Federico Marini
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_19 |
| git_last_commit: dd4c5de |
| git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 820/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.8.0 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | 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 | | ||||||||
|
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: 2.8.0 |
| 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_2.8.0.tar.gz |
| StartedAt: 2024-06-10 16:39:12 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 16:55:48 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 995.2 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_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.8.0’
* 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
GeneTonic 8.986 0.247 14.898
summarize_ggs_hubgenes 8.016 0.281 12.587
ggs_backbone 7.533 0.268 11.709
ggs_graph 7.452 0.236 11.318
gs_mds 7.391 0.197 11.497
gs_heatmap 7.336 0.188 11.282
gs_upset 6.590 0.171 10.116
gs_alluvial 6.192 0.189 8.915
enhance_table 6.028 0.178 9.606
gs_dendro 5.701 0.156 9.172
signature_volcano 5.433 0.192 8.591
gs_volcano 5.367 0.152 8.624
gs_horizon 5.367 0.130 7.553
gs_scoresheat 5.065 0.186 7.797
gs_scores 5.025 0.162 7.913
gs_summary_overview_pair 5.003 0.143 7.707
gs_radar 4.928 0.210 7.656
distill_enrichment 4.973 0.149 7.641
export_for_iSEE 4.971 0.118 7.078
get_aggrscores 4.771 0.135 7.543
enrichment_map 4.707 0.124 6.071
GeneTonicList 4.595 0.136 7.265
checkup_gtl 4.560 0.126 6.922
checkup_GeneTonic 4.498 0.134 6.816
gene_plot 3.898 0.133 5.516
gs_summary_overview 3.757 0.129 5.641
create_kappa_matrix 3.719 0.142 5.867
get_expression_values 3.727 0.116 5.763
gs_summary_heat 3.693 0.139 6.018
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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)
>
> 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
215.344 8.904 295.407
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.986 | 0.247 | 14.898 | |
| GeneTonicList | 4.595 | 0.136 | 7.265 | |
| check_colors | 0.009 | 0.002 | 0.014 | |
| checkup_GeneTonic | 4.498 | 0.134 | 6.816 | |
| checkup_gtl | 4.560 | 0.126 | 6.922 | |
| cluster_markov | 0.102 | 0.007 | 0.169 | |
| create_jaccard_matrix | 0.855 | 0.057 | 1.329 | |
| create_kappa_matrix | 3.719 | 0.142 | 5.867 | |
| create_upsetdata | 0.036 | 0.029 | 0.087 | |
| deseqresult2df | 0.177 | 0.007 | 0.289 | |
| distill_enrichment | 4.973 | 0.149 | 7.641 | |
| enhance_table | 6.028 | 0.178 | 9.606 | |
| enrichment_map | 4.707 | 0.124 | 6.071 | |
| export_for_iSEE | 4.971 | 0.118 | 7.078 | |
| export_to_sif | 0.034 | 0.003 | 0.039 | |
| gene_plot | 3.898 | 0.133 | 5.516 | |
| geneinfo_2_html | 0.007 | 0.001 | 0.009 | |
| get_aggrscores | 4.771 | 0.135 | 7.543 | |
| get_expression_values | 3.727 | 0.116 | 5.763 | |
| ggs_backbone | 7.533 | 0.268 | 11.709 | |
| ggs_graph | 7.452 | 0.236 | 11.318 | |
| go_2_html | 0.020 | 0.001 | 0.022 | |
| gs_alluvial | 6.192 | 0.189 | 8.915 | |
| gs_dendro | 5.701 | 0.156 | 9.172 | |
| gs_fuzzyclustering | 0.809 | 0.029 | 1.303 | |
| gs_heatmap | 7.336 | 0.188 | 11.282 | |
| gs_horizon | 5.367 | 0.130 | 7.553 | |
| gs_mds | 7.391 | 0.197 | 11.497 | |
| gs_radar | 4.928 | 0.210 | 7.656 | |
| gs_scores | 5.025 | 0.162 | 7.913 | |
| gs_scoresheat | 5.065 | 0.186 | 7.797 | |
| gs_simplify | 1.195 | 0.038 | 1.924 | |
| gs_summary_heat | 3.693 | 0.139 | 6.018 | |
| gs_summary_overview | 3.757 | 0.129 | 5.641 | |
| gs_summary_overview_pair | 5.003 | 0.143 | 7.707 | |
| gs_upset | 6.590 | 0.171 | 10.116 | |
| gs_volcano | 5.367 | 0.152 | 8.624 | |
| happy_hour | 3.290 | 0.120 | 4.643 | |
| map2color | 0.014 | 0.003 | 0.016 | |
| overlap_coefficient | 0.001 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.014 | 0.002 | 0.023 | |
| shake_enrichResult | 1.922 | 0.048 | 2.693 | |
| shake_enrichrResult | 0.064 | 0.004 | 0.093 | |
| shake_fgseaResult | 0.243 | 0.004 | 0.405 | |
| shake_gprofilerResult | 0.108 | 0.007 | 0.174 | |
| shake_gsenrichResult | 1.992 | 0.066 | 3.088 | |
| shake_topGOtableResult | 0.008 | 0.002 | 0.021 | |
| signature_volcano | 5.433 | 0.192 | 8.591 | |
| styleColorBar_divergent | 0.252 | 0.036 | 0.413 | |
| summarize_ggs_hubgenes | 8.016 | 0.281 | 12.587 | |