Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-23 11:40 -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 1278/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mistyR 1.15.0  (landing page)
Jovan Tanevski
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/mistyR
git_branch: devel
git_last_commit: 89f8c5d
git_last_commit_date: 2024-10-29 11:00:49 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for mistyR on nebbiolo1

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: 1.15.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mistyR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mistyR_1.15.0.tar.gz
StartedAt: 2024-12-22 23:58:07 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-23 00:11:04 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 777.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: mistyR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mistyR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mistyR_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mistyR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 loading without being on the library search path ... 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 132.167  6.579 138.728
reexports        45.011  2.258  47.252
run_misty        43.643  2.210  45.840
remove_views     25.416  0.353  25.773
add_paraview     20.596  0.096  20.698
add_juxtaview     6.151  0.106   6.257
create_view       5.677  0.030   5.710
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Generating paraview
  
  Generating paraview
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-misty.R:212:3'): k for cv , n.bags for bagging can be changed and approx works ──
  first.run < second.run is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/mistyR.Rcheck/00check.log’
for details.


Installation output

mistyR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mistyR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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.fail


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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Collecting importances

Aggregating

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Collecting improvements

Collecting contributions

Collecting importances

Aggregating

Training models

Collecting improvements

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Collecting importances

Aggregating

Training models

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

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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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Aggregating

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Aggregating

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Collecting importances

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Generating paraview

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Generating paraview

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Generating paraview

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Aggregating
Aggregating subset

Generating paraview

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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 1 | WARN 4 | SKIP 0 | PASS 172 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-misty.R:212:3'): k for cv , n.bags for bagging can be changed and approx works ──
first.run < second.run is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
Error: Test failures
Execution halted

Example timings

mistyR.Rcheck/mistyR-Ex.timings

nameusersystemelapsed
add_juxtaview6.1510.1066.257
add_paraview20.596 0.09620.698
add_views0.0090.0050.013
clear_cache0.0010.0010.002
collect_results132.167 6.579138.728
create_initial_view0.3500.0110.360
create_view5.6770.0305.710
extract_signature1.6720.2441.918
filter_views0.9650.0070.975
plot_contrast_heatmap2.2760.2352.515
plot_contrast_results2.3970.2392.637
plot_improvement_stats3.5870.4544.042
plot_interaction_communities1.9720.2762.251
plot_interaction_heatmap2.0190.2422.267
plot_view_contributions1.7780.2792.059
reexports45.011 2.25847.252
remove_views25.416 0.35325.773
rename_view0.0140.0020.016
run_misty43.643 2.21045.840
select_markers0.3160.0060.323