Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1285/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mistyR 1.14.0 (landing page) Jovan Tanevski
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
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. |
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: 2024-12-20 06:09:35 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:36:16 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1600.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mistyR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 281.685 28.489 321.809 reexports 93.115 9.143 107.404 run_misty 92.740 9.125 103.751 remove_views 58.378 8.427 67.840 add_paraview 47.044 5.196 53.119 create_view 14.201 0.115 15.033 add_juxtaview 13.191 0.659 14.027 plot_improvement_stats 8.264 0.412 8.906 plot_contrast_results 5.788 0.244 6.522 plot_contrast_heatmap 5.374 0.221 5.837 plot_interaction_heatmap 4.520 0.210 5.225 * 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.
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)
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 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 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 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 760.377 8.901 798.574
mistyR.Rcheck/mistyR-Ex.timings
name | user | system | elapsed | |
add_juxtaview | 13.191 | 0.659 | 14.027 | |
add_paraview | 47.044 | 5.196 | 53.119 | |
add_views | 0.021 | 0.020 | 0.042 | |
clear_cache | 0.005 | 0.004 | 0.008 | |
collect_results | 281.685 | 28.489 | 321.809 | |
create_initial_view | 0.729 | 0.018 | 0.785 | |
create_view | 14.201 | 0.115 | 15.033 | |
extract_signature | 3.906 | 0.216 | 4.297 | |
filter_views | 2.331 | 0.028 | 2.485 | |
plot_contrast_heatmap | 5.374 | 0.221 | 5.837 | |
plot_contrast_results | 5.788 | 0.244 | 6.522 | |
plot_improvement_stats | 8.264 | 0.412 | 8.906 | |
plot_interaction_communities | 4.169 | 0.223 | 4.730 | |
plot_interaction_heatmap | 4.520 | 0.210 | 5.225 | |
plot_view_contributions | 4.231 | 0.216 | 4.939 | |
reexports | 93.115 | 9.143 | 107.404 | |
remove_views | 58.378 | 8.427 | 67.840 | |
rename_view | 0.031 | 0.004 | 0.035 | |
run_misty | 92.740 | 9.125 | 103.751 | |
select_markers | 0.599 | 0.017 | 0.621 | |