Federico Marini
| Snapshot Date: 2025-01-23 13:00 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_20 |
| git_last_commit: d04704c |
| git_last_commit_date: 2024-10-29 10:43:15 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-27 12:10 -0500 (Mon, 27 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4395 |
| 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 810/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.0.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the GeneTonic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneTonic.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: GeneTonic |
| Version: 3.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.0.0.tar.gz |
| StartedAt: 2025-01-24 20:22:50 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 20:35:44 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 773.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.0.0’
* 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 ‘GeneTonic’ 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 ... 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 whether startup messages can be suppressed ... 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 ... 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 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
gs_mds 8.784 0.561 9.347
summarize_ggs_hubgenes 7.672 0.298 7.984
gs_scores 7.685 0.276 7.966
ggs_graph 7.393 0.300 7.721
signature_volcano 7.175 0.327 7.528
GeneTonic 7.058 0.199 7.298
gs_upset 6.797 0.227 7.029
gs_heatmap 6.173 0.266 6.444
ggs_backbone 6.007 0.256 6.290
gs_dendro 5.800 0.197 6.030
enhance_table 5.655 0.231 5.955
gs_volcano 5.636 0.204 5.869
gs_summary_overview 5.589 0.210 5.816
distill_enrichment 5.494 0.179 5.680
gs_summary_overview_pair 5.388 0.184 5.580
gs_scoresheat 5.282 0.279 5.567
get_aggrscores 5.267 0.195 5.465
gs_horizon 5.267 0.175 5.450
enrichment_map 5.273 0.138 5.426
gs_alluvial 5.178 0.180 5.363
checkup_gtl 5.024 0.166 5.201
checkup_GeneTonic 4.936 0.172 5.119
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (GeneTonic)
GeneTonic.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(GeneTonic)
Welcome to GeneTonic v3.0.0
If you use GeneTonic in your work, please cite:
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
BMC Bioinformatics, 2021 - https://doi.org/10.1186/s12859-021-04461-5
and/or (if adopting the series of protocols as a whole)
Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, ideal, and GeneTonic
Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin Strauch, Federico Marini
Current Protocols, 2022 - https://doi.org/10.1002/cpz1.411
>
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
--- Running gseGO...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
---------------------------------
----- GeneTonicList object ------
---------------------------------
----- dds object -----
Providing an expression object (as DESeqDataset) of 17806 features over 24 samples
----- res_de object -----
Providing a DE result object (as DESeqResults), 17806 features tested, 1024 found as DE
Upregulated: 652
Downregulated: 372
----- res_enrich object -----
Providing an enrichment result object, 200 reported
----- annotation_obj object -----
Providing an annotation object of 58294 features with information on 2 identifier types
--- Test setup script completed!
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 262 ]
>
> proc.time()
user system elapsed
242.989 11.081 203.307
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.058 | 0.199 | 7.298 | |
| GeneTonicList | 4.787 | 0.137 | 4.954 | |
| check_colors | 0.010 | 0.001 | 0.011 | |
| checkup_GeneTonic | 4.936 | 0.172 | 5.119 | |
| checkup_gtl | 5.024 | 0.166 | 5.201 | |
| cluster_markov | 0.108 | 0.004 | 0.112 | |
| create_jaccard_matrix | 0.874 | 0.031 | 0.907 | |
| create_kappa_matrix | 3.267 | 0.392 | 3.668 | |
| create_upsetdata | 0.020 | 0.016 | 0.047 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.135 | 0.004 | 0.139 | |
| distill_enrichment | 5.494 | 0.179 | 5.680 | |
| enhance_table | 5.655 | 0.231 | 5.955 | |
| enrichment_map | 5.273 | 0.138 | 5.426 | |
| export_for_iSEE | 4.105 | 0.171 | 4.278 | |
| export_to_sif | 0.029 | 0.002 | 0.030 | |
| gene_plot | 4.413 | 0.174 | 4.607 | |
| geneinfo_2_html | 0.010 | 0.001 | 0.010 | |
| get_aggrscores | 5.267 | 0.195 | 5.465 | |
| get_expression_values | 3.972 | 0.115 | 4.115 | |
| ggs_backbone | 6.007 | 0.256 | 6.290 | |
| ggs_graph | 7.393 | 0.300 | 7.721 | |
| go_2_html | 0.022 | 0.001 | 0.023 | |
| gs_alluvial | 5.178 | 0.180 | 5.363 | |
| gs_dendro | 5.800 | 0.197 | 6.030 | |
| gs_fuzzyclustering | 2.182 | 0.110 | 2.293 | |
| gs_heatmap | 6.173 | 0.266 | 6.444 | |
| gs_horizon | 5.267 | 0.175 | 5.450 | |
| gs_mds | 8.784 | 0.561 | 9.347 | |
| gs_radar | 3.398 | 0.185 | 3.618 | |
| gs_scores | 7.685 | 0.276 | 7.966 | |
| gs_scoresheat | 5.282 | 0.279 | 5.567 | |
| gs_simplify | 0.932 | 0.039 | 0.974 | |
| gs_summary_heat | 3.637 | 0.187 | 3.834 | |
| gs_summary_overview | 5.589 | 0.210 | 5.816 | |
| gs_summary_overview_pair | 5.388 | 0.184 | 5.580 | |
| gs_upset | 6.797 | 0.227 | 7.029 | |
| gs_volcano | 5.636 | 0.204 | 5.869 | |
| happy_hour | 4.027 | 0.182 | 4.211 | |
| map2color | 0.019 | 0.003 | 0.022 | |
| overlap_coefficient | 0.001 | 0.000 | 0.000 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.013 | 0.001 | 0.014 | |
| shake_enrichResult | 2.657 | 0.072 | 2.732 | |
| shake_enrichrResult | 0.075 | 0.002 | 0.077 | |
| shake_fgseaResult | 0.174 | 0.008 | 0.182 | |
| shake_gprofilerResult | 0.133 | 0.009 | 0.142 | |
| shake_gsenrichResult | 2.700 | 0.089 | 2.790 | |
| shake_topGOtableResult | 0.009 | 0.005 | 0.015 | |
| signature_volcano | 7.175 | 0.327 | 7.528 | |
| styleColorBar_divergent | 0.270 | 0.034 | 0.308 | |
| summarize_ggs_hubgenes | 7.672 | 0.298 | 7.984 | |