Federico Marini
| Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 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 2024-07-09 17:41 -0400 (Tue, 09 Jul 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" | 4709 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 12.7.4 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: 2.8.0 |
| 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: 2024-07-08 05:05:26 -0400 (Mon, 08 Jul 2024) |
| EndedAt: 2024-07-08 05:26:36 -0400 (Mon, 08 Jul 2024) |
| EllapsedTime: 1270.5 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_2.8.0.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 12.7.4
* 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 13.564 0.544 16.015
gs_upset 12.828 0.258 15.776
ggs_graph 12.080 0.362 14.604
summarize_ggs_hubgenes 12.043 0.302 14.889
ggs_backbone 11.797 0.433 14.769
gs_heatmap 11.304 0.341 13.154
signature_volcano 9.886 0.329 12.668
GeneTonic 9.751 0.444 11.397
gs_scoresheat 9.328 0.249 11.013
gs_dendro 9.279 0.296 11.197
gs_scores 8.684 0.237 10.426
enhance_table 8.235 0.242 9.937
gs_horizon 7.903 0.245 9.298
gene_plot 7.885 0.238 9.175
GeneTonicList 7.344 0.243 8.689
distill_enrichment 7.177 0.195 8.582
gs_summary_overview 7.139 0.209 9.178
gs_alluvial 6.888 0.349 8.512
gs_radar 6.832 0.380 8.494
create_kappa_matrix 6.537 0.423 8.059
export_for_iSEE 6.628 0.173 7.756
enrichment_map 6.573 0.218 7.865
gs_volcano 6.574 0.171 7.875
checkup_gtl 6.480 0.251 7.753
get_aggrscores 6.495 0.178 7.723
checkup_GeneTonic 6.439 0.220 7.682
happy_hour 6.432 0.207 7.730
gs_summary_overview_pair 5.954 0.178 7.659
gs_summary_heat 5.897 0.193 7.236
get_expression_values 4.952 0.204 6.148
* 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
368.061 17.611 387.372
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.751 | 0.444 | 11.397 | |
| GeneTonicList | 7.344 | 0.243 | 8.689 | |
| check_colors | 0.017 | 0.003 | 0.021 | |
| checkup_GeneTonic | 6.439 | 0.220 | 7.682 | |
| checkup_gtl | 6.480 | 0.251 | 7.753 | |
| cluster_markov | 0.231 | 0.025 | 0.281 | |
| create_jaccard_matrix | 2.470 | 0.228 | 3.149 | |
| create_kappa_matrix | 6.537 | 0.423 | 8.059 | |
| create_upsetdata | 0.091 | 0.129 | 0.252 | |
| deseqresult2df | 0.262 | 0.007 | 0.311 | |
| distill_enrichment | 7.177 | 0.195 | 8.582 | |
| enhance_table | 8.235 | 0.242 | 9.937 | |
| enrichment_map | 6.573 | 0.218 | 7.865 | |
| export_for_iSEE | 6.628 | 0.173 | 7.756 | |
| export_to_sif | 0.038 | 0.004 | 0.047 | |
| gene_plot | 7.885 | 0.238 | 9.175 | |
| geneinfo_2_html | 0.016 | 0.001 | 0.019 | |
| get_aggrscores | 6.495 | 0.178 | 7.723 | |
| get_expression_values | 4.952 | 0.204 | 6.148 | |
| ggs_backbone | 11.797 | 0.433 | 14.769 | |
| ggs_graph | 12.080 | 0.362 | 14.604 | |
| go_2_html | 0.054 | 0.002 | 0.069 | |
| gs_alluvial | 6.888 | 0.349 | 8.512 | |
| gs_dendro | 9.279 | 0.296 | 11.197 | |
| gs_fuzzyclustering | 1.768 | 0.075 | 2.102 | |
| gs_heatmap | 11.304 | 0.341 | 13.154 | |
| gs_horizon | 7.903 | 0.245 | 9.298 | |
| gs_mds | 13.564 | 0.544 | 16.015 | |
| gs_radar | 6.832 | 0.380 | 8.494 | |
| gs_scores | 8.684 | 0.237 | 10.426 | |
| gs_scoresheat | 9.328 | 0.249 | 11.013 | |
| gs_simplify | 3.167 | 0.074 | 3.674 | |
| gs_summary_heat | 5.897 | 0.193 | 7.236 | |
| gs_summary_overview | 7.139 | 0.209 | 9.178 | |
| gs_summary_overview_pair | 5.954 | 0.178 | 7.659 | |
| gs_upset | 12.828 | 0.258 | 15.776 | |
| gs_volcano | 6.574 | 0.171 | 7.875 | |
| happy_hour | 6.432 | 0.207 | 7.730 | |
| map2color | 0.019 | 0.004 | 0.031 | |
| overlap_coefficient | 0.001 | 0.001 | 0.002 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.020 | 0.003 | 0.023 | |
| shake_enrichResult | 2.968 | 0.099 | 3.760 | |
| shake_enrichrResult | 0.113 | 0.004 | 0.135 | |
| shake_fgseaResult | 0.258 | 0.005 | 0.320 | |
| shake_gprofilerResult | 0.258 | 0.009 | 0.320 | |
| shake_gsenrichResult | 2.841 | 0.072 | 3.563 | |
| shake_topGOtableResult | 0.012 | 0.002 | 0.016 | |
| signature_volcano | 9.886 | 0.329 | 12.668 | |
| styleColorBar_divergent | 0.389 | 0.068 | 0.600 | |
| summarize_ggs_hubgenes | 12.043 | 0.302 | 14.889 | |