Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 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 1260/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mistyR 1.13.0 (landing page) Jovan Tanevski
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.13.0 |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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 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 333.92 39.78 376.85
mistyR.Rcheck/mistyR-Ex.timings
name | user | system | elapsed | |
add_juxtaview | 6.94 | 2.23 | 9.25 | |
add_paraview | 26.70 | 4.99 | 31.67 | |
add_views | 0.02 | 0.00 | 0.02 | |
clear_cache | 0 | 0 | 0 | |
collect_results | 145.75 | 25.42 | 171.48 | |
create_initial_view | 0.45 | 0.12 | 0.58 | |
create_view | 6.11 | 0.22 | 6.33 | |
extract_signature | 2.81 | 0.58 | 3.36 | |
filter_views | 1.32 | 0.08 | 1.39 | |
plot_contrast_heatmap | 3.42 | 0.58 | 3.91 | |
plot_contrast_results | 3.65 | 0.44 | 4.25 | |
plot_improvement_stats | 5.61 | 1.09 | 6.56 | |
plot_interaction_communities | 2.88 | 0.50 | 3.52 | |
plot_interaction_heatmap | 2.73 | 0.47 | 3.26 | |
plot_view_contributions | 2.82 | 0.45 | 3.33 | |
reexports | 46.98 | 7.88 | 54.94 | |
remove_views | 34.37 | 5.82 | 40.20 | |
rename_view | 0.02 | 0.00 | 0.02 | |
run_misty | 48.48 | 7.44 | 56.39 | |
select_markers | 0.32 | 0.05 | 0.39 | |