Federico Marini
| Snapshot Date: 2025-02-10 13:40 -0500 (Mon, 10 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: f1af392 |
| git_last_commit_date: 2025-01-09 16:20:19 -0500 (Thu, 09 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-11 11:42 -0500 (Tue, 11 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 810/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.1.2 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | 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: 3.1.2 |
| 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_3.1.2.tar.gz |
| StartedAt: 2025-02-10 21:15:33 -0500 (Mon, 10 Feb 2025) |
| EndedAt: 2025-02-10 21:27:55 -0500 (Mon, 10 Feb 2025) |
| EllapsedTime: 741.9 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_3.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 7.757 0.354 8.162
gs_upset 7.163 0.188 7.408
GeneTonic 6.535 0.257 6.858
ggs_graph 6.468 0.188 6.700
gs_heatmap 6.225 0.184 6.454
summarize_ggs_hubgenes 6.098 0.226 6.367
ggs_backbone 5.914 0.226 6.185
gs_scoresheat 5.542 0.183 5.769
enhance_table 5.523 0.166 5.742
gs_dendro 5.157 0.180 5.377
signature_volcano 4.934 0.160 5.131
gs_scores 4.771 0.208 5.014
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** this is package ‘GeneTonic’ version ‘3.1.2’ ** 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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 v3.1.2
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 264 ]
>
> proc.time()
user system elapsed
215.455 12.134 196.706
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.535 | 0.257 | 6.858 | |
| GeneTonicList | 2.912 | 0.170 | 3.102 | |
| check_colors | 0.007 | 0.001 | 0.009 | |
| checkup_GeneTonic | 4.252 | 0.165 | 4.450 | |
| checkup_gtl | 4.193 | 0.151 | 4.390 | |
| cluster_markov | 0.111 | 0.004 | 0.117 | |
| create_jaccard_matrix | 1.488 | 0.154 | 1.654 | |
| create_kappa_matrix | 3.562 | 0.325 | 3.911 | |
| create_upsetdata | 0.042 | 0.043 | 0.086 | |
| deprecated | 0.001 | 0.000 | 0.000 | |
| deseqresult2df | 0.140 | 0.004 | 0.144 | |
| distill_enrichment | 4.515 | 0.197 | 4.741 | |
| enhance_table | 5.523 | 0.166 | 5.742 | |
| enrichment_map | 4.495 | 0.139 | 4.690 | |
| export_for_iSEE | 4.735 | 0.143 | 4.926 | |
| export_to_sif | 0.030 | 0.002 | 0.033 | |
| gene_plot | 4.801 | 0.130 | 4.970 | |
| geneinfo_2_html | 0.010 | 0.001 | 0.011 | |
| get_aggrscores | 4.158 | 0.139 | 4.322 | |
| get_expression_values | 3.189 | 0.109 | 3.318 | |
| ggs_backbone | 5.914 | 0.226 | 6.185 | |
| ggs_graph | 6.468 | 0.188 | 6.700 | |
| go_2_html | 0.023 | 0.001 | 0.024 | |
| gs_alluvial | 3.180 | 0.208 | 3.417 | |
| gs_dendro | 5.157 | 0.180 | 5.377 | |
| gs_fuzzyclustering | 0.860 | 0.027 | 0.893 | |
| gs_heatmap | 6.225 | 0.184 | 6.454 | |
| gs_horizon | 3.650 | 0.138 | 3.816 | |
| gs_mds | 7.757 | 0.354 | 8.162 | |
| gs_radar | 3.115 | 0.207 | 3.347 | |
| gs_scores | 4.771 | 0.208 | 5.014 | |
| gs_scoresheat | 5.542 | 0.183 | 5.769 | |
| gs_simplify | 1.006 | 0.033 | 1.043 | |
| gs_summary_heat | 3.074 | 0.130 | 3.223 | |
| gs_summary_overview | 4.521 | 0.152 | 4.708 | |
| gs_summary_overview_pair | 3.200 | 0.140 | 3.359 | |
| gs_upset | 7.163 | 0.188 | 7.408 | |
| gs_volcano | 3.547 | 0.104 | 3.685 | |
| happy_hour | 3.200 | 0.134 | 3.358 | |
| map2color | 0.013 | 0.005 | 0.018 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.012 | 0.001 | 0.015 | |
| shake_enrichResult | 1.658 | 0.060 | 1.733 | |
| shake_enrichrResult | 0.053 | 0.002 | 0.055 | |
| shake_fgseaResult | 0.100 | 0.002 | 0.102 | |
| shake_gprofilerResult | 0.092 | 0.004 | 0.097 | |
| shake_gsenrichResult | 2.835 | 0.115 | 2.968 | |
| shake_topGOtableResult | 0.005 | 0.001 | 0.006 | |
| signature_volcano | 4.934 | 0.160 | 5.131 | |
| styleColorBar_divergent | 0.207 | 0.046 | 0.258 | |
| summarize_ggs_hubgenes | 6.098 | 0.226 | 6.367 | |