Federico Marini
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_20 |
| git_last_commit: d04704c |
| git_last_commit_date: 2024-10-29 10:43:15 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 810/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.0.0 (landing page) Federico Marini
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeneTonic |
| Version: 3.0.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneTonic_3.0.0.tar.gz |
| StartedAt: 2024-11-20 08:08:18 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 08:22:32 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 854.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneTonic_3.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.0.0’
* 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 loading without being on the library search path ... 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_upset 8.910 0.112 9.038
ggs_backbone 8.830 0.040 8.805
gs_heatmap 8.426 0.199 8.642
GeneTonic 8.311 0.168 8.497
gs_mds 8.206 0.040 8.168
summarize_ggs_hubgenes 7.402 0.044 7.461
ggs_graph 6.986 0.084 7.086
gs_scoresheat 6.914 0.084 7.009
distill_enrichment 6.750 0.088 6.789
signature_volcano 5.913 0.036 5.959
gs_scores 5.880 0.012 5.902
gs_horizon 5.660 0.060 5.731
export_for_iSEE 5.539 0.080 5.630
enhance_table 5.400 0.020 5.377
gs_dendro 5.375 0.040 5.426
gs_radar 5.222 0.056 5.290
get_aggrscores 5.092 0.107 5.214
GeneTonicList 5.091 0.096 5.196
enrichment_map 5.126 0.056 5.192
checkup_GeneTonic 5.032 0.107 5.149
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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-unknown-linux-gnu
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)
Welcome to GeneTonic v3.0.0
If you use GeneTonic in your work, please cite:
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
BMC Bioinformatics, 2021 - https://doi.org/10.1186/s12859-021-04461-5
and/or (if adopting the series of protocols as a whole)
Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, ideal, and GeneTonic
Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin Strauch, Federico Marini
Current Protocols, 2022 - https://doi.org/10.1002/cpz1.411
>
> 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 262 ]
>
> proc.time()
user system elapsed
263.445 10.033 222.402
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.311 | 0.168 | 8.497 | |
| GeneTonicList | 5.091 | 0.096 | 5.196 | |
| check_colors | 0.011 | 0.000 | 0.010 | |
| checkup_GeneTonic | 5.032 | 0.107 | 5.149 | |
| checkup_gtl | 3.734 | 0.044 | 3.784 | |
| cluster_markov | 0.105 | 0.004 | 0.109 | |
| create_jaccard_matrix | 1.118 | 0.020 | 1.140 | |
| create_kappa_matrix | 3.912 | 0.036 | 3.955 | |
| create_upsetdata | 0.037 | 0.004 | 0.040 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.156 | 0.004 | 0.161 | |
| distill_enrichment | 6.750 | 0.088 | 6.789 | |
| enhance_table | 5.400 | 0.020 | 5.377 | |
| enrichment_map | 5.126 | 0.056 | 5.192 | |
| export_for_iSEE | 5.539 | 0.080 | 5.630 | |
| export_to_sif | 0.033 | 0.000 | 0.033 | |
| gene_plot | 4.705 | 0.044 | 4.757 | |
| geneinfo_2_html | 0.011 | 0.000 | 0.012 | |
| get_aggrscores | 5.092 | 0.107 | 5.214 | |
| get_expression_values | 2.798 | 0.020 | 2.824 | |
| ggs_backbone | 8.830 | 0.040 | 8.805 | |
| ggs_graph | 6.986 | 0.084 | 7.086 | |
| go_2_html | 0.030 | 0.003 | 0.033 | |
| gs_alluvial | 3.935 | 0.036 | 3.978 | |
| gs_dendro | 5.375 | 0.040 | 5.426 | |
| gs_fuzzyclustering | 1.067 | 0.000 | 1.070 | |
| gs_heatmap | 8.426 | 0.199 | 8.642 | |
| gs_horizon | 5.660 | 0.060 | 5.731 | |
| gs_mds | 8.206 | 0.040 | 8.168 | |
| gs_radar | 5.222 | 0.056 | 5.290 | |
| gs_scores | 5.880 | 0.012 | 5.902 | |
| gs_scoresheat | 6.914 | 0.084 | 7.009 | |
| gs_simplify | 1.510 | 0.000 | 1.513 | |
| gs_summary_heat | 3.910 | 0.028 | 3.945 | |
| gs_summary_overview | 4.125 | 0.016 | 4.149 | |
| gs_summary_overview_pair | 3.903 | 0.048 | 3.958 | |
| gs_upset | 8.910 | 0.112 | 9.038 | |
| gs_volcano | 4.189 | 0.008 | 4.203 | |
| happy_hour | 3.650 | 0.043 | 3.701 | |
| map2color | 0.013 | 0.000 | 0.013 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.011 | 0.000 | 0.013 | |
| shake_enrichResult | 1.994 | 0.028 | 2.026 | |
| shake_enrichrResult | 0.059 | 0.004 | 0.064 | |
| shake_fgseaResult | 0.135 | 0.000 | 0.135 | |
| shake_gprofilerResult | 0.095 | 0.000 | 0.096 | |
| shake_gsenrichResult | 3.246 | 0.008 | 3.260 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.007 | |
| signature_volcano | 5.913 | 0.036 | 5.959 | |
| styleColorBar_divergent | 0.24 | 0.00 | 0.25 | |
| summarize_ggs_hubgenes | 7.402 | 0.044 | 7.461 | |