| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
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To the developers/maintainers of the mixOmics package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1183/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mixOmics 6.19.1 (landing page) Al J Abadi
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: mixOmics |
| Version: 6.19.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mixOmics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mixOmics_6.19.1.tar.gz |
| StartedAt: 2022-03-17 19:37:24 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:41:14 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 230.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mixOmics.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mixOmics.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mixOmics_6.19.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mixOmics.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mixOmics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mixOmics' version '6.19.1'
* 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 whether package 'mixOmics' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 3.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
biplot 8.79 0.05 8.84
background.predict 6.13 1.75 7.88
circosPlot 6.49 0.33 6.86
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/mixOmics.Rcheck/00check.log'
for details.
mixOmics.Rcheck/00install.out
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###
### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mixOmics
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mixOmics' ...
** using staged installation
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mixOmics'
finding HTML links ... done
Koren.16S html
S3methods-print html
auroc html
background.predict html
biplot html
block.pls html
block.plsda html
block.spls html
block.splsda html
breast.TCGA html
breast.tumors html
cim html
cimDiablo html
circosPlot html
colors html
diverse.16S html
explained_variance html
get.confusion_matrix html
image.tune.rcc html
imgCor html
impute.nipals html
ipca html
linnerud html
liver.toxicity html
logratio-transformations html
map html
mat.rank html
mint.block.pls html
mint.block.plsda html
mint.block.spls html
mint.block.splsda html
mint.pca html
mint.pls html
mint.plsda html
mint.spls html
mint.splsda html
mixOmics-package html
mixOmics html
multidrug html
nearZeroVar html
network html
nipals html
nutrimouse html
pca html
perf html
plot.pca html
plot.perf html
plot.perf.pls html
plot.rcc html
plot.tune html
plotArrow html
plotDiablo html
plotIndiv html
plotLoadings html
plotMarkers html
plotVar html
pls html
plsda html
predict html
rcc html
finding level-2 HTML links ... done
selectVar html
sipca html
spca html
spls html
splsda html
srbct html
stemcells html
study_split html
summary html
tune html
tune.block.splsda html
tune.mint.splsda html
tune.pca html
tune.rcc html
tune.spca html
tune.spls html
tune.splsda html
tune.splslevel html
unmap html
vac18 html
vac18.simulated html
vip html
withinVariation html
wrapper.rgcca html
wrapper.sgcca html
yeast html
zz-defunct html
** 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)
Making 'packages.html' ... done
mixOmics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 6.19.1
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")
$Comp1
AUC p-value
AF vs BE 0.863 2.473e-05
$Comp2
AUC p-value
AF vs BE 0.9981 7.124e-09
adding block name to feature names in the output similarity matrix as there are similar feature names across blocks.
Performing repeated cross-validation with nrepeat = 3...
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Performing repeated cross-validation with nrepeat = 3...
|
| | 0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
33.45 1.32 42.48
mixOmics.Rcheck/mixOmics-Ex.timings
| name | user | system | elapsed | |
| S3methods-print | 0.00 | 0.02 | 0.01 | |
| auroc | 0.77 | 0.06 | 0.83 | |
| background.predict | 6.13 | 1.75 | 7.88 | |
| biplot | 8.79 | 0.05 | 8.84 | |
| block.pls | 0.36 | 0.00 | 0.36 | |
| block.plsda | 0.52 | 0.00 | 0.52 | |
| block.spls | 3.59 | 0.04 | 3.65 | |
| block.splsda | 4.19 | 0.05 | 4.24 | |
| cim | 0.05 | 0.00 | 0.05 | |
| cimDiablo | 0.18 | 0.03 | 0.21 | |
| circosPlot | 6.49 | 0.33 | 6.86 | |
| colors | 0.01 | 0.00 | 0.02 | |
| explained_variance | 0.10 | 0.00 | 0.09 | |
| get.confusion_matrix | 0.36 | 0.00 | 0.36 | |
| image.tune.rcc | 1.54 | 0.02 | 1.56 | |
| imgCor | 0.10 | 0.00 | 0.09 | |
| impute.nipals | 0 | 0 | 0 | |
| ipca | 0.56 | 0.02 | 0.58 | |
| logratio-transformations | 0.05 | 0.03 | 0.08 | |
| map | 0 | 0 | 0 | |
| mat.rank | 0.01 | 0.00 | 0.02 | |
| mint.block.pls | 0.10 | 0.00 | 0.09 | |
| mint.block.plsda | 0.11 | 0.00 | 0.11 | |
| mint.block.spls | 0.14 | 0.01 | 0.16 | |
| mint.block.splsda | 0.14 | 0.02 | 0.15 | |
| mint.pca | 0.42 | 0.00 | 0.42 | |
| mint.pls | 0.58 | 0.01 | 0.60 | |
| mint.plsda | 0.51 | 0.00 | 0.51 | |
| mint.spls | 0.36 | 0.00 | 0.36 | |
| mint.splsda | 0.43 | 0.00 | 0.45 | |
| mixOmics | 0.33 | 0.05 | 0.38 | |
| nearZeroVar | 0.60 | 0.03 | 0.62 | |
| network | 0.01 | 0.00 | 0.02 | |
| pca | 3.83 | 0.05 | 3.87 | |
| perf | 1.91 | 0.28 | 2.19 | |
| plot.rcc | 0.01 | 0.00 | 0.02 | |
| plot.tune | 0 | 0 | 0 | |
| plotArrow | 2.67 | 0.02 | 2.68 | |
| plotDiablo | 0.11 | 0.03 | 0.14 | |
| plotIndiv | 0.21 | 0.00 | 0.21 | |
| plotLoadings | 0.28 | 0.03 | 0.31 | |
| plotMarkers | 0 | 0 | 0 | |
| plotVar | 0.36 | 0.00 | 0.36 | |
| pls | 0 | 0 | 0 | |
| plsda | 0.23 | 0.01 | 0.25 | |
| predict | 0.13 | 0.02 | 0.14 | |
| rcc | 0 | 0 | 0 | |
| selectVar | 0.39 | 0.09 | 0.48 | |
| sipca | 0.31 | 0.02 | 0.33 | |
| spca | 2.39 | 0.19 | 2.58 | |
| spls | 0.13 | 0.03 | 0.16 | |
| splsda | 0.23 | 0.01 | 0.25 | |
| study_split | 0.00 | 0.02 | 0.01 | |
| summary | 0.02 | 0.00 | 0.02 | |
| tune | 3.73 | 0.19 | 3.92 | |
| tune.block.splsda | 0 | 0 | 0 | |
| tune.mint.splsda | 1.92 | 0.00 | 1.93 | |
| tune.pca | 0.14 | 0.02 | 0.15 | |
| tune.rcc | 1.44 | 0.04 | 1.49 | |
| tune.spca | 0.48 | 0.02 | 0.50 | |
| tune.spls | 0 | 0 | 0 | |
| tune.splsda | 4.04 | 0.09 | 4.12 | |
| tune.splslevel | 0.78 | 0.08 | 0.86 | |
| unmap | 0 | 0 | 0 | |
| vip | 0.01 | 0.00 | 0.02 | |
| withinVariation | 0.71 | 0.02 | 0.72 | |
| wrapper.rgcca | 0.04 | 0.00 | 0.04 | |
| wrapper.sgcca | 0.11 | 0.00 | 0.11 | |