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This page was generated on 2024-12-19 12:06 -0500 (Thu, 19 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4743
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4486
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4466
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 1285/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mistyR 1.14.0  (landing page)
Jovan Tanevski
Snapshot Date: 2024-12-16 13:00 -0500 (Mon, 16 Dec 2024)
git_url: https://git.bioconductor.org/packages/mistyR
git_branch: RELEASE_3_20
git_last_commit: b65acaa
git_last_commit_date: 2024-10-29 11:00:49 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for mistyR on merida1

To the developers/maintainers of the mistyR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mistyR.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: mistyR
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mistyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mistyR_1.14.0.tar.gz
StartedAt: 2024-12-17 05:53:27 -0500 (Tue, 17 Dec 2024)
EndedAt: 2024-12-17 06:20:09 -0500 (Tue, 17 Dec 2024)
EllapsedTime: 1601.6 seconds
RetCode: 0
Status:   OK  
CheckDir: mistyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mistyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mistyR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.14.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mistyR’ 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 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aggregate_results: no visible binding for global variable ‘measure’
aggregate_results: no visible binding for global variable ‘target’
aggregate_results: no visible binding for global variable ‘value’
aggregate_results: no visible binding for global variable ‘sd’
aggregate_results: no visible binding for global variable ‘view’
aggregate_results: no visible binding for global variable ‘.PT’
aggregate_results: no visible binding for global variable ‘Importance’
aggregate_results_subset: no visible binding for global variable ‘view’
aggregate_results_subset: no visible binding for global variable ‘.PT’
aggregate_results_subset: no visible binding for global variable
  ‘Importance’
bagged_mars_model: no visible binding for global variable ‘index’
bagged_mars_model: no visible binding for global variable ‘prediction’
collect_results : <anonymous>: no visible binding for global variable
  ‘intra.RMSE’
collect_results : <anonymous>: no visible binding for global variable
  ‘multi.RMSE’
collect_results : <anonymous>: no visible binding for global variable
  ‘multi.R2’
collect_results : <anonymous>: no visible binding for global variable
  ‘intra.R2’
collect_results: no visible binding for global variable ‘target’
collect_results : <anonymous>: no visible binding for global variable
  ‘target’
collect_results : <anonymous>: no visible binding for global variable
  ‘view’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘value’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Predictor’
collect_results : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Importance’
extract_signature: no visible binding for global variable ‘measure’
extract_signature: no visible binding for global variable ‘target’
extract_signature: no visible binding for global variable ‘ts’
extract_signature: no visible binding for global variable ‘view’
extract_signature: no visible binding for global variable ‘value’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Importance’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Target’
extract_signature : <anonymous>: no visible binding for global variable
  ‘ts’
extract_signature : <anonymous>: no visible binding for global variable
  ‘Predictor’
gradient_boosting_model: no visible binding for global variable ‘index’
linear_model: no visible binding for global variable ‘index’
mars_model: no visible binding for global variable ‘index’
mlp_model: no visible binding for global variable ‘index’
plot_contrast_heatmap: no visible binding for global variable ‘view’
plot_contrast_heatmap: no visible binding for global variable ‘measure’
plot_contrast_heatmap: no visible binding for global variable ‘target’
plot_contrast_heatmap: no visible binding for global variable ‘Target’
plot_contrast_heatmap: no visible binding for global variable
  ‘nsamples’
plot_contrast_heatmap: no visible binding for global variable
  ‘Predictor’
plot_contrast_heatmap: no visible binding for global variable
  ‘Importance’
plot_contrast_results: no visible binding for global variable ‘view’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘view’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Predictor’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Target’
plot_contrast_results: no visible binding for global variable ‘measure’
plot_contrast_results: no visible binding for global variable ‘target’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘nsamples’
plot_contrast_results : <anonymous>: no visible binding for global
  variable ‘Importance’
plot_improvement_stats: no visible binding for global variable ‘target’
plot_improvement_stats: no visible binding for global variable ‘sd’
plot_interaction_communities: no visible binding for global variable
  ‘nsamples’
plot_interaction_communities: no visible binding for global variable
  ‘Predictor’
plot_interaction_heatmap: no visible binding for global variable
  ‘measure’
plot_interaction_heatmap: no visible binding for global variable
  ‘target’
plot_interaction_heatmap: no visible binding for global variable
  ‘Target’
plot_interaction_heatmap: no visible binding for global variable
  ‘Importance’
plot_interaction_heatmap: no visible binding for global variable
  ‘Predictor’
plot_interaction_heatmap: no visible binding for global variable
  ‘total’
plot_view_contributions: no visible binding for global variable
  ‘measure’
plot_view_contributions: no visible binding for global variable
  ‘target’
plot_view_contributions: no visible binding for global variable
  ‘fraction’
plot_view_contributions: no visible binding for global variable ‘view’
run_misty : <anonymous>: no visible binding for global variable ‘p’
run_misty : <anonymous>: no visible binding for global variable
  ‘intra.RMSE’
run_misty : <anonymous>: no visible binding for global variable
  ‘multi.RMSE’
run_misty : <anonymous>: no visible binding for global variable
  ‘intra.R2’
run_misty : <anonymous>: no visible binding for global variable
  ‘multi.R2’
svm_model: no visible binding for global variable ‘index’
Undefined global functions or variables:
  .PT Importance Predictor Target fraction index intra.R2 intra.RMSE
  measure multi.R2 multi.RMSE nsamples p prediction sd target total ts
  value view
Consider adding
  importFrom("stats", "sd", "ts")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) collect_results.Rd:32: Lost braces; missing escapes or markup?
    32 |             for all performance measures for each {target} over all samples.}
       |                                                   ^
* 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
collect_results          280.731 27.450 321.564
run_misty                 92.487  9.696 104.022
reexports                 92.592  9.544 106.079
remove_views              57.945  8.525  67.387
add_paraview              46.713  5.215  52.883
add_juxtaview             13.614  0.710  14.497
create_view               14.015  0.080  14.795
plot_improvement_stats     8.308  0.411   9.057
plot_contrast_results      6.060  0.272   6.741
plot_contrast_heatmap      5.592  0.227   6.103
plot_interaction_heatmap   4.496  0.212   5.120
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck/00check.log’
for details.


Installation output

mistyR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘mistyR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (mistyR)

Tests output

mistyR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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(mistyR)
mistyR is able to run computationally intensive functions
  in parallel. Please consider specifying a future::plan(). For example by running
  future::plan(future::multisession) before calling mistyR functions.
> 
> test_check("mistyR")

Generating paraview

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null


Training models

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Aggregating

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Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

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Collecting importances

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Aggregating

Generating paraview

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Generating paraview

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Computing triangulation

Generating juxtaview

Generating paraview

Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Computing triangulation

Generating juxtaview

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Computing triangulation

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Computing triangulation

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Generating paraview using 2 nearest neighbors per unit

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Generating paraview
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
760.675   9.035 801.113 

Example timings

mistyR.Rcheck/mistyR-Ex.timings

nameusersystemelapsed
add_juxtaview13.614 0.71014.497
add_paraview46.713 5.21552.883
add_views0.0210.0200.040
clear_cache0.0040.0010.005
collect_results280.731 27.450321.564
create_initial_view0.7290.0210.786
create_view14.015 0.08014.795
extract_signature3.9390.2054.127
filter_views2.3520.0282.499
plot_contrast_heatmap5.5920.2276.103
plot_contrast_results6.0600.2726.741
plot_improvement_stats8.3080.4119.057
plot_interaction_communities4.2380.2124.670
plot_interaction_heatmap4.4960.2125.120
plot_view_contributions4.2270.2154.891
reexports 92.592 9.544106.079
remove_views57.945 8.52567.387
rename_view0.0310.0040.036
run_misty 92.487 9.696104.022
select_markers0.5530.0140.572