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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1260/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mistyR 1.13.0  (landing page)
Jovan Tanevski
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/mistyR
git_branch: devel
git_last_commit: 142139d
git_last_commit_date: 2024-04-30 11:35:00 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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 palomino4

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: 1.13.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mistyR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mistyR_1.13.0.tar.gz
StartedAt: 2024-06-10 05:31:42 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:47:45 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 962.8 seconds
RetCode: 0
Status:   OK  
CheckDir: mistyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mistyR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mistyR_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mistyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mistyR' version '1.13.0'
* 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 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        145.75  25.42  171.48
run_misty               48.48   7.44   56.39
reexports               46.98   7.88   54.94
remove_views            34.37   5.82   40.20
add_paraview            26.70   4.99   31.67
add_juxtaview            6.94   2.23    9.25
plot_improvement_stats   5.61   1.09    6.56
create_view              6.11   0.22    6.33
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/mistyR.Rcheck/00check.log'
for details.


Installation output

mistyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mistyR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Generating paraview

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Generating paraview

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

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Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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Collecting improvements

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Collecting importances

Aggregating

Generating paraview

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Generating paraview

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Collecting improvements

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Generating paraview

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Collecting importances

Aggregating

Generating paraview

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Collecting improvements

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Collecting importances

Aggregating
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Generating paraview

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Training models

Collecting improvements

Collecting contributions

Collecting importances

Aggregating

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

Generating paraview

Computing triangulation

Generating juxtaview

Generating paraview

Computing triangulation

Generating paraview

Generating paraview

Generating paraview using 2 nearest neighbors per unit

Generating paraview

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

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
 333.92   39.78  376.85 

Example timings

mistyR.Rcheck/mistyR-Ex.timings

nameusersystemelapsed
add_juxtaview6.942.239.25
add_paraview26.70 4.9931.67
add_views0.020.000.02
clear_cache000
collect_results145.75 25.42171.48
create_initial_view0.450.120.58
create_view6.110.226.33
extract_signature2.810.583.36
filter_views1.320.081.39
plot_contrast_heatmap3.420.583.91
plot_contrast_results3.650.444.25
plot_improvement_stats5.611.096.56
plot_interaction_communities2.880.503.52
plot_interaction_heatmap2.730.473.26
plot_view_contributions2.820.453.33
reexports46.98 7.8854.94
remove_views34.37 5.8240.20
rename_view0.020.000.02
run_misty48.48 7.4456.39
select_markers0.320.050.39