Federico Marini
| Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 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 2024-06-07 20:27 -0400 (Fri, 07 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" | 4755 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
| kjohnson3 | macOS 13.6.5 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 | | ||||||||
| 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: 2024-06-05 20:35:59 -0400 (Wed, 05 Jun 2024) |
| EndedAt: 2024-06-05 20:46:20 -0400 (Wed, 05 Jun 2024) |
| EllapsedTime: 621.9 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 12.7.1
* 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 7.346 0.289 7.666
ggs_graph 7.353 0.227 7.615
summarize_ggs_hubgenes 7.227 0.285 7.543
ggs_backbone 7.192 0.260 7.495
gs_mds 6.947 0.399 7.372
gs_heatmap 6.578 0.216 6.823
gs_upset 6.484 0.197 6.716
enhance_table 5.699 0.186 5.907
signature_volcano 5.487 0.212 5.732
gs_alluvial 5.211 0.314 5.546
gs_dendro 5.264 0.223 5.509
gs_scoresheat 5.107 0.236 5.368
gs_scores 4.968 0.184 5.167
* 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
191.495 10.380 175.651
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.346 | 0.289 | 7.666 | |
| GeneTonicList | 4.179 | 0.161 | 4.360 | |
| check_colors | 0.009 | 0.002 | 0.011 | |
| checkup_GeneTonic | 3.829 | 0.165 | 4.009 | |
| checkup_gtl | 4.281 | 0.155 | 4.456 | |
| cluster_markov | 0.113 | 0.004 | 0.118 | |
| create_jaccard_matrix | 0.959 | 0.070 | 1.032 | |
| create_kappa_matrix | 3.515 | 0.427 | 3.956 | |
| create_upsetdata | 0.039 | 0.048 | 0.087 | |
| deseqresult2df | 0.172 | 0.003 | 0.177 | |
| distill_enrichment | 4.670 | 0.165 | 4.872 | |
| enhance_table | 5.699 | 0.186 | 5.907 | |
| enrichment_map | 4.499 | 0.156 | 4.682 | |
| export_for_iSEE | 4.741 | 0.145 | 4.899 | |
| export_to_sif | 0.026 | 0.002 | 0.028 | |
| gene_plot | 4.206 | 0.191 | 4.435 | |
| geneinfo_2_html | 0.008 | 0.000 | 0.007 | |
| get_aggrscores | 4.526 | 0.160 | 4.731 | |
| get_expression_values | 3.458 | 0.150 | 3.632 | |
| ggs_backbone | 7.192 | 0.260 | 7.495 | |
| ggs_graph | 7.353 | 0.227 | 7.615 | |
| go_2_html | 0.020 | 0.001 | 0.021 | |
| gs_alluvial | 5.211 | 0.314 | 5.546 | |
| gs_dendro | 5.264 | 0.223 | 5.509 | |
| gs_fuzzyclustering | 0.870 | 0.056 | 0.931 | |
| gs_heatmap | 6.578 | 0.216 | 6.823 | |
| gs_horizon | 4.649 | 0.156 | 4.828 | |
| gs_mds | 6.947 | 0.399 | 7.372 | |
| gs_radar | 4.325 | 0.285 | 4.628 | |
| gs_scores | 4.968 | 0.184 | 5.167 | |
| gs_scoresheat | 5.107 | 0.236 | 5.368 | |
| gs_simplify | 1.353 | 0.048 | 1.416 | |
| gs_summary_heat | 3.799 | 0.143 | 3.962 | |
| gs_summary_overview | 3.835 | 0.145 | 3.999 | |
| gs_summary_overview_pair | 4.485 | 0.157 | 4.665 | |
| gs_upset | 6.484 | 0.197 | 6.716 | |
| gs_volcano | 4.700 | 0.178 | 4.910 | |
| happy_hour | 3.349 | 0.118 | 3.477 | |
| map2color | 0.013 | 0.004 | 0.018 | |
| overlap_coefficient | 0.001 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.000 | |
| shake_davidResult | 0.013 | 0.001 | 0.014 | |
| shake_enrichResult | 1.922 | 0.036 | 1.968 | |
| shake_enrichrResult | 0.069 | 0.003 | 0.073 | |
| shake_fgseaResult | 0.243 | 0.002 | 0.246 | |
| shake_gprofilerResult | 0.112 | 0.005 | 0.121 | |
| shake_gsenrichResult | 1.986 | 0.085 | 2.082 | |
| shake_topGOtableResult | 0.008 | 0.012 | 0.027 | |
| signature_volcano | 5.487 | 0.212 | 5.732 | |
| styleColorBar_divergent | 0.239 | 0.045 | 0.290 | |
| summarize_ggs_hubgenes | 7.227 | 0.285 | 7.543 | |