Federico Marini
| Snapshot Date: 2024-09-26 13:40 -0400 (Thu, 26 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 67e5c4a |
| git_last_commit_date: 2024-09-22 05:11:49 -0400 (Sun, 22 Sep 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-27 12:24 -0400 (Fri, 27 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
| 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 803/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.99.0 (landing page) Federico Marini
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2.99.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.99.0.tar.gz |
| StartedAt: 2024-09-27 01:49:24 -0400 (Fri, 27 Sep 2024) |
| EndedAt: 2024-09-27 01:58:48 -0400 (Fri, 27 Sep 2024) |
| EllapsedTime: 564.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.99.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.99.0’
* 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 loading without being on the library search path ... 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
GeneTonic 5.449 0.271 5.723
* 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: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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(GeneTonic)
Welcome to GeneTonic v2.99.0
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
136.012 4.569 119.698
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 5.449 | 0.271 | 5.723 | |
| GeneTonicList | 3.009 | 0.124 | 3.134 | |
| check_colors | 0.005 | 0.000 | 0.006 | |
| checkup_GeneTonic | 2.878 | 0.058 | 2.937 | |
| checkup_gtl | 2.807 | 0.059 | 2.866 | |
| cluster_markov | 0.059 | 0.001 | 0.059 | |
| create_jaccard_matrix | 0.548 | 0.017 | 0.565 | |
| create_kappa_matrix | 1.769 | 0.037 | 1.806 | |
| create_upsetdata | 0.024 | 0.007 | 0.032 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.098 | 0.003 | 0.101 | |
| distill_enrichment | 3.074 | 0.094 | 3.170 | |
| enhance_table | 3.521 | 0.055 | 3.577 | |
| enrichment_map | 1.916 | 0.095 | 2.012 | |
| export_for_iSEE | 3.297 | 0.073 | 3.371 | |
| export_to_sif | 0.016 | 0.000 | 0.016 | |
| gene_plot | 3.454 | 0.049 | 3.503 | |
| geneinfo_2_html | 0.007 | 0.000 | 0.008 | |
| get_aggrscores | 1.853 | 0.058 | 1.912 | |
| get_expression_values | 2.536 | 0.035 | 2.572 | |
| ggs_backbone | 4.584 | 0.075 | 4.661 | |
| ggs_graph | 4.412 | 0.119 | 4.531 | |
| go_2_html | 0.015 | 0.000 | 0.015 | |
| gs_alluvial | 1.920 | 0.063 | 1.986 | |
| gs_dendro | 3.681 | 0.077 | 3.759 | |
| gs_fuzzyclustering | 0.479 | 0.001 | 0.480 | |
| gs_heatmap | 3.351 | 0.038 | 3.390 | |
| gs_horizon | 3.383 | 0.043 | 3.427 | |
| gs_mds | 4.919 | 0.043 | 4.963 | |
| gs_radar | 1.943 | 0.079 | 2.022 | |
| gs_scores | 3.771 | 0.069 | 3.842 | |
| gs_scoresheat | 2.656 | 0.011 | 2.668 | |
| gs_simplify | 0.718 | 0.000 | 0.717 | |
| gs_summary_heat | 3.133 | 0.076 | 3.211 | |
| gs_summary_overview | 2.078 | 0.041 | 2.119 | |
| gs_summary_overview_pair | 3.257 | 0.066 | 3.323 | |
| gs_upset | 3.869 | 0.021 | 3.891 | |
| gs_volcano | 3.459 | 0.118 | 3.796 | |
| happy_hour | 1.905 | 0.074 | 2.559 | |
| map2color | 0.009 | 0.001 | 0.010 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.006 | 0.001 | 0.014 | |
| shake_enrichResult | 1.223 | 0.048 | 1.287 | |
| shake_enrichrResult | 0.031 | 0.001 | 0.034 | |
| shake_fgseaResult | 0.085 | 0.001 | 0.087 | |
| shake_gprofilerResult | 0.057 | 0.003 | 0.062 | |
| shake_gsenrichResult | 2.269 | 0.041 | 2.627 | |
| shake_topGOtableResult | 0.005 | 0.000 | 0.005 | |
| signature_volcano | 3.273 | 0.031 | 3.801 | |
| styleColorBar_divergent | 0.138 | 0.010 | 0.157 | |
| summarize_ggs_hubgenes | 3.623 | 0.068 | 3.740 | |