Federico Marini
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 9473081 |
| git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 794/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.9.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 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: 2.9.0 |
| 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_2.9.0.tar.gz |
| StartedAt: 2024-06-10 04:00:19 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 04:20:44 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 1224.5 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_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.9.0’
* 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
summarize_ggs_hubgenes 12.865 0.319 15.342
gs_mds 12.836 0.318 14.449
gs_upset 12.761 0.267 15.525
ggs_backbone 12.645 0.305 14.147
gs_heatmap 12.369 0.248 14.543
ggs_graph 12.188 0.246 13.752
GeneTonic 10.211 0.426 11.538
gs_dendro 9.170 0.227 10.499
signature_volcano 9.000 0.272 10.144
enhance_table 8.906 0.201 9.806
gs_scores 8.777 0.173 9.616
gs_scoresheat 8.435 0.305 9.678
gs_horizon 7.896 0.219 9.034
gs_alluvial 7.742 0.321 8.877
export_for_iSEE 7.579 0.192 8.810
gs_volcano 7.429 0.198 8.587
distill_enrichment 7.323 0.220 8.367
gs_radar 6.880 0.354 8.037
gene_plot 6.991 0.187 7.942
create_kappa_matrix 6.648 0.333 7.802
gs_summary_overview_pair 6.774 0.207 8.239
enrichment_map 6.673 0.179 8.133
GeneTonicList 6.522 0.211 7.274
get_aggrscores 6.496 0.193 7.294
checkup_gtl 6.432 0.158 7.114
checkup_GeneTonic 6.374 0.196 6.969
gs_summary_overview 6.150 0.179 6.938
gs_summary_heat 5.860 0.150 6.827
happy_hour 5.283 0.147 5.700
get_expression_values 4.850 0.160 5.470
* 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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
359.228 16.663 370.419
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 10.211 | 0.426 | 11.538 | |
| GeneTonicList | 6.522 | 0.211 | 7.274 | |
| check_colors | 0.016 | 0.003 | 0.023 | |
| checkup_GeneTonic | 6.374 | 0.196 | 6.969 | |
| checkup_gtl | 6.432 | 0.158 | 7.114 | |
| cluster_markov | 0.180 | 0.006 | 0.203 | |
| create_jaccard_matrix | 2.559 | 0.180 | 2.917 | |
| create_kappa_matrix | 6.648 | 0.333 | 7.802 | |
| create_upsetdata | 0.091 | 0.118 | 0.223 | |
| deseqresult2df | 0.259 | 0.007 | 0.280 | |
| distill_enrichment | 7.323 | 0.220 | 8.367 | |
| enhance_table | 8.906 | 0.201 | 9.806 | |
| enrichment_map | 6.673 | 0.179 | 8.133 | |
| export_for_iSEE | 7.579 | 0.192 | 8.810 | |
| export_to_sif | 0.043 | 0.004 | 0.048 | |
| gene_plot | 6.991 | 0.187 | 7.942 | |
| geneinfo_2_html | 0.016 | 0.001 | 0.019 | |
| get_aggrscores | 6.496 | 0.193 | 7.294 | |
| get_expression_values | 4.85 | 0.16 | 5.47 | |
| ggs_backbone | 12.645 | 0.305 | 14.147 | |
| ggs_graph | 12.188 | 0.246 | 13.752 | |
| go_2_html | 0.052 | 0.001 | 0.060 | |
| gs_alluvial | 7.742 | 0.321 | 8.877 | |
| gs_dendro | 9.170 | 0.227 | 10.499 | |
| gs_fuzzyclustering | 1.724 | 0.080 | 2.123 | |
| gs_heatmap | 12.369 | 0.248 | 14.543 | |
| gs_horizon | 7.896 | 0.219 | 9.034 | |
| gs_mds | 12.836 | 0.318 | 14.449 | |
| gs_radar | 6.880 | 0.354 | 8.037 | |
| gs_scores | 8.777 | 0.173 | 9.616 | |
| gs_scoresheat | 8.435 | 0.305 | 9.678 | |
| gs_simplify | 3.206 | 0.065 | 3.511 | |
| gs_summary_heat | 5.860 | 0.150 | 6.827 | |
| gs_summary_overview | 6.150 | 0.179 | 6.938 | |
| gs_summary_overview_pair | 6.774 | 0.207 | 8.239 | |
| gs_upset | 12.761 | 0.267 | 15.525 | |
| gs_volcano | 7.429 | 0.198 | 8.587 | |
| happy_hour | 5.283 | 0.147 | 5.700 | |
| map2color | 0.019 | 0.003 | 0.023 | |
| overlap_coefficient | 0.001 | 0.001 | 0.002 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.002 | |
| shake_davidResult | 0.020 | 0.003 | 0.024 | |
| shake_enrichResult | 2.910 | 0.070 | 3.473 | |
| shake_enrichrResult | 0.112 | 0.005 | 0.123 | |
| shake_fgseaResult | 0.348 | 0.005 | 0.518 | |
| shake_gprofilerResult | 0.162 | 0.009 | 0.200 | |
| shake_gsenrichResult | 2.872 | 0.101 | 3.633 | |
| shake_topGOtableResult | 0.013 | 0.010 | 0.033 | |
| signature_volcano | 9.000 | 0.272 | 10.144 | |
| styleColorBar_divergent | 0.387 | 0.072 | 0.574 | |
| summarize_ggs_hubgenes | 12.865 | 0.319 | 15.342 | |