Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-02-06 12:53:39 -0500 (Tue, 06 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4631 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4373 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4400 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4336 |
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 1420/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.5.0 (landing page) Sokratis Kariotis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the omada package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omada.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: omada |
Version: 1.5.0 |
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_1.5.0.tar.gz |
StartedAt: 2024-02-06 06:22:43 -0500 (Tue, 06 Feb 2024) |
EndedAt: 2024-02-06 06:45:43 -0500 (Tue, 06 Feb 2024) |
EllapsedTime: 1380.9 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_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.5.0’ * 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 74.961 0.656 79.310 get_feature_selection_optimal_number_of_features 74.201 0.711 76.694 plot_partition_agreement 53.398 0.728 64.689 get_cluster_voting_k_votes 51.052 0.572 53.073 get_cluster_voting_memberships 51.016 0.527 52.702 plot_feature_selection 50.448 1.036 85.236 get_signature_feature_coefs 50.567 0.504 52.955 get_partition_agreement_scores 50.218 0.542 51.667 get_sample_memberships 49.740 0.527 51.895 get_cluster_voting_scores 49.791 0.468 50.859 plot_signature_feature 49.529 0.448 62.059 get_feature_selection_optimal_features 49.378 0.505 50.852 get_cluster_voting_metric_votes 48.475 0.551 49.459 omada 40.337 0.461 42.327 plot_cluster_voting 38.962 0.628 70.862 get_optimal_features 17.017 0.148 17.396 plot_average_stabilities 16.422 0.159 18.824 get_optimal_number_of_features 15.431 0.151 16.150 get_optimal_memberships 14.944 0.126 15.338 get_optimal_parameter_used 14.819 0.113 15.631 get_optimal_stability_score 14.216 0.117 15.045 featureSelection 12.430 0.162 12.672 get_average_feature_k_stabilities 8.657 0.087 8.801 clusterVoting 7.392 0.685 8.286 get_generated_dataset 5.858 0.027 6.001 feasibilityAnalysisDataBased 5.285 0.144 5.506 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/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/4.4-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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(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 143.014 2.020 181.389
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 7.392 | 0.685 | 8.286 | |
clusteringMethodSelection | 2.106 | 0.052 | 2.205 | |
feasibilityAnalysis | 2.688 | 0.036 | 2.759 | |
feasibilityAnalysisDataBased | 5.285 | 0.144 | 5.506 | |
featureSelection | 12.430 | 0.162 | 12.672 | |
geneSignatures | 1.774 | 0.012 | 1.809 | |
get_agreement_scores | 0.261 | 0.001 | 0.265 | |
get_average_feature_k_stabilities | 8.657 | 0.087 | 8.801 | |
get_average_stabilities_per_k | 1.880 | 0.011 | 1.899 | |
get_average_stability | 1.900 | 0.007 | 1.929 | |
get_cluster_memberships_k | 1.669 | 0.106 | 1.925 | |
get_cluster_voting_k_votes | 51.052 | 0.572 | 53.073 | |
get_cluster_voting_memberships | 51.016 | 0.527 | 52.702 | |
get_cluster_voting_metric_votes | 48.475 | 0.551 | 49.459 | |
get_cluster_voting_scores | 49.791 | 0.468 | 50.859 | |
get_coefficient_dataset | 0.822 | 0.004 | 0.830 | |
get_feature_selection_optimal_features | 49.378 | 0.505 | 50.852 | |
get_feature_selection_optimal_number_of_features | 74.201 | 0.711 | 76.694 | |
get_feature_selection_scores | 74.961 | 0.656 | 79.310 | |
get_generated_dataset | 5.858 | 0.027 | 6.001 | |
get_internal_metric_scores | 1.642 | 0.203 | 1.858 | |
get_max_stability | 1.901 | 0.009 | 1.925 | |
get_metric_votes_k | 1.649 | 0.154 | 1.821 | |
get_optimal_features | 17.017 | 0.148 | 17.396 | |
get_optimal_memberships | 14.944 | 0.126 | 15.338 | |
get_optimal_number_of_features | 15.431 | 0.151 | 16.150 | |
get_optimal_parameter_used | 14.819 | 0.113 | 15.631 | |
get_optimal_stability_score | 14.216 | 0.117 | 15.045 | |
get_partition_agreement_scores | 50.218 | 0.542 | 51.667 | |
get_sample_memberships | 49.740 | 0.527 | 51.895 | |
get_signature_feature_coefs | 50.567 | 0.504 | 52.955 | |
get_vote_frequencies_k | 1.636 | 0.097 | 1.754 | |
omada | 40.337 | 0.461 | 42.327 | |
optimalClustering | 0.176 | 0.006 | 0.184 | |
partitionAgreement | 0.544 | 0.009 | 0.562 | |
plot_average_stabilities | 16.422 | 0.159 | 18.824 | |
plot_cluster_voting | 38.962 | 0.628 | 70.862 | |
plot_feature_selection | 50.448 | 1.036 | 85.236 | |
plot_partition_agreement | 53.398 | 0.728 | 64.689 | |
plot_signature_feature | 49.529 | 0.448 | 62.059 | |
plot_top30percent_coefficients | 1.350 | 0.008 | 1.362 | |
plot_vote_frequencies | 2.043 | 0.159 | 2.249 | |
toy_gene_memberships | 0.027 | 0.008 | 0.035 | |
toy_genes | 0.002 | 0.004 | 0.007 | |