Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-09-24 22:59 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
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 1457/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.6.0 (landing page) Sokratis Kariotis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | 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: 1.6.0 |
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_1.6.0.tar.gz |
StartedAt: 2024-09-24 04:43:01 -0400 (Tue, 24 Sep 2024) |
EndedAt: 2024-09-24 04:55:09 -0400 (Tue, 24 Sep 2024) |
EllapsedTime: 727.4 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_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/omada.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.6.0’ * 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 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘dplyr’ ‘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’ Undefined global functions or variables: Frequency as.dist calinhara dist featureSet generalised_dunn_index k means median methods negated_davies_bouldin_index silhouette_index value 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 48.207 1.804 50.286 get_feature_selection_optimal_number_of_features 47.641 1.918 49.670 get_cluster_voting_k_votes 34.636 0.787 35.635 get_cluster_voting_memberships 33.967 0.984 35.354 get_cluster_voting_scores 34.019 0.709 35.133 get_feature_selection_optimal_features 32.780 0.935 33.879 plot_partition_agreement 32.612 0.936 34.078 plot_feature_selection 31.942 1.398 33.554 get_sample_memberships 32.485 0.652 33.272 get_partition_agreement_scores 32.381 0.658 33.199 get_cluster_voting_metric_votes 29.307 0.749 30.408 omada 26.160 0.496 26.771 plot_cluster_voting 25.368 0.734 26.223 get_optimal_features 10.310 0.178 10.556 get_optimal_number_of_features 10.331 0.153 10.620 get_optimal_stability_score 10.384 0.100 10.527 plot_average_stabilities 10.083 0.347 10.477 get_optimal_parameter_used 9.482 0.110 9.667 featureSelection 8.503 0.126 8.683 get_optimal_memberships 8.401 0.196 8.632 get_average_feature_k_stabilities 5.128 0.082 5.274 * 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-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 89.832 2.511 93.303
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 4.302 | 0.545 | 4.864 | |
clusteringMethodSelection | 1.328 | 0.047 | 1.380 | |
feasibilityAnalysis | 1.106 | 0.012 | 1.122 | |
feasibilityAnalysisDataBased | 3.353 | 0.089 | 3.471 | |
featureSelection | 8.503 | 0.126 | 8.683 | |
get_agreement_scores | 0.188 | 0.006 | 0.196 | |
get_average_feature_k_stabilities | 5.128 | 0.082 | 5.274 | |
get_average_stabilities_per_k | 0.793 | 0.010 | 0.806 | |
get_average_stability | 0.783 | 0.006 | 0.791 | |
get_cluster_memberships_k | 0.984 | 0.137 | 1.130 | |
get_cluster_voting_k_votes | 34.636 | 0.787 | 35.635 | |
get_cluster_voting_memberships | 33.967 | 0.984 | 35.354 | |
get_cluster_voting_metric_votes | 29.307 | 0.749 | 30.408 | |
get_cluster_voting_scores | 34.019 | 0.709 | 35.133 | |
get_feature_selection_optimal_features | 32.780 | 0.935 | 33.879 | |
get_feature_selection_optimal_number_of_features | 47.641 | 1.918 | 49.670 | |
get_feature_selection_scores | 48.207 | 1.804 | 50.286 | |
get_generated_dataset | 3.025 | 0.030 | 3.070 | |
get_internal_metric_scores | 0.989 | 0.120 | 1.119 | |
get_max_stability | 0.772 | 0.017 | 0.792 | |
get_metric_votes_k | 0.982 | 0.165 | 1.158 | |
get_optimal_features | 10.310 | 0.178 | 10.556 | |
get_optimal_memberships | 8.401 | 0.196 | 8.632 | |
get_optimal_number_of_features | 10.331 | 0.153 | 10.620 | |
get_optimal_parameter_used | 9.482 | 0.110 | 9.667 | |
get_optimal_stability_score | 10.384 | 0.100 | 10.527 | |
get_partition_agreement_scores | 32.381 | 0.658 | 33.199 | |
get_sample_memberships | 32.485 | 0.652 | 33.272 | |
get_vote_frequencies_k | 0.971 | 0.122 | 1.097 | |
omada | 26.160 | 0.496 | 26.771 | |
optimalClustering | 0.069 | 0.005 | 0.074 | |
partitionAgreement | 0.383 | 0.033 | 0.416 | |
plot_average_stabilities | 10.083 | 0.347 | 10.477 | |
plot_cluster_voting | 25.368 | 0.734 | 26.223 | |
plot_feature_selection | 31.942 | 1.398 | 33.554 | |
plot_partition_agreement | 32.612 | 0.936 | 34.078 | |
plot_vote_frequencies | 1.121 | 0.218 | 1.348 | |
toy_gene_memberships | 0.017 | 0.006 | 0.024 | |
toy_genes | 0.001 | 0.003 | 0.004 | |