Kim-Anh Le Cao
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/mixOmics |
| Branch: RELEASE_3_8 |
| Last Commit: 240e862 |
| Last Changed Date: 2019-02-28 18:45:38 -0400 (Thu, 28 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:54 -0400 (Sat, 13 Apr 2019).
| Package 980/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mixOmics 6.6.2 Kim-Anh Le Cao
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mixOmics |
| Version: 6.6.2 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mixOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mixOmics_6.6.2.tar.gz |
| StartedAt: 2019-04-13 03:55:18 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:00:01 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 283.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mixOmics.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mixOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mixOmics_6.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/mixOmics.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '6.6.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 5.5Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 3.0Mb
* 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 or elapsed time > 5s
user system elapsed
background.predict 6.74 0.32 7.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
background.predict 6.78 0.06 6.84
* 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-3.8-bioc/meat/mixOmics.Rcheck/00check.log'
for details.
mixOmics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/mixOmics_6.6.2.tar.gz && rm -rf mixOmics.buildbin-libdir && mkdir mixOmics.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mixOmics.buildbin-libdir mixOmics_6.6.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mixOmics_6.6.2.zip && rm mixOmics_6.6.2.tar.gz mixOmics_6.6.2.zip
###
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install for i386
* installing *source* package 'mixOmics' ...
files 'R/MCVfold.R', 'R/multilevel.R', 'R/plotContrib.R', 'R/scatterutil.R', 'R/tune.multilevel.R', 'man/multilevel.Rd', 'man/plotContrib.Rd', 'man/scatterutil.Rd', 'man/tune.multilevel.Rd' are missing
files 'DESCRIPTION', 'NAMESPACE', 'NEWS', 'R/LOGOCV.R', 'R/bin.color.R', 'R/block.pls.R', 'R/block.plsda.R', 'R/block.spls.R', 'R/block.splsda.R', 'R/check_entry.R', 'R/cim.R', 'R/cimDiablo.R', 'R/circosPlot.R', 'R/color.GreenRed.R', 'R/color.jet.R', 'R/color.mixo.R', 'R/color.spectral.R', 'R/explained_variance.R', 'R/ica.def.par.R', 'R/image.tune.rcc.R', 'R/imageMap.R', 'R/imgCor.R', 'R/internal_graphicModule.R', 'R/internal_mint.block.R', 'R/internal_mint.block_helpers.R', 'R/internal_predict.DA.R', 'R/internal_wrapper.mint.R', 'R/internal_wrapper.mint.block.R', 'R/mat.rank.R', 'R/mint.block.pls.R', 'R/mint.block.plsda.R', 'R/mint.block.spls.R', 'R/mint.block.splsda.R', 'R/mint.pls.R', 'R/mint.plsda.R', 'R/mint.spls.R', 'R/mint.splsda.R', 'R/mixOmics.R', 'R/network.R', 'R/nipals.R', 'R/pca.R', 'R/pcasvd.R', 'R/perf.R', 'R/perf.diablo.R', 'R/perf.mint.splsda.R', 'R/plot.pca.R', 'R/plot.perf.R', 'R/plotArrow.R', 'R/plotDiablo.R', 'R/plotIndiv.R', 'R/plotIndiv.mint.R', 'R/plotIndiv.pca.R', 'R/plotIndiv.pls.R', 'R/plotIndiv.sgcca.R', 'R/plotLoadings.R', 'R/plotLoadings.mint.spls.R', 'R/plotLoadings.mint.splsda.R', 'R/plotLoadings.spls.R', 'R/plotLoadings.splsda.R', 'R/plotVar.R', 'R/pls.R', 'R/plsda.R', 'R/predict.mint.block.pls.R', 'R/print.methods.R', 'R/selectVar.R', 'R/sipca.R', 'R/spca.R', 'R/spls.R', 'R/splsda.R', 'R/summary.R', 'R/tune.R', 'R/tune.mint.splsda.R', 'R/tune.rcc.R', 'R/tune.splsda.R', 'R/tune.splslevel.R', 'R/vip.R', 'R/wrapper.ilr.R', 'R/wrapper.rgcca.R', 'R/wrapper.sgcca.R', 'R/zzz.R', 'data/Koren.16S.rda', 'data/datalist', 'data/diverse.16S.rda', 'data/vac18.simulated.rda', 'man/Koren.16S.Rd', 'man/block.pls.Rd', 'man/block.plsda.Rd', 'man/block.spls.Rd', 'man/block.splsda.Rd', 'man/breast.TCGA.Rd', 'man/breast.tumors.Rd', 'man/cim.Rd', 'man/cimDiablo.Rd', 'man/circosPlot.Rd', 'man/colors.Rd', 'man/diverse.16S.Rd', 'man/estim.regul.Rd', 'man/explained_variance.Rd', 'man/image.estim.regul.Rd', 'man/image.tune.rcc.Rd', 'man/imgCor.Rd', 'man/ipca.Rd', 'man/linnerud.Rd', 'man/liver.toxicity.Rd', 'man/logratio.transfo.Rd', 'man/map.Rd', 'man/mat.rank.Rd', 'man/mint.block.pls.Rd', 'man/mint.block.plsda.Rd', 'man/mint.block.spls.Rd', 'man/mint.block.splsda.Rd', 'man/mint.pls.Rd', 'man/mint.plsda.Rd', 'man/mint.spls.Rd', 'man/mint.splsda.Rd', 'man/mixOmics.Rd', 'man/multidrug.Rd', 'man/nearZeroVar.Rd', 'man/network.Rd', 'man/nipals.Rd', 'man/nutrimouse.Rd', 'man/pca.Rd', 'man/pcatune.Rd', 'man/perf.Rd', 'man/plot.perf.Rd', 'man/plot.rcc.Rd', 'man/plotArrow.Rd', 'man/plotDiablo.Rd', 'man/plotIndiv.Rd', 'man/plotLoadings.Rd', 'man/plotVar.Rd', 'man/pls.Rd', 'man/plsda.Rd', 'man/predict.Rd', 'man/print.methods.Rd', 'man/rcc.Rd', 'man/selectVar.Rd', 'man/sipca.Rd', 'man/spca.Rd', 'man/spls.Rd', 'man/splsda.Rd', 'man/srbct.Rd', 'man/stemcells.Rd', 'man/study_split.Rd', 'man/summary.Rd', 'man/tune.Rd', 'man/tune.mint.splsda.Rd', 'man/tune.pca.Rd', 'man/tune.rcc.Rd', 'man/tune.splsda.Rd', 'man/unmap.Rd', 'man/vac18.Rd', 'man/vac18.simulated.Rd', 'man/vip.Rd', 'man/withinVariation.Rd', 'man/wrapper.rgcca.Rd', 'man/wrapper.sgcca.Rd', 'man/yeast.Rd' have the wrong MD5 checksums
** 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
auroc html
background.predict 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
estim.regul html
explained_variance html
get.confusion_matrix html
image.estim.regul html
image.tune.rcc html
imgCor html
ipca html
linnerud html
liver.toxicity html
logratio.transfo 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 html
multidrug html
nearZeroVar html
network html
nipals html
nutrimouse html
pca html
pcatune html
perf html
plot.perf html
plot.rcc html
plot.tune html
plotArrow html
plotDiablo html
plotIndiv html
plotLoadings html
plotVar html
pls html
plsda html
predict html
print.methods html
rcc html
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.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
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'mixOmics' ...
files 'R/MCVfold.R', 'R/multilevel.R', 'R/plotContrib.R', 'R/scatterutil.R', 'R/tune.multilevel.R', 'man/multilevel.Rd', 'man/plotContrib.Rd', 'man/scatterutil.Rd', 'man/tune.multilevel.Rd' are missing
files 'DESCRIPTION', 'NAMESPACE', 'NEWS', 'R/LOGOCV.R', 'R/bin.color.R', 'R/block.pls.R', 'R/block.plsda.R', 'R/block.spls.R', 'R/block.splsda.R', 'R/check_entry.R', 'R/cim.R', 'R/cimDiablo.R', 'R/circosPlot.R', 'R/color.GreenRed.R', 'R/color.jet.R', 'R/color.mixo.R', 'R/color.spectral.R', 'R/explained_variance.R', 'R/ica.def.par.R', 'R/image.tune.rcc.R', 'R/imageMap.R', 'R/imgCor.R', 'R/internal_graphicModule.R', 'R/internal_mint.block.R', 'R/internal_mint.block_helpers.R', 'R/internal_predict.DA.R', 'R/internal_wrapper.mint.R', 'R/internal_wrapper.mint.block.R', 'R/mat.rank.R', 'R/mint.block.pls.R', 'R/mint.block.plsda.R', 'R/mint.block.spls.R', 'R/mint.block.splsda.R', 'R/mint.pls.R', 'R/mint.plsda.R', 'R/mint.spls.R', 'R/mint.splsda.R', 'R/mixOmics.R', 'R/network.R', 'R/nipals.R', 'R/pca.R', 'R/pcasvd.R', 'R/perf.R', 'R/perf.diablo.R', 'R/perf.mint.splsda.R', 'R/plot.pca.R', 'R/plot.perf.R', 'R/plotArrow.R', 'R/plotDiablo.R', 'R/plotIndiv.R', 'R/plotIndiv.mint.R', 'R/plotIndiv.pca.R', 'R/plotIndiv.pls.R', 'R/plotIndiv.sgcca.R', 'R/plotLoadings.R', 'R/plotLoadings.mint.spls.R', 'R/plotLoadings.mint.splsda.R', 'R/plotLoadings.spls.R', 'R/plotLoadings.splsda.R', 'R/plotVar.R', 'R/pls.R', 'R/plsda.R', 'R/predict.mint.block.pls.R', 'R/print.methods.R', 'R/selectVar.R', 'R/sipca.R', 'R/spca.R', 'R/spls.R', 'R/splsda.R', 'R/summary.R', 'R/tune.R', 'R/tune.mint.splsda.R', 'R/tune.rcc.R', 'R/tune.splsda.R', 'R/tune.splslevel.R', 'R/vip.R', 'R/wrapper.ilr.R', 'R/wrapper.rgcca.R', 'R/wrapper.sgcca.R', 'R/zzz.R', 'data/Koren.16S.rda', 'data/datalist', 'data/diverse.16S.rda', 'data/vac18.simulated.rda', 'man/Koren.16S.Rd', 'man/block.pls.Rd', 'man/block.plsda.Rd', 'man/block.spls.Rd', 'man/block.splsda.Rd', 'man/breast.TCGA.Rd', 'man/breast.tumors.Rd', 'man/cim.Rd', 'man/cimDiablo.Rd', 'man/circosPlot.Rd', 'man/colors.Rd', 'man/diverse.16S.Rd', 'man/estim.regul.Rd', 'man/explained_variance.Rd', 'man/image.estim.regul.Rd', 'man/image.tune.rcc.Rd', 'man/imgCor.Rd', 'man/ipca.Rd', 'man/linnerud.Rd', 'man/liver.toxicity.Rd', 'man/logratio.transfo.Rd', 'man/map.Rd', 'man/mat.rank.Rd', 'man/mint.block.pls.Rd', 'man/mint.block.plsda.Rd', 'man/mint.block.spls.Rd', 'man/mint.block.splsda.Rd', 'man/mint.pls.Rd', 'man/mint.plsda.Rd', 'man/mint.spls.Rd', 'man/mint.splsda.Rd', 'man/mixOmics.Rd', 'man/multidrug.Rd', 'man/nearZeroVar.Rd', 'man/network.Rd', 'man/nipals.Rd', 'man/nutrimouse.Rd', 'man/pca.Rd', 'man/pcatune.Rd', 'man/perf.Rd', 'man/plot.perf.Rd', 'man/plot.rcc.Rd', 'man/plotArrow.Rd', 'man/plotDiablo.Rd', 'man/plotIndiv.Rd', 'man/plotLoadings.Rd', 'man/plotVar.Rd', 'man/pls.Rd', 'man/plsda.Rd', 'man/predict.Rd', 'man/print.methods.Rd', 'man/rcc.Rd', 'man/selectVar.Rd', 'man/sipca.Rd', 'man/spca.Rd', 'man/spls.Rd', 'man/splsda.Rd', 'man/srbct.Rd', 'man/stemcells.Rd', 'man/study_split.Rd', 'man/summary.Rd', 'man/tune.Rd', 'man/tune.mint.splsda.Rd', 'man/tune.pca.Rd', 'man/tune.rcc.Rd', 'man/tune.splsda.Rd', 'man/unmap.Rd', 'man/vac18.Rd', 'man/vac18.simulated.Rd', 'man/vip.Rd', 'man/withinVariation.Rd', 'man/wrapper.rgcca.Rd', 'man/wrapper.sgcca.Rd', 'man/yeast.Rd' have the wrong MD5 checksums
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mixOmics' as mixOmics_6.6.2.zip
* DONE (mixOmics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mixOmics' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
mixOmics.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 6.6.2
Thank you for using mixOmics! Learn how to apply our methods with our tutorials on www.mixOmics.org, vignette and bookdown on https://github.com/mixOmicsTeam/mixOmics
Questions: email us at mixomics[at]math.univ-toulouse.fr
Bugs, Issues? https://github.com/mixOmicsTeam/mixOmics/issues
Cite us: citation('mixOmics')
>
> test_check("mixOmics")
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
3.48 0.23 3.70
|
mixOmics.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 6.6.2
Thank you for using mixOmics! Learn how to apply our methods with our tutorials on www.mixOmics.org, vignette and bookdown on https://github.com/mixOmicsTeam/mixOmics
Questions: email us at mixomics[at]math.univ-toulouse.fr
Bugs, Issues? https://github.com/mixOmicsTeam/mixOmics/issues
Cite us: citation('mixOmics')
>
> test_check("mixOmics")
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
3.29 0.26 3.54
|
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mixOmics.Rcheck/examples_i386/mixOmics-Ex.timings
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mixOmics.Rcheck/examples_x64/mixOmics-Ex.timings
|