Marouen Ben Guebila
| Snapshot Date: 2026-03-02 13:45 -0500 (Mon, 02 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/netZooR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 42aeb7f |
| git_last_commit_date: 2026-02-27 18:02:44 -0500 (Fri, 27 Feb 2026) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-03 11:57 -0500 (Tue, 03 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4892 |
| 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 1460/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Marouen Ben Guebila
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| See other builds for netZooR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the netZooR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.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: netZooR |
| Version: 1.14.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings netZooR_1.14.1.tar.gz |
| StartedAt: 2026-03-03 02:05:44 -0500 (Tue, 03 Mar 2026) |
| EndedAt: 2026-03-03 02:08:49 -0500 (Tue, 03 Mar 2026) |
| EllapsedTime: 184.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: netZooR.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings netZooR_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.14.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘netZooR’ can be installed ... OK
* checking installed package size ... INFO
installed size is 8.1Mb
sub-directories of 1Mb or more:
data 4.3Mb
extdata 2.9Mb
* 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 ... 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘cmdstanr’
'loadNamespace' or 'requireNamespace' call not declared from: ‘cmdstanr’
* 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 ... 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 ... WARNING
'::' or ':::' import not declared from: ‘cmdstanr’
'library' or 'require' call not declared from: ‘cmdstanr’
* 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
puma 6.742 0.109 6.852
spider 6.560 0.064 6.624
* 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 WARNINGs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’
for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘netZooR’ ... ** this is package ‘netZooR’ version ‘1.14.1’ ** 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 (netZooR)
netZooR.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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(netZooR)
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: reticulate
Loading required package: pandaR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:igraph':
components, union
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> # Download shared test data with error handling and caching
> test_data_dir <- file.path("testthat")
> dir.create(test_data_dir, showWarnings = FALSE, recursive = TRUE)
>
> download_if_missing <- function(url, dest) {
+ dest_path <- file.path(test_data_dir, dest)
+ if (!file.exists(dest_path)) {
+ tryCatch(
+ download.file(url, dest_path, quiet = TRUE, mode = "wb"),
+ error = function(e) {
+ warning("Could not download ", dest, ": ", conditionMessage(e))
+ }
+ )
+ }
+ }
>
> if (!identical(Sys.getenv("NETZOOR_SKIP_DOWNLOADS"), "true")) {
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt', 'ppi_medium.txt')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData', 'testDataset.RData')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv', 'dragon_test_get_shrunken_covariance.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv', 'dragon_layer1.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv', 'dragon_layer2.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv', 'dragon_python_cov.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv', 'dragon_python_prec.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv', 'dragon_python_parcor.csv')
+ download_if_missing('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv', 'risk_grid_netzoopy.csv')
+ }
>
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.0223684210526318"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.9279
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.132231404958678"
[1] "Q = 0.148760330578512"
[1] "Q = 0.148760330578512"
[1] 0.231405 0.231405
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] "Applying Alpha = 0.1"
[1] "Constructing Iteratuvely Perturbed Network"
[1] "Sorting Nodes"
[1] "Applying Alpha = 0.1"
[1] "Constructing Iteratuvely Perturbed Network"
[1] "Sorting Nodes"
[1] "Applying Alpha = 0"
[1] "ROW ERROR Alpha limit has been reached"
[1] "Applying Alpha = 0.1"
[1] "Constructing Iteratuvely Perturbed Network"
[1] "ROW ERROR Alpha limit has been reached"
[1] "Applying Alpha = 0"
[1] "ROW ERROR Alpha limit has been reached"
[1] "Converting Edgelist to Adj Matrix"
[1] "Applying Alpha = 0.1"
[1] "Constructing Iteratuvely Perturbed Network"
[1] "Sorting Nodes"
[1] 0.79 0.00
final value 375.120000
converged
[1] 0.31 0.29
final value 36.897493
converged
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 27822 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 27822 100 27822 0 0 145k 0 --:--:-- --:--:-- --:--:-- 145k
[1] "Computing network for sample 1"
[1] "Computing network for sample 2"
[1] "Computing network for sample 3"
[1] "Computing network for sample 4"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1085k 100 1085k 0 0 3143k 0 --:--:-- --:--:-- --:--:-- 3145k
Time difference of 1.740456e-05 secs
Time difference of 1.396792 secs
Time difference of 0.946418 secs
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MONSTER object
2555 genes
20 baseline samples
20 final samples
Transition driven by 53 transcription factors
Run with 10 randomized permutations.
[1] "1001 network transitions to be estimated"
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[1] "Using OLS method"
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[1] "Using OLS method"
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Time difference of 3.871094 secs
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
[1] 2
[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
[ FAIL 0 | WARN 1 | SKIP 11 | PASS 186 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• Alpha limit reached, result is NULL (3): 'test-crane.R:34:3',
'test-crane.R:48:3', 'test-crane.R:62:3'
• On CRAN (6): 'test-egret.R:2:3', 'test-puma.R:4:3', 'test-puma.R:31:3',
'test-source.PPI.R:4:3', 'test-spider.R:4:3', 'test-spider.R:40:3'
• Python pandas module not available (1): 'test-panda.R:6:3'
• empty test (1): 'test-lioness.R:45:1'
[ FAIL 0 | WARN 1 | SKIP 11 | PASS 186 ]
>
> proc.time()
user system elapsed
33.433 1.454 41.044
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.632 | 0.023 | 0.656 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaCrane | 0 | 0 | 0 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.276 | 0.044 | 0.320 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0 | 0 | 0 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0 | 0 | 0 | |
| alpacaRotationAnalysis | 0 | 0 | 0 | |
| alpacaRotationAnalysisLouvain | 0 | 0 | 0 | |
| alpacaSimulateNetwork | 0 | 0 | 0 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0.001 | 0.000 | 0.001 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |
| annotateFromBiomart | 0 | 0 | 0 | |
| checkMisAnnotation | 0 | 0 | 0 | |
| checkTissuesToMerge | 0 | 0 | 0 | |
| cobra | 0.013 | 0.000 | 0.014 | |
| condorCluster | 0.276 | 0.001 | 0.278 | |
| condorCoreEnrich | 0.983 | 0.005 | 0.988 | |
| condorMatrixModularity | 0.007 | 0.001 | 0.008 | |
| condorModularityMax | 0.019 | 0.000 | 0.019 | |
| condorPlotCommunities | 0.287 | 0.001 | 0.290 | |
| condorPlotHeatmap | 0.193 | 0.011 | 0.205 | |
| condorQscore | 0.302 | 0.001 | 0.303 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0.002 | 0.000 | 0.003 | |
| domonster | 0 | 0 | 0 | |
| downloadGTEx | 0 | 0 | 0 | |
| extractMatrix | 0 | 0 | 0 | |
| filterGenes | 0 | 0 | 0 | |
| filterLowGenes | 0 | 0 | 0 | |
| filterMissingGenes | 0 | 0 | 0 | |
| filterSamples | 0 | 0 | 0 | |
| lioness | 2.059 | 0.153 | 2.222 | |
| lionessPy | 0.003 | 0.000 | 0.002 | |
| monster | 0.021 | 0.000 | 0.020 | |
| monsterBereFull | 3.549 | 0.017 | 3.566 | |
| monsterCalculateTmPValues | 0.014 | 0.001 | 0.016 | |
| monsterCalculateTmStats | 0.015 | 0.000 | 0.016 | |
| monsterCheckDataType | 0.105 | 0.079 | 0.184 | |
| monsterGetTm | 0.004 | 0.000 | 0.003 | |
| monsterHclHeatmapPlot | 0.649 | 0.001 | 0.649 | |
| monsterMonsterNI | 1.808 | 0.067 | 1.874 | |
| monsterPlotMonsterAnalysis | 0.019 | 0.001 | 0.019 | |
| monsterPrintMonsterAnalysis | 0.018 | 0.001 | 0.020 | |
| monsterTransformationMatrix | 0.612 | 0.011 | 0.623 | |
| monsterTransitionNetworkPlot | 0.276 | 0.007 | 0.283 | |
| monsterTransitionPCAPlot | 0.212 | 0.005 | 0.218 | |
| monsterdTFIPlot | 0.458 | 0.003 | 0.462 | |
| normalizeTissueAware | 0.000 | 0.000 | 0.001 | |
| otter | 0.002 | 0.000 | 0.002 | |
| pandaDiffEdges | 0.004 | 0.000 | 0.003 | |
| pandaPy | 0.004 | 0.000 | 0.003 | |
| pandaToAlpaca | 0.003 | 0.000 | 0.003 | |
| pandaToCondorObject | 0.002 | 0.000 | 0.003 | |
| plotCMDS | 0 | 0 | 0 | |
| plotDensity | 0 | 0 | 0 | |
| plotHeatmap | 0 | 0 | 0 | |
| puma | 6.742 | 0.109 | 6.852 | |
| qsmooth | 0 | 0 | 0 | |
| runEgret | 0.013 | 0.000 | 0.014 | |
| sambar | 1.682 | 0.009 | 1.692 | |
| seahorse | 0.148 | 0.003 | 0.151 | |
| sourcePPI | 0.007 | 0.001 | 0.008 | |
| spider | 6.560 | 0.064 | 6.624 | |
| tiger | 0.000 | 0.000 | 0.001 | |