| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 1254/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mistyR 1.8.1 (landing page) Jovan Tanevski
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
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. |
| 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 |
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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
###
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* 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.
mistyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mistyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
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
Training models
Training models
Training models
Training models
Training models
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Training models
Training models
Training models
Training models
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
Training models
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
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Generating paraview
Training models
Generating paraview
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
Training models
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
Training models
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
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Generating paraview
Training models
Training models
Training models
Training models
Training models
Training models
Training models
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Training models
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Training models
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Training models
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Training models
Generating paraview
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Generating paraview
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Generating paraview
Generating paraview
Training models
Generating paraview
Training models
Generating paraview
Training models
Collecting improvements
Collecting contributions
Collecting importances
Aggregating
Aggregating subset
Generating paraview
Training models
Generating paraview
Training models
Generating paraview
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
394.792 8.309 621.603
mistyR.Rcheck/mistyR-Ex.timings
| name | user | system | elapsed |