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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1254/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mistyR 1.8.1  (landing page)
Jovan Tanevski
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/mistyR
git_branch: RELEASE_3_17
git_last_commit: 21ac394
git_last_commit_date: 2023-07-26 04:25:02 -0400 (Wed, 26 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for mistyR on kjohnson2


To the developers/maintainers of the mistyR package:
- 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: 1.8.1
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_1.8.1.tar.gz
StartedAt: 2023-10-18 08:13:30 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 08:25:22 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 712.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: mistyR.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### 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_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mistyR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mistyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mistyR’ version ‘1.8.1’
* 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 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 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘mistyR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_juxtaview
> ### Title: Generate and add a juxtaview to the current view composition
> ### Aliases: add_juxtaview
> 
> ### ** Examples
> 
> # Create a view composition of an intraview and a juxtaview.
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> # get the expression data
> data("synthetic")
> expr <- synthetic[[1]] %>% select(-c(row, col, type))
> # get the coordinates for each cell
> pos <- synthetic[[1]] %>% select(row, col)
> 
> # compose
> misty.views <- create_initial_view(expr) %>% add_juxtaview(pos, neighbor.thr = 1.5)

Computing triangulation
Line from midpoint to circumcenter
does not intersect rectangle boundary!
But it HAS to!!!
Error in deldir::deldir(as.data.frame(positions)) : 
  Bailing out of dirseg.
Calls: %>% -> add_juxtaview -> <Anonymous>
Execution halted
* 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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mistyR.Rcheck/00check.log’
for details.


Installation output

mistyR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(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


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Computing triangulation

Generating juxtaview

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Generating paraview using 20 nearest neighbors per unit

Approximating RBF matrix using the Nystrom method

Computing triangulation

Generating juxtaview

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

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
394.792   8.309 621.603 

Example timings

mistyR.Rcheck/mistyR-Ex.timings

nameusersystemelapsed