Federico Marini
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: eae9a03 |
| git_last_commit_date: 2024-10-29 10:43:15 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 803/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 3.1.0 (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 | | ||||||||
|
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: 3.1.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GeneTonic_3.1.0.tar.gz |
| StartedAt: 2024-11-28 00:49:32 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 01:03:42 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 850.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GeneTonic_3.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneTonic/DESCRIPTION' ... OK
* this is package 'GeneTonic' version '3.1.0'
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
export_for_iSEE.Rd: DESeqDataSet, DESeqResults
map2color.Rd: brewer.pal
signature_volcano.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 8.41 0.68 9.05
summarize_ggs_hubgenes 8.44 0.43 8.86
ggs_graph 8.51 0.30 8.82
gs_upset 8.22 0.48 8.67
GeneTonic 8.21 0.40 8.94
gs_heatmap 7.42 0.89 7.50
gs_dendro 6.60 0.58 7.17
signature_volcano 6.89 0.28 7.17
gs_scores 6.87 0.28 7.17
enhance_table 6.66 0.33 7.03
ggs_backbone 6.64 0.27 7.85
gs_volcano 6.36 0.19 6.55
gs_summary_overview 5.88 0.28 6.16
gs_radar 5.44 0.39 5.81
export_for_iSEE 5.49 0.19 5.67
gs_scoresheat 5.32 0.31 5.63
GeneTonicList 5.19 0.31 5.50
get_aggrscores 4.93 0.36 5.30
checkup_GeneTonic 4.98 0.27 5.25
checkup_gtl 4.83 0.20 5.03
gs_horizon 4.75 0.28 5.05
gs_alluvial 4.19 0.22 6.57
* 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: 1 NOTE
See
'E:/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck/00check.log'
for details.
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 v3.1.0
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 1 | SKIP 0 | PASS 262 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 262 ]
>
> proc.time()
user system elapsed
189.03 14.15 245.53
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.21 | 0.40 | 8.94 | |
| GeneTonicList | 5.19 | 0.31 | 5.50 | |
| check_colors | 0 | 0 | 0 | |
| checkup_GeneTonic | 4.98 | 0.27 | 5.25 | |
| checkup_gtl | 4.83 | 0.20 | 5.03 | |
| cluster_markov | 0.14 | 0.00 | 0.19 | |
| create_jaccard_matrix | 1.04 | 0.14 | 1.19 | |
| create_kappa_matrix | 3.71 | 0.53 | 4.22 | |
| create_upsetdata | 0.03 | 0.07 | 0.09 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.14 | 0.01 | 0.16 | |
| distill_enrichment | 4.02 | 0.38 | 4.39 | |
| enhance_table | 6.66 | 0.33 | 7.03 | |
| enrichment_map | 3.69 | 0.20 | 3.89 | |
| export_for_iSEE | 5.49 | 0.19 | 5.67 | |
| export_to_sif | 0.05 | 0.00 | 0.04 | |
| gene_plot | 4.64 | 0.32 | 4.97 | |
| geneinfo_2_html | 0 | 0 | 0 | |
| get_aggrscores | 4.93 | 0.36 | 5.30 | |
| get_expression_values | 2.52 | 0.30 | 2.79 | |
| ggs_backbone | 6.64 | 0.27 | 7.85 | |
| ggs_graph | 8.51 | 0.30 | 8.82 | |
| go_2_html | 0.03 | 0.00 | 0.03 | |
| gs_alluvial | 4.19 | 0.22 | 6.57 | |
| gs_dendro | 6.60 | 0.58 | 7.17 | |
| gs_fuzzyclustering | 1.15 | 0.26 | 1.42 | |
| gs_heatmap | 7.42 | 0.89 | 7.50 | |
| gs_horizon | 4.75 | 0.28 | 5.05 | |
| gs_mds | 8.41 | 0.68 | 9.05 | |
| gs_radar | 5.44 | 0.39 | 5.81 | |
| gs_scores | 6.87 | 0.28 | 7.17 | |
| gs_scoresheat | 5.32 | 0.31 | 5.63 | |
| gs_simplify | 1.56 | 0.05 | 1.61 | |
| gs_summary_heat | 4.28 | 0.22 | 4.50 | |
| gs_summary_overview | 5.88 | 0.28 | 6.16 | |
| gs_summary_overview_pair | 3.90 | 0.28 | 4.19 | |
| gs_upset | 8.22 | 0.48 | 8.67 | |
| gs_volcano | 6.36 | 0.19 | 6.55 | |
| happy_hour | 3.98 | 0.19 | 4.17 | |
| map2color | 0.02 | 0.00 | 0.02 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.01 | 0.00 | 0.04 | |
| shake_enrichResult | 2.20 | 0.18 | 2.37 | |
| shake_enrichrResult | 0.08 | 0.00 | 0.11 | |
| shake_fgseaResult | 0.16 | 0.00 | 0.16 | |
| shake_gprofilerResult | 0.13 | 0.00 | 0.14 | |
| shake_gsenrichResult | 1.97 | 0.15 | 2.11 | |
| shake_topGOtableResult | 0.01 | 0.00 | 0.02 | |
| signature_volcano | 6.89 | 0.28 | 7.17 | |
| styleColorBar_divergent | 0.30 | 0.07 | 1.53 | |
| summarize_ggs_hubgenes | 8.44 | 0.43 | 8.86 | |