Build/check report for BioC 3.23 - CHECK results for DNEA on nebbiolo1

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*

CHECK results for DNEA on nebbiolo1

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: 1.1.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DNEA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DNEA_1.1.0.tar.gz

StartedAt: 2025-11-04 22:54:47 -0500 (Tue, 04 Nov 2025)

EndedAt: 2025-11-04 23:04:10 -0500 (Tue, 04 Nov 2025)

EllapsedTime: 563.7 seconds

RetCode: 0

Status: OK

CheckDir: DNEA.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DNEA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DNEA_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/DNEA.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 ‘DNEA/DESCRIPTION’ ... OK
* this is package ‘DNEA’ version ‘1.1.0’
* 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 19.769  3.627  12.193
BICtune-methods    19.954  2.422  10.911
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/DNEA.Rcheck/00check.log’
for details.

Installation output

DNEA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DNEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DNEA’ ...
** this is package ‘DNEA’ version ‘1.1.0’
** 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 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.

> # 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...
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_input_data expression data will be used for analysis.
The log_input_data expression data will be used for analysis.
Vectors to compare are not the same length!
Vectors to compare are not the same length!
DM:control network specific edges: 11
DM:case network specific edges: 7
-----------------------------------
Number of edges shared by both networks: 10
Total number of edges in dataset: 28
DM:control network specific edges: 11
DM:case network specific edges: 7
-----------------------------------
Number of edges shared by both networks: 10
Total number of edges in dataset: 28
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 53 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
517.075  20.811 236.624

Example timings

DNEA.Rcheck/DNEA-Ex.timings

name	user	system	elapsed
BICscores-methods	0.176	0.029	0.205
BICtune-methods	19.954	2.422	10.911
CCsummary-methods	0.185	0.004	0.189
DNEA-class	0.913	0.059	0.971
DNEAinputSummary-class	0.896	0.073	0.969
addExpressionData	0.976	0.115	1.092
adjacencyGraph-methods	0.171	0.008	0.179
adjacencyMatrix-methods	0.224	0.229	0.453
aggregateFeatures	2.242	0.033	2.275
clusterNet	3.412	0.226	3.638
collapsed_DNEA-class	2.258	0.104	2.362
createDNEAobject	0.910	0.044	0.954
datasetSummary-methods	0.892	0.013	0.906
diagnostics-methods	0.927	0.041	0.968
edgeList-methods	0.173	0.000	0.172
expressionData-methods	1.155	0.915	2.071
featureNames-methods	0.921	0.017	0.938
filterNetworks-methods	0.220	0.002	0.221
getNetworkFiles	0.166	0.002	0.167
getNetworks	0.380	0.012	0.392
includeMetadata	0.910	0.022	0.932
lambdas2Test-methods	0.900	0.021	0.921
massDataset2DNEA	0.052	0.004	0.055
metaData-methods	0.925	0.028	0.953
netGSAresults-methods	0.180	0.006	0.186
networkGroupIDs-methods	0.904	0.009	0.913
networkGroups-methods	0.939	0.004	0.943
nodeList-methods	0.907	0.026	0.933
numFeatures-methods	0.897	0.012	0.909
numSamples-methods	0.963	0.049	1.011
optimizedLambda-methods	0.897	0.012	0.911
plotNetworks	0.278	0.006	0.284
projectName-methods	0.905	0.007	0.911
runNetGSA	2.327	0.042	2.369
sampleNames-methods	0.913	0.021	0.934
selectionProbabilities-methods	0.249	0.205	0.453
selectionResults-methods	0.261	0.200	0.460
stabilitySelection	19.769	3.627	12.193
subnetworkMembership-methods	1.359	0.747	0.208
sumExp2DNEA	2.439	0.202	2.641