Federico Marini
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | | ||||||||
| palomino7 | 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: 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: 2024-10-17 05:48:03 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 06:08:50 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 1246.3 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 4.4.1 (2024-06-14)
* 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 ‘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
gs_mds 12.945 0.479 15.244
gs_upset 12.600 0.265 15.266
summarize_ggs_hubgenes 11.706 0.318 14.091
ggs_graph 11.682 0.281 13.847
ggs_backbone 11.498 0.321 13.672
gs_heatmap 10.808 0.415 12.513
signature_volcano 9.728 0.349 12.144
GeneTonic 9.340 0.451 11.235
gs_scoresheat 9.191 0.293 12.336
gs_dendro 8.839 0.222 10.278
gs_scores 8.315 0.264 10.257
enhance_table 7.739 0.200 8.741
gene_plot 7.674 0.226 8.997
gs_horizon 7.626 0.233 9.067
GeneTonicList 7.084 0.250 8.110
gs_summary_overview 6.990 0.247 8.490
distill_enrichment 6.822 0.186 7.843
gs_radar 6.528 0.399 7.847
create_kappa_matrix 6.276 0.480 7.815
gs_volcano 6.548 0.173 8.286
gs_alluvial 6.379 0.316 7.553
export_for_iSEE 6.469 0.154 7.657
enrichment_map 6.344 0.181 7.147
happy_hour 6.324 0.200 8.468
checkup_GeneTonic 6.202 0.203 7.162
checkup_gtl 6.130 0.237 7.480
get_aggrscores 6.184 0.162 7.221
gs_summary_overview_pair 5.819 0.187 7.089
gs_summary_heat 5.706 0.174 7.175
get_expression_values 4.762 0.179 5.678
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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)
>
> 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
363.455 16.049 388.814
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.340 | 0.451 | 11.235 | |
| GeneTonicList | 7.084 | 0.250 | 8.110 | |
| check_colors | 0.016 | 0.003 | 0.020 | |
| checkup_GeneTonic | 6.202 | 0.203 | 7.162 | |
| checkup_gtl | 6.130 | 0.237 | 7.480 | |
| cluster_markov | 0.230 | 0.026 | 0.297 | |
| create_jaccard_matrix | 2.397 | 0.213 | 3.070 | |
| create_kappa_matrix | 6.276 | 0.480 | 7.815 | |
| create_upsetdata | 0.090 | 0.127 | 0.246 | |
| deseqresult2df | 0.257 | 0.006 | 0.322 | |
| distill_enrichment | 6.822 | 0.186 | 7.843 | |
| enhance_table | 7.739 | 0.200 | 8.741 | |
| enrichment_map | 6.344 | 0.181 | 7.147 | |
| export_for_iSEE | 6.469 | 0.154 | 7.657 | |
| export_to_sif | 0.036 | 0.003 | 0.047 | |
| gene_plot | 7.674 | 0.226 | 8.997 | |
| geneinfo_2_html | 0.015 | 0.001 | 0.019 | |
| get_aggrscores | 6.184 | 0.162 | 7.221 | |
| get_expression_values | 4.762 | 0.179 | 5.678 | |
| ggs_backbone | 11.498 | 0.321 | 13.672 | |
| ggs_graph | 11.682 | 0.281 | 13.847 | |
| go_2_html | 0.054 | 0.001 | 0.063 | |
| gs_alluvial | 6.379 | 0.316 | 7.553 | |
| gs_dendro | 8.839 | 0.222 | 10.278 | |
| gs_fuzzyclustering | 1.708 | 0.055 | 1.999 | |
| gs_heatmap | 10.808 | 0.415 | 12.513 | |
| gs_horizon | 7.626 | 0.233 | 9.067 | |
| gs_mds | 12.945 | 0.479 | 15.244 | |
| gs_radar | 6.528 | 0.399 | 7.847 | |
| gs_scores | 8.315 | 0.264 | 10.257 | |
| gs_scoresheat | 9.191 | 0.293 | 12.336 | |
| gs_simplify | 3.198 | 0.089 | 4.264 | |
| gs_summary_heat | 5.706 | 0.174 | 7.175 | |
| gs_summary_overview | 6.990 | 0.247 | 8.490 | |
| gs_summary_overview_pair | 5.819 | 0.187 | 7.089 | |
| gs_upset | 12.600 | 0.265 | 15.266 | |
| gs_volcano | 6.548 | 0.173 | 8.286 | |
| happy_hour | 6.324 | 0.200 | 8.468 | |
| map2color | 0.019 | 0.003 | 0.031 | |
| overlap_coefficient | 0.001 | 0.001 | 0.002 | |
| overlap_jaccard_index | 0.001 | 0.001 | 0.001 | |
| shake_davidResult | 0.021 | 0.002 | 0.029 | |
| shake_enrichResult | 2.971 | 0.101 | 4.002 | |
| shake_enrichrResult | 0.112 | 0.005 | 0.148 | |
| shake_fgseaResult | 0.259 | 0.006 | 0.334 | |
| shake_gprofilerResult | 0.255 | 0.009 | 0.333 | |
| shake_gsenrichResult | 2.815 | 0.068 | 3.515 | |
| shake_topGOtableResult | 0.013 | 0.002 | 0.022 | |
| signature_volcano | 9.728 | 0.349 | 12.144 | |
| styleColorBar_divergent | 0.401 | 0.076 | 0.567 | |
| summarize_ggs_hubgenes | 11.706 | 0.318 | 14.091 | |