Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:18 -0000 (Wed, 08 Feb 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" | 4164 |
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Package 1371/2164 | 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: 2023-02-07 10:10:56 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 10:28:21 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 1044.6 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_scores 55.993 0.120 56.142 get_feature_selection_optimal_number_of_features 55.318 0.044 55.375 get_partition_agreement_scores 38.832 0.036 38.920 get_cluster_voting_memberships 37.720 1.086 45.345 get_cluster_voting_k_votes 38.067 0.304 41.571 get_cluster_voting_scores 38.292 0.049 38.343 get_cluster_voting_metric_votes 37.240 0.354 41.089 plot_feature_selection 37.236 0.064 37.358 plot_partition_agreement 37.131 0.056 37.222 get_sample_memberships 36.255 0.064 36.337 plot_signature_feature 36.225 0.056 36.291 get_feature_selection_optimal_features 34.849 0.089 34.940 get_signature_feature_coefs 34.736 0.060 34.881 omada 29.810 0.040 29.900 plot_cluster_voting 27.473 0.048 27.572 get_optimal_number_of_features 13.239 0.012 13.255 get_optimal_features 12.620 0.024 12.650 plot_average_stabilities 12.593 0.016 12.620 get_optimal_memberships 11.842 0.000 11.846 get_optimal_parameter_used 11.180 0.024 11.282 get_optimal_stability_score 10.371 0.020 10.402 featureSelection 8.839 0.008 8.856 get_average_feature_k_stabilities 7.366 0.008 7.616 * 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 95.787 0.328 98.115
omada.Rcheck/omada-Ex.timings
name | user | system | elapsed | |
clusterVoting | 2.129 | 0.020 | 2.363 | |
clusteringMethodSelection | 1.287 | 0.004 | 1.294 | |
feasibilityAnalysis | 1.764 | 0.008 | 1.774 | |
feasibilityAnalysisDataBased | 3.471 | 0.036 | 3.526 | |
featureSelection | 8.839 | 0.008 | 8.856 | |
geneSignatures | 1.212 | 0.036 | 1.259 | |
get_agreement_scores | 0.203 | 0.004 | 0.206 | |
get_average_feature_k_stabilities | 7.366 | 0.008 | 7.616 | |
get_average_stabilities_per_k | 1.227 | 0.008 | 1.609 | |
get_average_stability | 1.278 | 0.004 | 1.391 | |
get_cluster_memberships_k | 0.370 | 0.004 | 0.473 | |
get_cluster_voting_k_votes | 38.067 | 0.304 | 41.571 | |
get_cluster_voting_memberships | 37.720 | 1.086 | 45.345 | |
get_cluster_voting_metric_votes | 37.240 | 0.354 | 41.089 | |
get_cluster_voting_scores | 38.292 | 0.049 | 38.343 | |
get_coefficient_dataset | 0.602 | 0.004 | 0.606 | |
get_feature_selection_optimal_features | 34.849 | 0.089 | 34.940 | |
get_feature_selection_optimal_number_of_features | 55.318 | 0.044 | 55.375 | |
get_feature_selection_scores | 55.993 | 0.120 | 56.142 | |
get_generated_dataset | 3.851 | 0.012 | 3.865 | |
get_internal_metric_scores | 0.366 | 0.000 | 0.366 | |
get_max_stability | 1.223 | 0.004 | 1.228 | |
get_metric_votes_k | 0.361 | 0.004 | 0.365 | |
get_optimal_features | 12.620 | 0.024 | 12.650 | |
get_optimal_memberships | 11.842 | 0.000 | 11.846 | |
get_optimal_number_of_features | 13.239 | 0.012 | 13.255 | |
get_optimal_parameter_used | 11.180 | 0.024 | 11.282 | |
get_optimal_stability_score | 10.371 | 0.020 | 10.402 | |
get_partition_agreement_scores | 38.832 | 0.036 | 38.920 | |
get_sample_memberships | 36.255 | 0.064 | 36.337 | |
get_signature_feature_coefs | 34.736 | 0.060 | 34.881 | |
get_vote_frequencies_k | 0.362 | 0.003 | 0.366 | |
omada | 29.81 | 0.04 | 29.90 | |
optimalClustering | 0.534 | 0.008 | 0.541 | |
partitionAgreement | 0.414 | 0.008 | 0.422 | |
plot_average_stabilities | 12.593 | 0.016 | 12.620 | |
plot_cluster_voting | 27.473 | 0.048 | 27.572 | |
plot_feature_selection | 37.236 | 0.064 | 37.358 | |
plot_partition_agreement | 37.131 | 0.056 | 37.222 | |
plot_signature_feature | 36.225 | 0.056 | 36.291 | |
plot_top30percent_coefficients | 0.940 | 0.004 | 0.944 | |
plot_vote_frequencies | 0.602 | 0.012 | 0.614 | |
toy_gene_memberships | 0.012 | 0.008 | 0.023 | |
toy_genes | 0.002 | 0.000 | 0.001 | |