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 17:43 -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 20:40:22 -0400 (Mon, 08 Jul 2024) |
| EndedAt: 2024-07-08 20:51:40 -0400 (Mon, 08 Jul 2024) |
| EllapsedTime: 677.3 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: aarch64-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 Ventura 13.6.6
* 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 8.180 0.361 8.638
GeneTonic 7.970 0.232 8.316
ggs_graph 7.327 0.303 7.696
gs_upset 6.980 0.218 7.261
signature_volcano 6.791 0.234 7.047
gs_heatmap 6.257 0.241 6.643
summarize_ggs_hubgenes 6.265 0.231 6.504
gs_scoresheat 5.931 0.235 6.264
GeneTonicList 5.885 0.176 6.087
ggs_backbone 5.736 0.307 6.101
gs_horizon 5.802 0.181 6.054
gene_plot 5.621 0.229 5.964
gs_dendro 5.637 0.212 5.949
gs_scores 5.473 0.286 5.832
gs_summary_overview 5.522 0.214 5.847
gs_radar 5.303 0.211 5.614
distill_enrichment 5.301 0.204 5.554
gs_alluvial 5.219 0.201 5.464
enhance_table 5.109 0.226 5.374
happy_hour 4.981 0.164 5.183
get_aggrscores 4.893 0.197 5.114
checkup_GeneTonic 4.920 0.149 5.119
checkup_gtl 4.877 0.154 5.049
* 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-arm64/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: aarch64-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
230.531 11.694 201.286
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.970 | 0.232 | 8.316 | |
| GeneTonicList | 5.885 | 0.176 | 6.087 | |
| check_colors | 0.010 | 0.001 | 0.011 | |
| checkup_GeneTonic | 4.920 | 0.149 | 5.119 | |
| checkup_gtl | 4.877 | 0.154 | 5.049 | |
| cluster_markov | 0.142 | 0.013 | 0.156 | |
| create_jaccard_matrix | 0.856 | 0.049 | 0.922 | |
| create_kappa_matrix | 3.379 | 0.238 | 3.664 | |
| create_upsetdata | 0.041 | 0.039 | 0.082 | |
| deseqresult2df | 0.213 | 0.005 | 0.219 | |
| distill_enrichment | 5.301 | 0.204 | 5.554 | |
| enhance_table | 5.109 | 0.226 | 5.374 | |
| enrichment_map | 4.572 | 0.197 | 4.929 | |
| export_for_iSEE | 4.306 | 0.214 | 4.736 | |
| export_to_sif | 0.024 | 0.002 | 0.026 | |
| gene_plot | 5.621 | 0.229 | 5.964 | |
| geneinfo_2_html | 0.007 | 0.001 | 0.008 | |
| get_aggrscores | 4.893 | 0.197 | 5.114 | |
| get_expression_values | 3.920 | 0.148 | 4.085 | |
| ggs_backbone | 5.736 | 0.307 | 6.101 | |
| ggs_graph | 7.327 | 0.303 | 7.696 | |
| go_2_html | 0.019 | 0.001 | 0.020 | |
| gs_alluvial | 5.219 | 0.201 | 5.464 | |
| gs_dendro | 5.637 | 0.212 | 5.949 | |
| gs_fuzzyclustering | 0.691 | 0.055 | 0.773 | |
| gs_heatmap | 6.257 | 0.241 | 6.643 | |
| gs_horizon | 5.802 | 0.181 | 6.054 | |
| gs_mds | 8.180 | 0.361 | 8.638 | |
| gs_radar | 5.303 | 0.211 | 5.614 | |
| gs_scores | 5.473 | 0.286 | 5.832 | |
| gs_scoresheat | 5.931 | 0.235 | 6.264 | |
| gs_simplify | 1.174 | 0.046 | 1.237 | |
| gs_summary_heat | 4.137 | 0.168 | 4.362 | |
| gs_summary_overview | 5.522 | 0.214 | 5.847 | |
| gs_summary_overview_pair | 3.784 | 0.163 | 3.980 | |
| gs_upset | 6.980 | 0.218 | 7.261 | |
| gs_volcano | 4.294 | 0.184 | 4.545 | |
| happy_hour | 4.981 | 0.164 | 5.183 | |
| map2color | 0.018 | 0.002 | 0.020 | |
| overlap_coefficient | 0.000 | 0.001 | 0.001 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.014 | 0.001 | 0.016 | |
| shake_enrichResult | 2.642 | 0.078 | 2.728 | |
| shake_enrichrResult | 0.076 | 0.002 | 0.079 | |
| shake_fgseaResult | 0.173 | 0.002 | 0.174 | |
| shake_gprofilerResult | 0.235 | 0.005 | 0.240 | |
| shake_gsenrichResult | 2.538 | 0.053 | 2.592 | |
| shake_topGOtableResult | 0.010 | 0.001 | 0.011 | |
| signature_volcano | 6.791 | 0.234 | 7.047 | |
| styleColorBar_divergent | 0.148 | 0.020 | 0.171 | |
| summarize_ggs_hubgenes | 6.265 | 0.231 | 6.504 | |