Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the omada package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1373/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
omada 1.1.0 (landing page) Sokratis Kariotis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: omada |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings omada_1.1.0.tar.gz |
StartedAt: 2023-02-28 10:13:55 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 10:31:25 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1049.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: omada.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings omada_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.1.0’ * 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', 'clusterCrit', '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 ... OK * 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’ ‘clusterCrit’ ‘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 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 featureSet features k means methods value variable where Consider adding 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_optimal_number_of_features 55.638 0.144 57.795 get_feature_selection_scores 52.953 0.140 60.622 get_cluster_voting_memberships 38.950 0.151 43.267 get_partition_agreement_scores 38.811 0.136 42.759 get_cluster_voting_k_votes 38.334 0.571 40.468 plot_partition_agreement 38.538 0.088 38.628 get_sample_memberships 37.920 0.088 40.280 get_cluster_voting_metric_votes 37.334 0.256 39.574 get_signature_feature_coefs 36.835 0.352 38.826 get_feature_selection_optimal_features 35.784 0.156 39.536 get_cluster_voting_scores 35.438 0.184 36.933 plot_signature_feature 34.597 0.084 34.682 plot_feature_selection 34.309 0.056 34.366 omada 29.245 0.084 30.495 plot_cluster_voting 28.376 0.064 28.440 get_optimal_number_of_features 13.367 0.016 13.845 get_optimal_features 13.090 0.008 13.098 plot_average_stabilities 12.626 0.048 13.016 get_optimal_parameter_used 10.724 0.008 10.842 get_optimal_stability_score 10.412 0.032 11.326 get_optimal_memberships 9.952 0.048 10.000 featureSelection 9.461 0.204 10.882 get_average_feature_k_stabilities 6.096 0.160 6.428 * 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 ... ‘omada-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck/00check.log’ for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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: clusterCrit 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 4.1-6 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 39 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 39 ] > > proc.time() user system elapsed 97.485 1.175 98.645
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 2.149 | 0.044 | 2.353 | |
clusteringMethodSelection | 1.289 | 0.000 | 1.409 | |
feasibilityAnalysis | 1.808 | 0.004 | 1.956 | |
feasibilityAnalysisDataBased | 3.796 | 0.108 | 4.056 | |
featureSelection | 9.461 | 0.204 | 10.882 | |
geneSignatures | 1.252 | 0.024 | 1.464 | |
get_agreement_scores | 0.210 | 0.008 | 0.313 | |
get_average_feature_k_stabilities | 6.096 | 0.160 | 6.428 | |
get_average_stabilities_per_k | 1.261 | 0.000 | 1.371 | |
get_average_stability | 1.252 | 0.004 | 1.257 | |
get_cluster_memberships_k | 0.385 | 0.004 | 0.440 | |
get_cluster_voting_k_votes | 38.334 | 0.571 | 40.468 | |
get_cluster_voting_memberships | 38.950 | 0.151 | 43.267 | |
get_cluster_voting_metric_votes | 37.334 | 0.256 | 39.574 | |
get_cluster_voting_scores | 35.438 | 0.184 | 36.933 | |
get_coefficient_dataset | 0.589 | 0.008 | 0.597 | |
get_feature_selection_optimal_features | 35.784 | 0.156 | 39.536 | |
get_feature_selection_optimal_number_of_features | 55.638 | 0.144 | 57.795 | |
get_feature_selection_scores | 52.953 | 0.140 | 60.622 | |
get_generated_dataset | 3.914 | 0.012 | 4.542 | |
get_internal_metric_scores | 0.385 | 0.004 | 0.789 | |
get_max_stability | 1.281 | 0.012 | 1.741 | |
get_metric_votes_k | 0.376 | 0.020 | 0.412 | |
get_optimal_features | 13.090 | 0.008 | 13.098 | |
get_optimal_memberships | 9.952 | 0.048 | 10.000 | |
get_optimal_number_of_features | 13.367 | 0.016 | 13.845 | |
get_optimal_parameter_used | 10.724 | 0.008 | 10.842 | |
get_optimal_stability_score | 10.412 | 0.032 | 11.326 | |
get_partition_agreement_scores | 38.811 | 0.136 | 42.759 | |
get_sample_memberships | 37.920 | 0.088 | 40.280 | |
get_signature_feature_coefs | 36.835 | 0.352 | 38.826 | |
get_vote_frequencies_k | 0.361 | 0.008 | 0.368 | |
omada | 29.245 | 0.084 | 30.495 | |
optimalClustering | 0.561 | 0.000 | 0.561 | |
partitionAgreement | 0.445 | 0.016 | 0.478 | |
plot_average_stabilities | 12.626 | 0.048 | 13.016 | |
plot_cluster_voting | 28.376 | 0.064 | 28.440 | |
plot_feature_selection | 34.309 | 0.056 | 34.366 | |
plot_partition_agreement | 38.538 | 0.088 | 38.628 | |
plot_signature_feature | 34.597 | 0.084 | 34.682 | |
plot_top30percent_coefficients | 0.898 | 0.000 | 0.898 | |
plot_vote_frequencies | 0.573 | 0.012 | 0.585 | |
toy_gene_memberships | 0.017 | 0.000 | 0.018 | |
toy_genes | 0.001 | 0.000 | 0.002 | |