Multiple platform build/check report for BioC 3.12 - CHECK report for mixOmics on tokay1

Package: mixOmics

Version: 6.14.1

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mixOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mixOmics_6.14.1.tar.gz

StartedAt: 2021-05-06 04:44:11 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:52:22 -0400 (Thu, 06 May 2021)

EllapsedTime: 491.6 seconds

RetCode: 0

Status: OK

CheckDir: mixOmics.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mixOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings mixOmics_6.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/mixOmics.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '6.14.1'
* 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  6.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
biplot             17.33   0.08   17.41
background.predict 11.67   0.43   12.12
tune                5.22   0.14    5.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
biplot             14.18   0.09   14.28
background.predict  7.71   0.08    7.78
tune.splsda         5.27   0.01    5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/mixOmics.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/mixOmics_6.14.1.tar.gz && rm -rf mixOmics.buildbin-libdir && mkdir mixOmics.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mixOmics.buildbin-libdir mixOmics_6.14.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL mixOmics_6.14.1.zip && rm mixOmics_6.14.1.tar.gz mixOmics_6.14.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 4330k  100 4330k    0     0  68.4M      0 --:--:-- --:--:-- --:--:-- 69.3M

install for i386

* installing *source* package 'mixOmics' ...
** using staged installation
** 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  
    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

install for x64

* installing *source* package 'mixOmics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mixOmics' as mixOmics_6.14.1.zip
* DONE (mixOmics)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'mixOmics' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 6.14.1
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


Performing repeated cross-validation...

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  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
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  |======================================================================| 100%
Performing repeated cross-validation...

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  |                                                                      |   0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
  42.76    1.31   72.48


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 6.14.1
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


Performing repeated cross-validation...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
Performing repeated cross-validation...

  |                                                                            
  |                                                                      |   0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
  53.18    1.39   87.15

name	user	system	elapsed
S3methods-print	0.03	0.00	0.03
auroc	0.63	0.04	0.66
background.predict	11.67	0.43	12.12
biplot	17.33	0.08	17.41
block.pls	0.58	0.02	0.59
block.plsda	1.06	0.00	1.07
block.spls	0.62	0.01	0.64
block.splsda	0.61	0.00	0.61
cim	0.07	0.00	0.06
cimDiablo	0.17	0.02	0.19
circosPlot	1.22	0.00	1.21
colors	0.03	0.00	0.04
explained_variance	0.14	0.01	0.15
get.confusion_matrix	0.17	0.02	0.19
image.tune.rcc	2.42	0.00	2.42
imgCor	0.16	0.00	0.16
impute.nipals	0.01	0.01	0.03
ipca	1.27	0.02	1.28
logratio-transformations	0.12	0.02	0.14
map	0.02	0.00	0.02
mat.rank	0	0	0
mint.block.pls	0.23	0.00	0.24
mint.block.plsda	0.17	0.00	0.17
mint.block.spls	0.22	0.01	0.24
mint.block.splsda	0.2	0.0	0.2
mint.pca	0.42	0.00	0.42
mint.pls	0.72	0.00	0.72
mint.plsda	0.78	0.02	0.79
mint.spls	0.48	0.00	0.49
mint.splsda	0.61	0.01	0.62
mixOmics	0.59	0.02	0.61
nearZeroVar	0.86	0.01	0.88
network	0.02	0.02	0.03
pca	4.25	0.02	4.26
perf	3.62	0.17	3.80
plot.rcc	0.02	0.00	0.02
plot.tune	0	0	0
plotArrow	3.06	0.04	3.12
plotDiablo	0.21	0.02	0.22
plotIndiv	0.25	0.02	0.27
plotLoadings	0.17	0.00	0.17
plotVar	0.47	0.01	0.48
pls	0.01	0.00	0.02
plsda	0.35	0.00	0.34
predict	0.17	0.03	0.21
rcc	0.00	0.02	0.01
selectVar	0.89	0.06	0.95
sipca	0.40	0.05	0.46
spca	3.08	0.14	3.22
spls	0.25	0.03	0.28
splsda	0.33	0.00	0.33
study_split	0.01	0.00	0.02
summary	0.02	0.00	0.01
tune	5.22	0.14	5.36
tune.block.splsda	0	0	0
tune.mint.splsda	2.5	0.0	2.5
tune.pca	0.21	0.00	0.20
tune.rcc	2.23	0.02	2.25
tune.spca	0.72	0.00	0.72
tune.spls	0	0	0
tune.splsda	4.48	0.01	4.50
tune.splslevel	0.80	0.02	0.81
unmap	0	0	0
vip	0.02	0.00	0.02
withinVariation	0.78	0.01	0.79
wrapper.rgcca	0.06	0.02	0.08
wrapper.sgcca	0.12	0.01	0.14

name	user	system	elapsed
S3methods-print	0.03	0.00	0.04
auroc	0.58	0.00	0.57
background.predict	7.71	0.08	7.78
biplot	14.18	0.09	14.28
block.pls	0.50	0.02	0.52
block.plsda	0.91	0.00	0.90
block.spls	0.81	0.00	0.82
block.splsda	0.60	0.00	0.59
cim	0.04	0.00	0.05
cimDiablo	0.13	0.01	0.14
circosPlot	1.09	0.04	1.12
colors	0.03	0.00	0.03
explained_variance	0.11	0.00	0.11
get.confusion_matrix	0.22	0.03	0.25
image.tune.rcc	2.84	0.00	2.85
imgCor	0.13	0.00	0.12
impute.nipals	0.01	0.00	0.02
ipca	0.80	0.04	0.84
logratio-transformations	0.11	0.00	0.11
map	0	0	0
mat.rank	0	0	0
mint.block.pls	0.16	0.02	0.17
mint.block.plsda	0.09	0.00	0.10
mint.block.spls	0.14	0.02	0.15
mint.block.splsda	0.13	0.00	0.13
mint.pca	0.34	0.00	0.34
mint.pls	0.45	0.00	0.45
mint.plsda	0.55	0.01	0.57
mint.spls	0.53	0.00	0.53
mint.splsda	0.55	0.02	0.56
mixOmics	0.58	0.03	0.61
nearZeroVar	0.84	0.01	0.86
network	0.02	0.00	0.01
pca	4.62	0.07	4.69
perf	2.84	0.15	3.00
plot.rcc	0.02	0.00	0.02
plot.tune	0	0	0
plotArrow	3.23	0.08	3.31
plotDiablo	0.19	0.00	0.19
plotIndiv	0.30	0.00	0.29
plotLoadings	0.11	0.00	0.11
plotVar	0.56	0.00	0.57
pls	0.02	0.00	0.01
plsda	0.34	0.00	0.35
predict	0.16	0.02	0.17
rcc	0.00	0.01	0.01
selectVar	0.42	0.02	0.44
sipca	0.44	0.03	0.47
spca	3.26	0.05	3.31
spls	0.19	0.01	0.21
splsda	0.36	0.00	0.35
study_split	0	0	0
summary	0.01	0.00	0.02
tune	4.94	0.04	4.98
tune.block.splsda	0	0	0
tune.mint.splsda	2.61	0.00	2.63
tune.pca	0.19	0.02	0.20
tune.rcc	2.44	0.00	2.44
tune.spca	0.68	0.00	0.68
tune.spls	0	0	0
tune.splsda	5.27	0.01	5.28
tune.splslevel	1.05	0.00	1.05
unmap	0	0	0
vip	0.01	0.00	0.02
withinVariation	1.38	0.02	1.39
wrapper.rgcca	0.11	0.00	0.11
wrapper.sgcca	0.25	0.00	0.25

CHECK report for mixOmics on tokay1

Summary

Command output

Installation output

Tests output

Example timings