Federico Marini
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| 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 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| 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" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | | ||||||||
|
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: 2024-12-20 03:50:50 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 04:12:36 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 1306.0 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: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.0.0’
* 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 13.392 0.664 14.196
gs_upset 13.685 0.241 14.597
summarize_ggs_hubgenes 12.719 0.306 13.225
ggs_backbone 12.023 0.300 12.622
gs_heatmap 10.707 0.216 11.757
ggs_graph 10.574 0.248 11.172
enhance_table 9.992 0.203 11.013
gs_scoresheat 9.293 0.245 9.747
gs_dendro 9.033 0.237 9.378
GeneTonic 8.734 0.398 9.734
signature_volcano 8.733 0.284 9.347
gs_scores 8.230 0.203 8.991
gs_volcano 7.477 0.148 7.828
distill_enrichment 7.355 0.174 8.426
gs_summary_overview 7.331 0.190 7.733
export_for_iSEE 7.176 0.130 7.339
gs_alluvial 6.679 0.323 7.147
gene_plot 6.666 0.168 6.905
gs_horizon 6.636 0.170 6.929
create_kappa_matrix 6.350 0.341 7.549
GeneTonicList 6.428 0.197 6.686
checkup_GeneTonic 6.408 0.204 6.790
get_aggrscores 6.459 0.151 6.692
enrichment_map 6.400 0.151 6.789
checkup_gtl 6.276 0.161 6.725
gs_summary_overview_pair 5.824 0.168 6.405
gs_radar 5.646 0.344 6.589
gs_summary_heat 5.668 0.157 5.906
happy_hour 5.226 0.165 5.562
get_expression_values 4.924 0.134 5.507
* 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-x86_64/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: 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 v3.0.0
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
364.656 14.786 348.787
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.734 | 0.398 | 9.734 | |
| GeneTonicList | 6.428 | 0.197 | 6.686 | |
| check_colors | 0.016 | 0.003 | 0.018 | |
| checkup_GeneTonic | 6.408 | 0.204 | 6.790 | |
| checkup_gtl | 6.276 | 0.161 | 6.725 | |
| cluster_markov | 0.175 | 0.007 | 0.192 | |
| create_jaccard_matrix | 2.361 | 0.100 | 2.683 | |
| create_kappa_matrix | 6.350 | 0.341 | 7.549 | |
| create_upsetdata | 0.085 | 0.115 | 0.212 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.257 | 0.006 | 0.289 | |
| distill_enrichment | 7.355 | 0.174 | 8.426 | |
| enhance_table | 9.992 | 0.203 | 11.013 | |
| enrichment_map | 6.400 | 0.151 | 6.789 | |
| export_for_iSEE | 7.176 | 0.130 | 7.339 | |
| export_to_sif | 0.039 | 0.004 | 0.043 | |
| gene_plot | 6.666 | 0.168 | 6.905 | |
| geneinfo_2_html | 0.018 | 0.001 | 0.020 | |
| get_aggrscores | 6.459 | 0.151 | 6.692 | |
| get_expression_values | 4.924 | 0.134 | 5.507 | |
| ggs_backbone | 12.023 | 0.300 | 12.622 | |
| ggs_graph | 10.574 | 0.248 | 11.172 | |
| go_2_html | 0.057 | 0.002 | 0.076 | |
| gs_alluvial | 6.679 | 0.323 | 7.147 | |
| gs_dendro | 9.033 | 0.237 | 9.378 | |
| gs_fuzzyclustering | 2.852 | 0.083 | 2.971 | |
| gs_heatmap | 10.707 | 0.216 | 11.757 | |
| gs_horizon | 6.636 | 0.170 | 6.929 | |
| gs_mds | 13.392 | 0.664 | 14.196 | |
| gs_radar | 5.646 | 0.344 | 6.589 | |
| gs_scores | 8.230 | 0.203 | 8.991 | |
| gs_scoresheat | 9.293 | 0.245 | 9.747 | |
| gs_simplify | 3.153 | 0.095 | 3.446 | |
| gs_summary_heat | 5.668 | 0.157 | 5.906 | |
| gs_summary_overview | 7.331 | 0.190 | 7.733 | |
| gs_summary_overview_pair | 5.824 | 0.168 | 6.405 | |
| gs_upset | 13.685 | 0.241 | 14.597 | |
| gs_volcano | 7.477 | 0.148 | 7.828 | |
| happy_hour | 5.226 | 0.165 | 5.562 | |
| map2color | 0.021 | 0.004 | 0.025 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.001 | 0.001 | 0.002 | |
| shake_davidResult | 0.018 | 0.002 | 0.020 | |
| shake_enrichResult | 2.913 | 0.076 | 3.017 | |
| shake_enrichrResult | 0.109 | 0.004 | 0.118 | |
| shake_fgseaResult | 0.251 | 0.003 | 0.265 | |
| shake_gprofilerResult | 0.157 | 0.006 | 0.174 | |
| shake_gsenrichResult | 2.918 | 0.106 | 3.174 | |
| shake_topGOtableResult | 0.012 | 0.009 | 0.021 | |
| signature_volcano | 8.733 | 0.284 | 9.347 | |
| styleColorBar_divergent | 0.379 | 0.060 | 0.445 | |
| summarize_ggs_hubgenes | 12.719 | 0.306 | 13.225 | |