.400 | |
tune.block.splsda | 0 | 0 | 0 | |
tune.mint.splsda | 2.215 | 0.028 | 2.244 | |
tune.pca | 0.156 | 0.002 | 0.158 | |
tune.rcc | 1.987 | 0.049 | 2.037 | |
tune.spca | 0.593 | 0.020 | 0.614 | |
tune.spls | 0 | 0 | 0 | |
tune.splsda | 3.801 | 0.088 | 3.910 | |
tune.splslevel | 0.774 | 0.023 | 0.797 | |
unmap | 0.004 | 0.000 | 0.004 | |
vip | 0.01 | 0.00 | 0.01 | |
withinVariation | 0.809 | 0.036 | 0.845 | |
wrapper.rgcca | 0.067 | 0.008 | 0.076 | |
wrapper.sgcca | 0.112 | 0.000 | 0.112 | |