Federico Marini
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_17 |
| git_last_commit: 55e4ea5 |
| git_last_commit_date: 2023-09-28 10:09:47 -0400 (Thu, 28 Sep 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:04 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 794/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.4.2 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2.4.2 |
| 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_2.4.2.tar.gz |
| StartedAt: 2023-10-16 02:00:42 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:22:59 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 1336.9 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_2.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GeneTonic.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.4.2’
* 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 R 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 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 13.122 0.526 16.601
gs_upset 12.708 0.255 16.735
ggs_backbone 11.732 0.342 15.324
summarize_ggs_hubgenes 11.495 0.303 15.649
gs_heatmap 10.732 0.308 13.961
ggs_graph 10.471 0.293 14.470
signature_volcano 9.525 0.326 14.013
gs_scoresheat 9.169 0.463 13.021
GeneTonic 8.914 0.421 11.935
gs_dendro 8.870 0.245 11.670
gs_scores 8.465 0.405 11.957
distill_enrichment 7.782 0.255 10.299
gs_horizon 7.727 0.276 9.725
enhance_table 7.604 0.172 9.844
gene_plot 7.257 0.186 9.351
gs_summary_overview 6.995 0.297 9.597
export_for_iSEE 7.103 0.160 9.182
gs_radar 6.785 0.469 9.672
gs_alluvial 6.475 0.326 9.095
gs_volcano 6.439 0.190 8.637
create_kappa_matrix 6.202 0.425 8.437
enrichment_map 6.288 0.162 8.129
GeneTonicList 6.229 0.212 8.226
checkup_gtl 6.171 0.182 7.933
checkup_GeneTonic 6.162 0.176 7.682
get_aggrscores 5.999 0.192 8.167
gs_summary_overview_pair 5.861 0.217 8.895
gs_summary_heat 5.778 0.216 7.939
happy_hour 5.361 0.177 7.836
get_expression_values 3.872 0.170 5.098
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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...
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, 928 found as DE
Upregulated: 599
Downregulated: 329
----- 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 2 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
352.437 15.411 420.079
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.914 | 0.421 | 11.935 | |
| GeneTonicList | 6.229 | 0.212 | 8.226 | |
| check_colors | 0.018 | 0.004 | 0.025 | |
| checkup_GeneTonic | 6.162 | 0.176 | 7.682 | |
| checkup_gtl | 6.171 | 0.182 | 7.933 | |
| cluster_markov | 0.231 | 0.023 | 0.329 | |
| create_jaccard_matrix | 2.257 | 0.195 | 3.141 | |
| create_kappa_matrix | 6.202 | 0.425 | 8.437 | |
| create_upsetdata | 0.085 | 0.129 | 0.262 | |
| deseqresult2df | 0.248 | 0.013 | 0.317 | |
| distill_enrichment | 7.782 | 0.255 | 10.299 | |
| enhance_table | 7.604 | 0.172 | 9.844 | |
| enrichment_map | 6.288 | 0.162 | 8.129 | |
| export_for_iSEE | 7.103 | 0.160 | 9.182 | |
| export_to_sif | 0.037 | 0.003 | 0.050 | |
| gene_plot | 7.257 | 0.186 | 9.351 | |
| geneinfo_2_html | 0.015 | 0.001 | 0.021 | |
| get_aggrscores | 5.999 | 0.192 | 8.167 | |
| get_expression_values | 3.872 | 0.170 | 5.098 | |
| ggs_backbone | 11.732 | 0.342 | 15.324 | |
| ggs_graph | 10.471 | 0.293 | 14.470 | |
| go_2_html | 0.045 | 0.001 | 0.058 | |
| gs_alluvial | 6.475 | 0.326 | 9.095 | |
| gs_dendro | 8.870 | 0.245 | 11.670 | |
| gs_fuzzyclustering | 1.711 | 0.081 | 2.314 | |
| gs_heatmap | 10.732 | 0.308 | 13.961 | |
| gs_horizon | 7.727 | 0.276 | 9.725 | |
| gs_mds | 13.122 | 0.526 | 16.601 | |
| gs_radar | 6.785 | 0.469 | 9.672 | |
| gs_scores | 8.465 | 0.405 | 11.957 | |
| gs_scoresheat | 9.169 | 0.463 | 13.021 | |
| gs_simplify | 2.937 | 0.117 | 4.278 | |
| gs_summary_heat | 5.778 | 0.216 | 7.939 | |
| gs_summary_overview | 6.995 | 0.297 | 9.597 | |
| gs_summary_overview_pair | 5.861 | 0.217 | 8.895 | |
| gs_upset | 12.708 | 0.255 | 16.735 | |
| gs_volcano | 6.439 | 0.190 | 8.637 | |
| happy_hour | 5.361 | 0.177 | 7.836 | |
| map2color | 0.018 | 0.004 | 0.029 | |
| overlap_coefficient | 0.001 | 0.001 | 0.001 | |
| overlap_jaccard_index | 0.001 | 0.001 | 0.001 | |
| shake_davidResult | 0.019 | 0.002 | 0.029 | |
| shake_enrichResult | 2.975 | 0.083 | 4.071 | |
| shake_enrichrResult | 0.110 | 0.004 | 0.167 | |
| shake_fgseaResult | 0.254 | 0.013 | 0.362 | |
| shake_gprofilerResult | 0.163 | 0.016 | 0.238 | |
| shake_gsenrichResult | 2.982 | 0.105 | 4.236 | |
| shake_topGOtableResult | 0.012 | 0.010 | 0.028 | |
| signature_volcano | 9.525 | 0.326 | 14.013 | |
| styleColorBar_divergent | 0.362 | 0.072 | 0.621 | |
| summarize_ggs_hubgenes | 11.495 | 0.303 | 15.649 | |