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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 605/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNEA 0.99.14  (landing page)
Christopher Patsalis
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/DNEA
git_branch: devel
git_last_commit: d511133
git_last_commit_date: 2025-07-01 13:19:29 -0400 (Tue, 01 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DNEA on nebbiolo2

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.

raw results


Summary

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: 2025-08-29 22:17:36 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 22:57:37 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 2400.6 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: DNEA.Rcheck
Warnings: NA

Command output

##############################################################################
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### 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
###
##############################################################################
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* 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
stabilitySelection 18.980  2.761   8.593
BICtune-methods    19.843  1.422  10.676
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

DNEA.Rcheck/00install.out

##############################################################################
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###
### 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)

Tests output

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...

Example timings

DNEA.Rcheck/DNEA-Ex.timings

nameusersystemelapsed
BICscores-methods0.1700.0030.173
BICtune-methods19.843 1.42210.676
CCsummary-methods0.1750.0030.178
DNEA-class0.9080.0680.977
DNEAinputSummary-class0.9150.0590.974
addExpressionData0.9730.0741.048
adjacencyGraph-methods0.1750.0030.178
adjacencyMatrix-methods0.2130.0210.233
aggregateFeatures2.2770.0872.364
clusterNet3.3900.2313.621
collapsed_DNEA-class2.3030.0612.363
createDNEAobject0.9320.0300.962
datasetSummary-methods0.9090.0300.937
diagnostics-methods0.9240.0460.969
edgeList-methods0.1740.0020.176
expressionData-methods1.1000.0981.198
featureNames-methods0.9060.0120.917
filterNetworks-methods0.2180.0060.224
getNetworkFiles0.1680.0020.169
getNetworks0.3810.0050.376
includeMetadata0.9220.0230.945
lambdas2Test-methods0.9220.0250.948
massDataset2DNEA0.0550.0010.055
metaData-methods0.9020.0080.911
netGSAresults-methods0.1670.0000.168
networkGroupIDs-methods0.9130.0070.918
networkGroups-methods0.9110.0050.917
nodeList-methods0.9060.0080.913
numFeatures-methods0.9100.0270.938
numSamples-methods0.9540.0260.980
optimizedLambda-methods0.8930.0070.901
plotNetworks0.2310.0000.231
projectName-methods0.9220.0110.933
runNetGSA3.0580.0472.143
sampleNames-methods0.9260.0010.927
selectionProbabilities-methods0.2440.0280.272
selectionResults-methods0.3430.0640.407
stabilitySelection18.980 2.761 8.593
subnetworkMembership-methods0.1790.0060.185
sumExp2DNEA2.4490.1482.597