Federico Marini
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 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 2024-06-25 17:42 -0400 (Tue, 25 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" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 | | ||||||||
| 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: 2024-06-24 04:59:41 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 05:21:42 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 1321.0 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_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: 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 12.860 0.365 15.110
gs_upset 12.845 0.247 14.992
summarize_ggs_hubgenes 12.493 0.315 14.017
gs_heatmap 12.288 0.270 14.789
ggs_backbone 11.442 0.346 26.422
ggs_graph 11.370 0.346 11.990
GeneTonic 10.363 0.494 12.790
signature_volcano 9.113 0.287 10.862
gs_dendro 9.134 0.262 11.021
enhance_table 9.148 0.221 10.526
gs_scores 8.563 0.178 9.766
gs_scoresheat 8.513 0.228 10.670
gs_horizon 7.901 0.182 9.365
gs_alluvial 7.714 0.356 9.385
gs_volcano 7.515 0.186 9.237
distill_enrichment 7.435 0.193 8.522
export_for_iSEE 7.435 0.159 8.404
gene_plot 6.973 0.190 7.769
gs_radar 6.761 0.395 8.167
gs_summary_overview_pair 6.801 0.196 8.112
create_kappa_matrix 6.556 0.384 8.159
GeneTonicList 6.606 0.243 7.975
get_aggrscores 6.519 0.212 7.569
enrichment_map 6.489 0.176 7.502
checkup_GeneTonic 6.433 0.219 7.457
checkup_gtl 6.414 0.188 7.607
gs_summary_overview 6.295 0.177 7.780
gs_summary_heat 5.885 0.162 7.266
happy_hour 5.394 0.148 6.708
get_expression_values 4.991 0.178 5.879
styleColorBar_divergent 0.390 0.087 15.095
* 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 (2024-04-24) -- "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
366.892 16.934 400.162
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 10.363 | 0.494 | 12.790 | |
| GeneTonicList | 6.606 | 0.243 | 7.975 | |
| check_colors | 0.018 | 0.003 | 0.024 | |
| checkup_GeneTonic | 6.433 | 0.219 | 7.457 | |
| checkup_gtl | 6.414 | 0.188 | 7.607 | |
| cluster_markov | 0.174 | 0.006 | 0.208 | |
| create_jaccard_matrix | 2.528 | 0.176 | 3.148 | |
| create_kappa_matrix | 6.556 | 0.384 | 8.159 | |
| create_upsetdata | 0.091 | 0.124 | 0.251 | |
| deseqresult2df | 0.262 | 0.007 | 0.315 | |
| distill_enrichment | 7.435 | 0.193 | 8.522 | |
| enhance_table | 9.148 | 0.221 | 10.526 | |
| enrichment_map | 6.489 | 0.176 | 7.502 | |
| export_for_iSEE | 7.435 | 0.159 | 8.404 | |
| export_to_sif | 0.040 | 0.004 | 0.050 | |
| gene_plot | 6.973 | 0.190 | 7.769 | |
| geneinfo_2_html | 0.015 | 0.001 | 0.017 | |
| get_aggrscores | 6.519 | 0.212 | 7.569 | |
| get_expression_values | 4.991 | 0.178 | 5.879 | |
| ggs_backbone | 11.442 | 0.346 | 26.422 | |
| ggs_graph | 11.370 | 0.346 | 11.990 | |
| go_2_html | 0.039 | 0.001 | 0.041 | |
| gs_alluvial | 7.714 | 0.356 | 9.385 | |
| gs_dendro | 9.134 | 0.262 | 11.021 | |
| gs_fuzzyclustering | 1.731 | 0.070 | 2.058 | |
| gs_heatmap | 12.288 | 0.270 | 14.789 | |
| gs_horizon | 7.901 | 0.182 | 9.365 | |
| gs_mds | 12.860 | 0.365 | 15.110 | |
| gs_radar | 6.761 | 0.395 | 8.167 | |
| gs_scores | 8.563 | 0.178 | 9.766 | |
| gs_scoresheat | 8.513 | 0.228 | 10.670 | |
| gs_simplify | 3.260 | 0.089 | 4.461 | |
| gs_summary_heat | 5.885 | 0.162 | 7.266 | |
| gs_summary_overview | 6.295 | 0.177 | 7.780 | |
| gs_summary_overview_pair | 6.801 | 0.196 | 8.112 | |
| gs_upset | 12.845 | 0.247 | 14.992 | |
| gs_volcano | 7.515 | 0.186 | 9.237 | |
| happy_hour | 5.394 | 0.148 | 6.708 | |
| map2color | 0.018 | 0.003 | 0.025 | |
| overlap_coefficient | 0.001 | 0.001 | 0.003 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.002 | |
| shake_davidResult | 0.020 | 0.003 | 0.029 | |
| shake_enrichResult | 2.896 | 0.065 | 3.620 | |
| shake_enrichrResult | 0.114 | 0.004 | 0.139 | |
| shake_fgseaResult | 0.354 | 0.005 | 0.441 | |
| shake_gprofilerResult | 0.166 | 0.008 | 0.219 | |
| shake_gsenrichResult | 2.951 | 0.100 | 3.811 | |
| shake_topGOtableResult | 0.012 | 0.009 | 0.032 | |
| signature_volcano | 9.113 | 0.287 | 10.862 | |
| styleColorBar_divergent | 0.390 | 0.087 | 15.095 | |
| summarize_ggs_hubgenes | 12.493 | 0.315 | 14.017 | |