| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1471/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| omada 1.13.0 (landing page) Sokratis Kariotis
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings omada_1.13.0.tar.gz |
| StartedAt: 2025-11-05 01:58:17 -0500 (Wed, 05 Nov 2025) |
| EndedAt: 2025-11-05 02:12:34 -0500 (Wed, 05 Nov 2025) |
| EllapsedTime: 857.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: omada.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings omada_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/omada.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘omada/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omada’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 ... 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 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 loading without being on the library search path ... 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_optimal_number_of_features 44.064 0.123 44.188
get_feature_selection_scores 38.771 0.057 38.828
get_cluster_voting_metric_votes 29.572 0.103 29.680
get_partition_agreement_scores 29.441 0.066 29.509
get_cluster_voting_k_votes 29.400 0.100 29.505
plot_partition_agreement 29.439 0.029 29.471
get_cluster_voting_scores 28.524 0.079 28.602
get_feature_selection_optimal_features 28.423 0.103 28.526
get_sample_memberships 27.621 0.055 27.677
plot_feature_selection 27.607 0.021 27.630
get_cluster_voting_memberships 27.295 0.092 27.387
omada 22.311 0.051 22.437
plot_cluster_voting 20.945 0.007 20.960
get_optimal_features 10.110 0.035 10.146
plot_average_stabilities 9.701 0.005 9.750
get_optimal_number_of_features 8.930 0.006 8.936
get_optimal_stability_score 8.275 0.005 8.280
get_optimal_memberships 7.694 0.007 7.701
get_optimal_parameter_used 7.360 0.005 7.365
featureSelection 6.392 0.017 6.411
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/omada.Rcheck/00check.log’
for details.
omada.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL omada ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘omada’ ... ** this is package ‘omada’ version ‘1.13.0’ ** 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 4.1-10
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
94.619 0.773 102.124
omada.Rcheck/omada-Ex.timings
| name | user | system | elapsed | |
| clusterVoting | 3.738 | 0.068 | 3.807 | |
| clusteringMethodSelection | 1.511 | 0.018 | 1.530 | |
| feasibilityAnalysis | 1.156 | 0.035 | 1.192 | |
| feasibilityAnalysisDataBased | 2.916 | 0.082 | 2.997 | |
| featureSelection | 6.392 | 0.017 | 6.411 | |
| get_agreement_scores | 0.158 | 0.005 | 0.163 | |
| get_average_feature_k_stabilities | 4.568 | 0.077 | 4.647 | |
| get_average_stabilities_per_k | 0.773 | 0.002 | 0.775 | |
| get_average_stability | 0.777 | 0.041 | 0.818 | |
| get_cluster_memberships_k | 0.736 | 0.048 | 0.784 | |
| get_cluster_voting_k_votes | 29.400 | 0.100 | 29.505 | |
| get_cluster_voting_memberships | 27.295 | 0.092 | 27.387 | |
| get_cluster_voting_metric_votes | 29.572 | 0.103 | 29.680 | |
| get_cluster_voting_scores | 28.524 | 0.079 | 28.602 | |
| get_feature_selection_optimal_features | 28.423 | 0.103 | 28.526 | |
| get_feature_selection_optimal_number_of_features | 44.064 | 0.123 | 44.188 | |
| get_feature_selection_scores | 38.771 | 0.057 | 38.828 | |
| get_generated_dataset | 2.586 | 0.040 | 2.626 | |
| get_internal_metric_scores | 0.714 | 0.007 | 0.720 | |
| get_max_stability | 0.765 | 0.003 | 0.768 | |
| get_metric_votes_k | 0.721 | 0.019 | 0.741 | |
| get_optimal_features | 10.110 | 0.035 | 10.146 | |
| get_optimal_memberships | 7.694 | 0.007 | 7.701 | |
| get_optimal_number_of_features | 8.930 | 0.006 | 8.936 | |
| get_optimal_parameter_used | 7.360 | 0.005 | 7.365 | |
| get_optimal_stability_score | 8.275 | 0.005 | 8.280 | |
| get_partition_agreement_scores | 29.441 | 0.066 | 29.509 | |
| get_sample_memberships | 27.621 | 0.055 | 27.677 | |
| get_vote_frequencies_k | 0.938 | 0.004 | 0.942 | |
| omada | 22.311 | 0.051 | 22.437 | |
| optimalClustering | 0.111 | 0.001 | 0.135 | |
| partitionAgreement | 0.429 | 0.018 | 0.465 | |
| plot_average_stabilities | 9.701 | 0.005 | 9.750 | |
| plot_cluster_voting | 20.945 | 0.007 | 20.960 | |
| plot_feature_selection | 27.607 | 0.021 | 27.630 | |
| plot_partition_agreement | 29.439 | 0.029 | 29.471 | |
| plot_vote_frequencies | 0.882 | 0.032 | 0.914 | |
| toy_gene_memberships | 0.012 | 0.002 | 0.013 | |
| toy_genes | 0.001 | 0.000 | 0.001 | |