Federico Marini
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_16 |
| git_last_commit: cbc0a9f |
| git_last_commit_date: 2022-11-01 11:21:18 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:08 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the GeneTonic package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 773/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.2.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneTonic |
| Version: 2.2.0 |
| 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_2.2.0.tar.gz |
| StartedAt: 2023-04-10 20:22:23 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:31:01 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 518.5 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_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.2.0’
* 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 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 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 6.110 0.458 6.586
GeneTonic 6.143 0.227 6.403
summarize_ggs_hubgenes 6.119 0.245 6.398
gs_upset 5.958 0.175 6.150
gs_heatmap 5.543 0.186 5.744
signature_volcano 5.497 0.193 5.710
ggs_backbone 5.419 0.226 5.673
ggs_graph 5.356 0.241 5.618
gs_scores 4.965 0.330 5.387
gene_plot 4.980 0.208 5.253
* 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/4.2/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 329
Downregulated: 599
----- 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 4 | SKIP 0 | PASS 258 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 258 ]
>
> proc.time()
user system elapsed
192.718 15.653 160.215
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.143 | 0.227 | 6.403 | |
| GeneTonicList | 3.682 | 0.172 | 3.872 | |
| check_colors | 0.007 | 0.001 | 0.008 | |
| checkup_GeneTonic | 3.651 | 0.131 | 3.795 | |
| checkup_gtl | 3.629 | 0.166 | 3.820 | |
| cluster_markov | 0.090 | 0.004 | 0.095 | |
| create_jaccard_matrix | 0.769 | 0.065 | 0.844 | |
| create_kappa_matrix | 2.783 | 0.441 | 3.233 | |
| create_upsetdata | 0.034 | 0.035 | 0.070 | |
| deseqresult2df | 0.138 | 0.003 | 0.141 | |
| distill_enrichment | 3.965 | 0.172 | 4.155 | |
| enhance_table | 4.056 | 0.133 | 4.211 | |
| enrichment_map | 3.774 | 0.148 | 3.939 | |
| export_for_iSEE | 4.131 | 0.159 | 4.330 | |
| export_to_sif | 0.020 | 0.002 | 0.022 | |
| gene_plot | 4.980 | 0.208 | 5.253 | |
| geneinfo_2_html | 0.006 | 0.001 | 0.007 | |
| get_aggrscores | 3.540 | 0.116 | 3.667 | |
| get_expression_values | 3.014 | 0.148 | 3.221 | |
| ggs_backbone | 5.419 | 0.226 | 5.673 | |
| ggs_graph | 5.356 | 0.241 | 5.618 | |
| go_2_html | 0.019 | 0.000 | 0.020 | |
| gs_alluvial | 3.600 | 0.177 | 3.785 | |
| gs_dendro | 4.480 | 0.242 | 4.736 | |
| gs_fuzzyclustering | 0.737 | 0.066 | 0.807 | |
| gs_heatmap | 5.543 | 0.186 | 5.744 | |
| gs_horizon | 4.091 | 0.238 | 4.343 | |
| gs_mds | 6.110 | 0.458 | 6.586 | |
| gs_radar | 3.703 | 0.255 | 3.971 | |
| gs_scores | 4.965 | 0.330 | 5.387 | |
| gs_scoresheat | 3.994 | 0.206 | 4.216 | |
| gs_simplify | 1.011 | 0.035 | 1.054 | |
| gs_summary_heat | 3.960 | 0.193 | 4.179 | |
| gs_summary_overview | 3.489 | 0.126 | 3.631 | |
| gs_summary_overview_pair | 4.014 | 0.251 | 4.299 | |
| gs_upset | 5.958 | 0.175 | 6.150 | |
| gs_volcano | 3.272 | 0.114 | 3.398 | |
| happy_hour | 3.650 | 0.141 | 3.800 | |
| map2color | 0.011 | 0.008 | 0.020 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.013 | 0.001 | 0.014 | |
| shake_enrichResult | 1.702 | 0.042 | 1.751 | |
| shake_enrichrResult | 0.055 | 0.002 | 0.058 | |
| shake_fgseaResult | 0.139 | 0.003 | 0.143 | |
| shake_gprofilerResult | 0.080 | 0.002 | 0.085 | |
| shake_gsenrichResult | 1.825 | 0.063 | 1.898 | |
| shake_topGOtableResult | 0.007 | 0.001 | 0.008 | |
| signature_volcano | 5.497 | 0.193 | 5.710 | |
| styleColorBar_divergent | 0.215 | 0.035 | 0.251 | |
| summarize_ggs_hubgenes | 6.119 | 0.245 | 6.398 | |