Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2024-12-23 11:44 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2136/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
timeOmics 1.19.0  (landing page)
Antoine Bodein
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/timeOmics
git_branch: devel
git_last_commit: 6546b5f
git_last_commit_date: 2024-10-29 10:45:29 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for timeOmics on lconway

To the developers/maintainers of the timeOmics package:
- 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 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.

raw results


Summary

Package: timeOmics
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2024-12-22 23:46:32 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 23:49:38 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 185.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: timeOmics.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/timeOmics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘timeOmics/DESCRIPTION’ ... OK
* this is package ‘timeOmics’ version ‘1.19.0’
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
getCluster:
  function(X, user.block, user.cluster)
getCluster.UpDown:
  function(X, user.block, user.cluster, .by, .preserve, ...)

filter:
  function(.data, ..., .by, .preserve)
filter.cluster.df:
  function(.data, user.block, user.cluster)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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.cluster.df: no visible binding for global variable ‘block’
filter.cluster.df: 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’
lmms.filter.lines: no visible global function definition for ‘all_of’
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 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’
to_lr2phs: no visible global function definition for ‘var’
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: no visible global function definition
  for ‘na.omit’
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 all_of 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 var
Consider adding
  importFrom("methods", "is", "slot")
  importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd", "var")
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getNcomp.Rd: silhouette
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘timeOmics.simdata’
Undocumented data sets:
  ‘timeOmics.simdata’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 14.443   0.13  14.684
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/timeOmics.Rcheck/00check.log’
for details.


Installation output

timeOmics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 6.31.0
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("timeOmics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 263 ]
> 
> proc.time()
   user  system elapsed 
 67.983   0.862  69.235 

Example timings

timeOmics.Rcheck/timeOmics-Ex.timings

nameusersystemelapsed
getCluster0.4080.0090.419
getNcomp3.2130.0723.304
getSilhouette1.9850.0162.019
getUpDownCluster0.3840.0100.397
get_demo_cluster0.2540.0030.259
get_demo_silhouette0.0020.0010.002
lmms.filter.lines0.1700.0110.182
plotLong2.6850.0522.765
proportionality3.2590.0353.321
remove.low.cv0.0020.0010.002
tuneCluster.block.spls14.443 0.13014.684
tuneCluster.spca2.2040.0212.242
tuneCluster.spls2.6760.0172.703
unscale0.0010.0000.001