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This page was generated on 2024-03-28 11:32:26 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 1441/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.4.0 (landing page) Sokratis Kariotis
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the omada 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: omada |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omada.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omada_1.4.0.tar.gz |
StartedAt: 2024-03-27 21:15:55 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:29:01 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 786.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omada.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omada_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/omada.Rcheck’ * using R version 4.3.3 (2024-02-29) * 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 Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'pdfCluster', 'kernlab', 'fpc', 'Rcpp', 'diceR', 'ggplot2', 'reshape', 'genieclust', 'clValid', 'glmnet', 'dplyr' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘omada’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘clValid’ A package should be listed in only one of these fields. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘genieclust’ ‘glmnet’ ‘kernlab’ ‘reshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Index.15and28: no visible global function definition for ‘dist’ Index.15and28: no visible global function definition for ‘as.dist’ Index.sPlussMoins: no visible global function definition for ‘dist’ Index.sPlussMoins: no visible global function definition for ‘as.dist’ Index.sPlussMoins: no visible global function definition for ‘median’ Indice.cindex: no visible global function definition for ‘dist’ clusterVoting: no visible global function definition for ‘calinhara’ clusterVoting: no visible global function definition for ‘generalised_dunn_index’ clusterVoting: no visible global function definition for ‘silhouette_index’ clusterVoting: no visible global function definition for ‘negated_davies_bouldin_index’ clusterVoting: no visible binding for global variable ‘k’ clusterVoting: no visible binding for global variable ‘Frequency’ clusteringMethodSelection: no visible binding for global variable ‘value’ clusteringMethodSelection: no visible binding for global variable ‘methods’ featureSelection: no visible binding for global variable ‘featureSet’ featureSelection: no visible binding for global variable ‘means’ geneSignatures: no visible global function definition for ‘where’ geneSignatures: no visible binding for global variable ‘features’ geneSignatures: no visible binding for global variable ‘value’ geneSignatures: no visible binding for global variable ‘variable’ Undefined global functions or variables: Frequency as.dist calinhara dist featureSet features generalised_dunn_index k means median methods negated_davies_bouldin_index silhouette_index value variable where Consider adding importFrom("stats", "as.dist", "dist", "median") importFrom("utils", "methods") 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 LazyData ... 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 get_feature_selection_scores 50.250 1.660 52.115 get_feature_selection_optimal_number_of_features 47.206 1.698 48.983 plot_signature_feature 37.146 1.218 38.420 plot_partition_agreement 33.877 1.272 35.305 get_partition_agreement_scores 32.665 1.123 33.980 get_signature_feature_coefs 32.614 1.062 33.725 get_cluster_voting_k_votes 32.479 1.136 33.656 get_feature_selection_optimal_features 32.124 1.323 33.515 get_cluster_voting_memberships 31.711 1.174 32.902 get_sample_memberships 31.383 0.957 32.358 plot_feature_selection 30.437 1.237 31.745 get_cluster_voting_metric_votes 30.332 1.259 31.742 get_cluster_voting_scores 30.345 1.120 31.521 omada 24.211 0.805 25.079 plot_cluster_voting 23.621 0.885 24.757 get_optimal_number_of_features 10.331 0.365 10.712 get_optimal_features 10.301 0.273 10.616 plot_average_stabilities 10.218 0.331 10.586 featureSelection 8.996 0.276 9.280 get_optimal_parameter_used 8.808 0.299 9.109 get_optimal_memberships 8.379 0.193 8.587 get_optimal_stability_score 8.184 0.293 8.480 get_average_feature_k_stabilities 5.325 0.147 5.477 clusterVoting 4.775 0.548 5.340 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/omada.Rcheck/00check.log’ for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘omada’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (omada)
omada.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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(omada) Loading required package: pdfCluster pdfCluster 1.0-4 Loading required package: kernlab Loading required package: fpc Loading required package: Rcpp Loading required package: diceR Loading required package: ggplot2 Attaching package: 'ggplot2' The following object is masked from 'package:kernlab': alpha Loading required package: reshape Loading required package: genieclust Loading required package: clValid Loading required package: cluster Loading required package: glmnet Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:reshape': expand Loaded glmnet 4.1-8 Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:reshape': rename The following object is masked from 'package:pdfCluster': groups The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("omada") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 86.937 3.600 90.961
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 4.775 | 0.548 | 5.340 | |
clusteringMethodSelection | 1.303 | 0.065 | 1.378 | |
feasibilityAnalysis | 1.022 | 0.017 | 1.039 | |
feasibilityAnalysisDataBased | 3.127 | 0.174 | 3.302 | |
featureSelection | 8.996 | 0.276 | 9.280 | |
geneSignatures | 0.838 | 0.024 | 0.863 | |
get_agreement_scores | 0.193 | 0.005 | 0.198 | |
get_average_feature_k_stabilities | 5.325 | 0.147 | 5.477 | |
get_average_stabilities_per_k | 0.736 | 0.020 | 0.756 | |
get_average_stability | 0.674 | 0.004 | 0.678 | |
get_cluster_memberships_k | 0.978 | 0.208 | 1.187 | |
get_cluster_voting_k_votes | 32.479 | 1.136 | 33.656 | |
get_cluster_voting_memberships | 31.711 | 1.174 | 32.902 | |
get_cluster_voting_metric_votes | 30.332 | 1.259 | 31.742 | |
get_cluster_voting_scores | 30.345 | 1.120 | 31.521 | |
get_coefficient_dataset | 0.454 | 0.008 | 0.461 | |
get_feature_selection_optimal_features | 32.124 | 1.323 | 33.515 | |
get_feature_selection_optimal_number_of_features | 47.206 | 1.698 | 48.983 | |
get_feature_selection_scores | 50.250 | 1.660 | 52.115 | |
get_generated_dataset | 2.331 | 0.050 | 2.389 | |
get_internal_metric_scores | 0.621 | 0.131 | 0.756 | |
get_max_stability | 0.711 | 0.010 | 0.723 | |
get_metric_votes_k | 0.992 | 0.176 | 1.189 | |
get_optimal_features | 10.301 | 0.273 | 10.616 | |
get_optimal_memberships | 8.379 | 0.193 | 8.587 | |
get_optimal_number_of_features | 10.331 | 0.365 | 10.712 | |
get_optimal_parameter_used | 8.808 | 0.299 | 9.109 | |
get_optimal_stability_score | 8.184 | 0.293 | 8.480 | |
get_partition_agreement_scores | 32.665 | 1.123 | 33.980 | |
get_sample_memberships | 31.383 | 0.957 | 32.358 | |
get_signature_feature_coefs | 32.614 | 1.062 | 33.725 | |
get_vote_frequencies_k | 0.965 | 0.143 | 1.109 | |
omada | 24.211 | 0.805 | 25.079 | |
optimalClustering | 0.073 | 0.006 | 0.079 | |
partitionAgreement | 0.398 | 0.019 | 0.417 | |
plot_average_stabilities | 10.218 | 0.331 | 10.586 | |
plot_cluster_voting | 23.621 | 0.885 | 24.757 | |
plot_feature_selection | 30.437 | 1.237 | 31.745 | |
plot_partition_agreement | 33.877 | 1.272 | 35.305 | |
plot_signature_feature | 37.146 | 1.218 | 38.420 | |
plot_top30percent_coefficients | 0.657 | 0.009 | 0.665 | |
plot_vote_frequencies | 1.091 | 0.166 | 1.257 | |
toy_gene_memberships | 0.017 | 0.006 | 0.024 | |
toy_genes | 0.001 | 0.003 | 0.003 | |