| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
| 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 825/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.2.1 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeneTonic |
| Version: 3.2.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneTonic_3.2.1.tar.gz |
| StartedAt: 2025-10-07 09:42:33 -0000 (Tue, 07 Oct 2025) |
| EndedAt: 2025-10-07 09:57:08 -0000 (Tue, 07 Oct 2025) |
| EllapsedTime: 875.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneTonic_3.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.2.1’
* 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 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
gs_mds 10.030 0.047 10.098
summarize_ggs_hubgenes 9.226 0.068 9.320
GeneTonic 8.454 0.176 8.651
ggs_graph 8.489 0.036 8.543
gs_heatmap 8.295 0.020 8.333
gs_upset 8.228 0.028 8.276
gs_scoresheat 7.308 0.112 7.439
ggs_backbone 7.324 0.068 7.409
gs_dendro 6.765 0.040 6.819
signature_volcano 6.176 0.040 6.229
gs_scores 6.027 0.040 6.083
gs_volcano 5.940 0.016 5.971
distill_enrichment 5.806 0.080 5.896
enhance_table 5.560 0.044 5.617
export_for_iSEE 5.497 0.020 5.530
happy_hour 5.126 0.076 5.214
enrichment_map 5.157 0.012 5.179
get_aggrscores 5.128 0.039 5.182
GeneTonicList 5.050 0.024 5.083
checkup_GeneTonic 5.018 0.044 5.071
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘GeneTonic’ ... ** this is package ‘GeneTonic’ version ‘3.2.1’ ** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 v3.2.1
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 265 ]
>
> proc.time()
user system elapsed
252.200 9.577 227.632
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.454 | 0.176 | 8.651 | |
| GeneTonicList | 5.050 | 0.024 | 5.083 | |
| check_colors | 0.010 | 0.000 | 0.011 | |
| checkup_GeneTonic | 5.018 | 0.044 | 5.071 | |
| checkup_gtl | 3.767 | 0.035 | 3.809 | |
| cluster_markov | 0.114 | 0.000 | 0.113 | |
| create_jaccard_matrix | 1.810 | 0.087 | 1.901 | |
| create_kappa_matrix | 4.749 | 0.016 | 4.773 | |
| create_upsetdata | 0.039 | 0.004 | 0.043 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.171 | 0.000 | 0.171 | |
| distill_enrichment | 5.806 | 0.080 | 5.896 | |
| enhance_table | 5.560 | 0.044 | 5.617 | |
| enrichment_map | 5.157 | 0.012 | 5.179 | |
| export_for_iSEE | 5.497 | 0.020 | 5.530 | |
| export_to_sif | 0.03 | 0.00 | 0.03 | |
| gene_plot | 4.795 | 0.020 | 4.827 | |
| geneinfo_2_html | 0.013 | 0.000 | 0.012 | |
| get_aggrscores | 5.128 | 0.039 | 5.182 | |
| get_expression_values | 3.903 | 0.028 | 3.940 | |
| ggs_backbone | 7.324 | 0.068 | 7.409 | |
| ggs_graph | 8.489 | 0.036 | 8.543 | |
| go_2_html | 0.036 | 0.000 | 0.036 | |
| gs_alluvial | 3.964 | 0.036 | 4.042 | |
| gs_dendro | 6.765 | 0.040 | 6.819 | |
| gs_fuzzyclustering | 1.229 | 0.000 | 1.232 | |
| gs_heatmap | 8.295 | 0.020 | 8.333 | |
| gs_horizon | 4.504 | 0.040 | 4.553 | |
| gs_mds | 10.030 | 0.047 | 10.098 | |
| gs_radar | 3.936 | 0.052 | 3.997 | |
| gs_scores | 6.027 | 0.040 | 6.083 | |
| gs_scoresheat | 7.308 | 0.112 | 7.439 | |
| gs_simplify | 1.544 | 0.000 | 1.547 | |
| gs_summary_heat | 4.005 | 0.032 | 4.048 | |
| gs_summary_overview | 4.306 | 0.059 | 4.379 | |
| gs_summary_overview_pair | 4.103 | 0.012 | 4.123 | |
| gs_upset | 8.228 | 0.028 | 8.276 | |
| gs_volcano | 5.940 | 0.016 | 5.971 | |
| happy_hour | 5.126 | 0.076 | 5.214 | |
| map2color | 0.011 | 0.002 | 0.014 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.012 | 0.000 | 0.014 | |
| shake_enrichResult | 1.977 | 0.016 | 1.997 | |
| shake_enrichrResult | 0.062 | 0.000 | 0.063 | |
| shake_fgseaResult | 0.132 | 0.004 | 0.135 | |
| shake_gprofilerResult | 0.091 | 0.004 | 0.101 | |
| shake_gsenrichResult | 1.906 | 0.028 | 1.939 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.007 | |
| signature_volcano | 6.176 | 0.040 | 6.229 | |
| styleColorBar_divergent | 0.250 | 0.012 | 0.271 | |
| summarize_ggs_hubgenes | 9.226 | 0.068 | 9.320 | |