Federico Marini
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: fe808f5 |
| git_last_commit_date: 2024-12-19 15:34:51 -0500 (Thu, 19 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 805/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.1.1 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 3.1.1 |
| 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_3.1.1.tar.gz |
| StartedAt: 2025-01-04 06:33:56 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 06:48:23 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 866.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### 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_3.1.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 9.835 0.048 9.905
ggs_graph 8.542 0.052 8.609
gs_heatmap 8.381 0.032 8.429
GeneTonic 8.181 0.191 8.393
gs_upset 7.983 0.048 8.045
ggs_backbone 7.471 0.048 7.533
summarize_ggs_hubgenes 7.339 0.060 7.410
gs_scoresheat 7.265 0.028 7.303
gs_dendro 6.622 0.020 6.653
gs_scores 6.211 0.028 6.252
signature_volcano 5.814 0.024 5.846
gs_volcano 5.738 0.092 5.838
gs_summary_overview 5.594 0.028 5.629
export_for_iSEE 5.560 0.056 5.629
create_kappa_matrix 5.539 0.068 5.617
enrichment_map 5.267 0.055 5.335
enhance_table 5.221 0.044 5.277
get_aggrscores 5.157 0.020 5.186
checkup_GeneTonic 5.111 0.047 5.167
GeneTonicList 5.056 0.072 5.138
* 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: 5 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck/00check.log’
for details.
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (GeneTonic)
GeneTonic.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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)
Warning: program compiled against libxml 212 using older 211
Welcome to GeneTonic v3.1.1
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 264 ]
>
> proc.time()
user system elapsed
258.583 9.683 233.199
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.181 | 0.191 | 8.393 | |
| GeneTonicList | 5.056 | 0.072 | 5.138 | |
| check_colors | 0.011 | 0.000 | 0.011 | |
| checkup_GeneTonic | 5.111 | 0.047 | 5.167 | |
| checkup_gtl | 3.798 | 0.044 | 3.850 | |
| cluster_markov | 0.115 | 0.000 | 0.116 | |
| create_jaccard_matrix | 1.496 | 0.032 | 1.531 | |
| create_kappa_matrix | 5.539 | 0.068 | 5.617 | |
| create_upsetdata | 0.034 | 0.008 | 0.042 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.155 | 0.000 | 0.155 | |
| distill_enrichment | 4.182 | 0.012 | 4.201 | |
| enhance_table | 5.221 | 0.044 | 5.277 | |
| enrichment_map | 5.267 | 0.055 | 5.335 | |
| export_for_iSEE | 5.560 | 0.056 | 5.629 | |
| export_to_sif | 0.031 | 0.000 | 0.031 | |
| gene_plot | 4.659 | 0.028 | 4.696 | |
| geneinfo_2_html | 0.012 | 0.000 | 0.012 | |
| get_aggrscores | 5.157 | 0.020 | 5.186 | |
| get_expression_values | 4.047 | 0.028 | 4.083 | |
| ggs_backbone | 7.471 | 0.048 | 7.533 | |
| ggs_graph | 8.542 | 0.052 | 8.609 | |
| go_2_html | 0.032 | 0.000 | 0.032 | |
| gs_alluvial | 4.053 | 0.032 | 4.128 | |
| gs_dendro | 6.622 | 0.020 | 6.653 | |
| gs_fuzzyclustering | 1.141 | 0.004 | 1.147 | |
| gs_heatmap | 8.381 | 0.032 | 8.429 | |
| gs_horizon | 4.635 | 0.032 | 4.678 | |
| gs_mds | 9.835 | 0.048 | 9.905 | |
| gs_radar | 4.016 | 0.036 | 4.061 | |
| gs_scores | 6.211 | 0.028 | 6.252 | |
| gs_scoresheat | 7.265 | 0.028 | 7.303 | |
| gs_simplify | 1.544 | 0.000 | 1.547 | |
| gs_summary_heat | 4.042 | 0.032 | 4.080 | |
| gs_summary_overview | 5.594 | 0.028 | 5.629 | |
| gs_summary_overview_pair | 3.969 | 0.019 | 3.995 | |
| gs_upset | 7.983 | 0.048 | 8.045 | |
| gs_volcano | 5.738 | 0.092 | 5.838 | |
| happy_hour | 3.684 | 0.012 | 3.700 | |
| map2color | 0.013 | 0.000 | 0.013 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.012 | 0.000 | 0.013 | |
| shake_enrichResult | 1.948 | 0.028 | 1.979 | |
| shake_enrichrResult | 0.060 | 0.000 | 0.062 | |
| shake_fgseaResult | 0.133 | 0.000 | 0.133 | |
| shake_gprofilerResult | 0.090 | 0.000 | 0.092 | |
| shake_gsenrichResult | 3.213 | 0.012 | 3.229 | |
| shake_topGOtableResult | 0.008 | 0.000 | 0.008 | |
| signature_volcano | 5.814 | 0.024 | 5.846 | |
| styleColorBar_divergent | 0.244 | 0.004 | 0.258 | |
| summarize_ggs_hubgenes | 7.339 | 0.060 | 7.410 | |