Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 605/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DNEA 0.99.14 (landing page) Christopher Patsalis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DNEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNEA.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: DNEA |
Version: 0.99.14 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DNEA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DNEA_0.99.14.tar.gz |
StartedAt: 2025-08-31 22:16:38 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 22:56:39 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 2400.5 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: DNEA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DNEA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DNEA_0.99.14.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DNEA.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘DNEA/DESCRIPTION’ ... OK * this is package ‘DNEA’ version ‘0.99.14’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package which this enhances but not available for checking: ‘massdataset’ * 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 ‘DNEA’ 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 ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: Cannot extract version info from the following section titles: DNEA v.0.99.12 * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BICtune-methods.Rd: BiocParallel adjacencyGraph-methods.Rd: igraph clusterNet.Rd: igraph consensusClusteringResults-class.Rd: igraph getNetworks.Rd: BiocParallel Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 BICtune-methods 20.265 1.547 11.209 stabilitySelection 19.123 2.639 8.473 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
DNEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DNEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘DNEA’ ... ** this is package ‘DNEA’ version ‘0.99.14’ ** using staged installation ** R ** data ** 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 (DNEA)
DNEA.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(DNEA) > > test_check("DNEA") Optimizing the lambda hyperparameter using Bayesian-Information Criterion outlined in Guo et al. (2011) A Link to this reference can be found in the function documentation by running ?BICtune() in the console. The log_scaled_data expression data will be used for analysis. Provided lambda values will be used for optimization... Optimizing the lambda hyperparameter using Bayesian-Information Criterion outlined in Guo et al. (2011) A Link to this reference can be found in the function documentation by running ?BICtune() in the console. The log_scaled_data expression data will be used for analysis. Provided lambda values will be used for optimization... The raw peak intensity data was used for aggregation The aggregated log-scaled data is in the @assay slot (The orginal DNEA object can be found in the @original_experiment slot) Data has been normalized for further analysis. New data can be found in the log_scaled_data assay! Data diagnostics was performed on log_scaled_data assay. To check a different assay, please specify the assay parameter. Diagnostic criteria are as follows: DNEAinputSummary Number of Samples - 322 Number of Features - 83 min_eigen condition_num all_data 9.870990e-02 7.028033e+01 DM:control 8.577548e-02 8.229973e+01 DM:case -2.833480e-15 6.999910e+17 The log_scaled_data expression data will be used for analysis. The log_scaled_data expression data will be used for analysis. The log_scaled_data expression data will be used for analysis. The log_scaled_data expression data will be used for analysis. Optimizing the lambda hyperparameter using Bayesian-Information Criterion outlined in Guo et al. (2011) A Link to this reference can be found in the function documentation by running ?BICtune() in the console NOTE: if your dataset contains fewer than ~500 samples per experimental condition, consider setting "aprox=TRUE". This will provide more reliable results TUNING LAMBDA FOR DM:control!: -------------------------------------------------- Estimating optimal c constant range for asymptotic lambda... Fine-tuning Lambda... The optimal Lambda hyper-parameter has been set to: 0.0199548849358947! TUNING LAMBDA FOR DM:case!: -------------------------------------------------- Estimating optimal c constant range for asymptotic lambda... Fine-tuning Lambda... The optimal Lambda hyper-parameter has been set to: 0.0495095483188967! selection_probabilites from stability selection will be used in glasso model! Estimating model for DM:control...using 0.0199548849358947 for lambda... model estimated! Estimating model for DM:case...using 0.0495095483188967 for lambda... model estimated! DM:control network specific edges: 463 DM:case network specific edges: 423 ----------------------------------- Number of edges shared by both networks: 434 Total number of edges in dataset: 1320 The log_scaled_data expression data will be used for analysis. Optimizing the lambda hyperparameter using Bayesian-Information Criterion outlined in Guo et al. (2011) A Link to this reference can be found in the function documentation by running ?BICtune() in the console NOTE: if your dataset contains fewer than ~500 samples per experimental condition, consider setting "aprox=TRUE". This will provide more reliable results TUNING LAMBDA FOR DM:control!: -------------------------------------------------- Estimating optimal c constant range for asymptotic lambda...
DNEA.Rcheck/DNEA-Ex.timings
name | user | system | elapsed | |
BICscores-methods | 0.172 | 0.017 | 0.189 | |
BICtune-methods | 20.265 | 1.547 | 11.209 | |
CCsummary-methods | 0.404 | 0.212 | 0.173 | |
DNEA-class | 0.894 | 0.055 | 0.949 | |
DNEAinputSummary-class | 0.901 | 0.056 | 0.957 | |
addExpressionData | 0.989 | 0.139 | 1.128 | |
adjacencyGraph-methods | 0.173 | 0.003 | 0.176 | |
adjacencyMatrix-methods | 0.205 | 0.022 | 0.227 | |
aggregateFeatures | 2.232 | 0.055 | 2.287 | |
clusterNet | 3.323 | 0.064 | 3.387 | |
collapsed_DNEA-class | 2.210 | 0.002 | 2.212 | |
createDNEAobject | 0.899 | 0.014 | 0.913 | |
datasetSummary-methods | 0.882 | 0.001 | 0.883 | |
diagnostics-methods | 0.900 | 0.016 | 0.916 | |
edgeList-methods | 0.159 | 0.003 | 0.162 | |
expressionData-methods | 1.096 | 0.123 | 1.219 | |
featureNames-methods | 0.909 | 0.027 | 0.935 | |
filterNetworks-methods | 0.213 | 0.003 | 0.217 | |
getNetworkFiles | 0.163 | 0.002 | 0.165 | |
getNetworks | 0.368 | 0.015 | 0.370 | |
includeMetadata | 0.942 | 0.020 | 0.962 | |
lambdas2Test-methods | 0.906 | 0.022 | 0.927 | |
massDataset2DNEA | 0.051 | 0.003 | 0.054 | |
metaData-methods | 0.895 | 0.013 | 0.907 | |
netGSAresults-methods | 0.159 | 0.004 | 0.163 | |
networkGroupIDs-methods | 0.898 | 0.011 | 0.909 | |
networkGroups-methods | 0.907 | 0.029 | 0.937 | |
nodeList-methods | 0.894 | 0.022 | 0.917 | |
numFeatures-methods | 0.888 | 0.008 | 0.896 | |
numSamples-methods | 0.912 | 0.020 | 0.931 | |
optimizedLambda-methods | 0.884 | 0.002 | 0.886 | |
plotNetworks | 0.230 | 0.001 | 0.231 | |
projectName-methods | 0.899 | 0.010 | 0.909 | |
runNetGSA | 2.945 | 0.051 | 2.051 | |
sampleNames-methods | 0.909 | 0.004 | 0.913 | |
selectionProbabilities-methods | 0.237 | 0.019 | 0.257 | |
selectionResults-methods | 0.294 | 0.050 | 0.344 | |
stabilitySelection | 19.123 | 2.639 | 8.473 | |
subnetworkMembership-methods | 0.181 | 0.007 | 0.188 | |
sumExp2DNEA | 2.363 | 0.166 | 2.529 | |