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This page was generated on 2022-01-19 13:08:56 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for timeOmics on machv2


To the developers/maintainers of the timeOmics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/timeOmics.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.

raw results

Package 1957/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
timeOmics 1.6.0  (landing page)
Antoine Bodein
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/timeOmics
git_branch: RELEASE_3_14
git_last_commit: 6d94bd4
git_last_commit_date: 2021-10-26 12:58:42 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: timeOmics
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings timeOmics_1.6.0.tar.gz
StartedAt: 2022-01-18 19:00:58 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 19:05:00 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 241.3 seconds
RetCode: 0
Status:   OK  
CheckDir: timeOmics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings timeOmics_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/timeOmics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘timeOmics/DESCRIPTION’ ... OK
* this is package ‘timeOmics’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘timeOmics’ can be installed ... OK
* checking installed package size ... OK
* 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
* 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 ... NOTE
.mutate_cluster: no visible binding for global variable ‘cluster’
.mutate_cluster: no visible binding for global variable ‘contrib.max’
check_legend.block.name: no visible global function definition for ‘is’
dmatrix.spearman.dissimilarity: no visible global function definition
  for ‘cor’
filter.getCluster: no visible binding for global variable ‘block’
filter.getCluster: no visible binding for global variable ‘cluster’
getCluster.block.pls: no visible binding for global variable ‘block’
getCluster.block.pls: no visible binding for global variable ‘molecule’
getCluster.block.pls: no visible binding for global variable ‘comp’
getCluster.block.spls: no visible binding for global variable ‘block’
getCluster.block.spls: no visible binding for global variable
  ‘molecule’
getCluster.block.spls: no visible binding for global variable ‘comp’
getCluster.mixo_pls: no visible binding for global variable ‘comp’
getCluster.mixo_spls: no visible binding for global variable ‘comp’
getCluster.pca: no visible binding for global variable ‘comp’
getCluster.spca: no visible binding for global variable ‘comp’
getNcomp: no visible global function definition for ‘is’
getUpDownCluster: no visible global function definition for ‘is’
get_MSE: no visible binding for global variable ‘feature’
get_MSE: no visible global function definition for ‘na.omit’
get_MSE: no visible binding for global variable ‘Y_i’
get_MSE: no visible binding for global variable ‘Y_hat’
get_MSE: no visible binding for global variable ‘error’
lmms.filter.lines: no visible global function definition for ‘is’
lmms.filter.lines: no visible global function definition for ‘slot’
lmms.filter.lines: no visible binding for global variable ‘feature’
lmms.filter.lines: no visible binding for global variable ‘BP.test’
lmms.filter.lines: no visible binding for global variable ‘MSE’
lmms.filter.lines: no visible binding for global variable ‘val’
plot.ncomp.tune.silhouette: no visible global function definition for
  ‘is’
plot.ncomp.tune.silhouette: no visible binding for global variable
  ‘ncomp’
plot.proportionality: no visible binding for global variable ‘cluster1’
plot.proportionality: no visible binding for global variable ‘value’
plot.proportionality: no visible binding for global variable
  ‘insideout’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘comp’
plot.spca.tune.silhouette: no visible binding for global variable ‘X’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘na.omit’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘contrib’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘value’
plotLong: no visible binding for global variable ‘block’
plotLong: no visible binding for global variable ‘new.block’
plotLong: no visible global function definition for ‘is’
plotLong: no visible binding for global variable ‘.’
plotLong: no visible binding for global variable ‘value’
plotLong: no visible binding for global variable ‘molecule’
proportionality: no visible global function definition for ‘is’
proportionality: no visible binding for global variable ‘molecule’
proportionality: no visible binding for global variable ‘cluster’
proportionality: no visible binding for global variable ‘.’
proportionality : <anonymous>: no visible binding for global variable
  ‘.’
proportionality: no visible binding for global variable ‘feature1’
proportionality: no visible binding for global variable ‘feature2’
proportionality: no visible binding for global variable ‘cluster1’
proportionality: no visible binding for global variable ‘cluster2’
proportionality: no visible global function definition for ‘na.omit’
remove.low.cv: no visible global function definition for ‘is’
remove.low.cv : <anonymous>: no visible global function definition for
  ‘sd’
sd_new: no visible global function definition for ‘sd’
silhouette: no visible binding for global variable ‘silhouette.coef’
stat_median: no visible binding for global variable ‘cluster1’
stat_median: no visible binding for global variable ‘cluster2’
stat_median: no visible binding for global variable ‘value’
stat_median: no visible global function definition for ‘median’
stat_median: no visible binding for global variable ‘Pvalue’
stat_median: no visible binding for global variable ‘na.omit’
tune.silhouette.get_choice_keepX: no visible global function definition
  for ‘na.omit’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘comp’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘direction’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.pos’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.neg’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘distance_from_origin’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.dir’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.value’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘Pval.value’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘distance_from_origin’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘.’
tune.silhouette.get_slopes: no visible global function definition for
  ‘is’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘origin’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘destination’
tune.silhouette.get_slopes: no visible binding for global variable ‘.’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘comp’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘direction’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘slope.pos’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘slope.neg’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘Z_score.pos’
tune.silhouette.get_slopes: no visible global function definition for
  ‘pnorm’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘Z_score.neg’
tuneCluster.block.spls: no visible binding for global variable
  ‘silhouette.coef’
tuneCluster.spca: no visible binding for global variable
  ‘silhouette.coef’
tuneCluster.spls: no visible binding for global variable
  ‘silhouette.coef’
unscale: no visible global function definition for ‘is’
Undefined global functions or variables:
  . BP.test MSE Pval.dir Pval.neg Pval.pos Pval.value Pvalue X Y_hat
  Y_i Z_score.neg Z_score.pos block cluster cluster1 cluster2 comp
  contrib contrib.max cor destination direction distance_from_origin
  error feature feature1 feature2 insideout is median molecule na.omit
  ncomp new.block origin pnorm sd silhouette.coef slope.neg slope.pos
  slot val value
Consider adding
  importFrom("methods", "is", "slot")
  importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
tuneCluster.block.spls 24.92  0.082  25.019
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/timeOmics.Rcheck/00check.log’
for details.



Installation output

timeOmics.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL timeOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘timeOmics’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '*' 
** help
*** installing help indices
*** copying figures
** 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 (timeOmics)

Tests output

timeOmics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(timeOmics)
Loading required package: mixOmics
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.18.1
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("timeOmics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 263 ]
> 
> proc.time()
   user  system elapsed 
 95.069   0.726  95.836 

Example timings

timeOmics.Rcheck/timeOmics-Ex.timings

nameusersystemelapsed
getCluster0.9020.0280.931
getNcomp4.7900.0924.892
getSilhouette3.4320.0133.448
getUpDownCluster0.5640.0070.572
get_demo_cluster0.4150.0070.422
get_demo_silhouette0.0020.0010.003
lmms.filter.lines0.2430.0110.255
plotLong3.7610.0193.787
proportionality2.8920.0542.950
remove.low.cv0.0030.0020.004
tuneCluster.block.spls24.920 0.08225.019
tuneCluster.spca3.5920.0133.609
tuneCluster.spls4.7860.0134.802
unscale0.0010.0000.001