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 11:41 -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. |
| Package: GeneTonic |
| Version: 3.1.1 |
| 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_3.1.1.tar.gz |
| StartedAt: 2025-01-04 01:15:55 -0500 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 01:29:57 -0500 (Sat, 04 Jan 2025) |
| EllapsedTime: 842.3 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_3.1.1.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 '3.1.1'
* 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 ... 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 9.39 0.30 9.71
gs_mds 8.76 0.90 9.64
summarize_ggs_hubgenes 9.00 0.35 9.37
GeneTonic 8.19 0.31 8.84
gs_heatmap 7.16 0.82 7.25
gs_scoresheat 7.23 0.25 7.49
ggs_graph 7.08 0.30 7.37
signature_volcano 6.88 0.37 7.25
gs_dendro 6.70 0.44 7.16
ggs_backbone 6.48 0.43 7.86
gs_horizon 6.08 0.21 6.31
enhance_table 6.03 0.23 6.31
gene_plot 5.70 0.28 5.97
gs_alluvial 5.48 0.47 8.10
gs_radar 5.55 0.34 5.92
gs_scores 5.55 0.31 5.86
GeneTonicList 5.23 0.19 5.43
happy_hour 5.09 0.29 5.39
get_aggrscores 5.02 0.27 5.29
* 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: ### ### 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 v3.1.1
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!
|
| | 0%
|
| | 1%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|== | 4%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======= | 11%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========= | 14%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================ | 24%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|===================== | 31%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 32%
|
|======================= | 33%
|
|======================= | 34%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|============================== | 44%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 49%
|
|=================================== | 50%
|
|=================================== | 51%
|
|==================================== | 51%
|
|==================================== | 52%
|
|===================================== | 52%
|
|===================================== | 53%
|
|===================================== | 54%
|
|====================================== | 54%
|
|====================================== | 55%
|
|======================================= | 55%
|
|======================================= | 56%
|
|======================================== | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 59%
|
|========================================== | 60%
|
|========================================== | 61%
|
|=========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================ | 64%
|
|============================================= | 64%
|
|============================================= | 65%
|
|============================================== | 65%
|
|============================================== | 66%
|
|=============================================== | 66%
|
|=============================================== | 67%
|
|=============================================== | 68%
|
|================================================ | 68%
|
|================================================ | 69%
|
|================================================= | 69%
|
|================================================= | 70%
|
|================================================= | 71%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|=================================================== | 74%
|
|==================================================== | 74%
|
|==================================================== | 75%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 79%
|
|======================================================== | 80%
|
|======================================================== | 81%
|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|========================================================== | 84%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================= | 94%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 99%
|
|======================================================================| 100%
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
188.87 13.73 245.92
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 8.19 | 0.31 | 8.84 | |
| GeneTonicList | 5.23 | 0.19 | 5.43 | |
| check_colors | 0.00 | 0.02 | 0.02 | |
| checkup_GeneTonic | 4.62 | 0.18 | 4.81 | |
| checkup_gtl | 4.65 | 0.35 | 5.00 | |
| cluster_markov | 0.16 | 0.00 | 0.20 | |
| create_jaccard_matrix | 1.39 | 0.10 | 1.49 | |
| create_kappa_matrix | 3.08 | 0.48 | 3.56 | |
| create_upsetdata | 0.03 | 0.03 | 0.06 | |
| deprecated | 0 | 0 | 0 | |
| deseqresult2df | 0.14 | 0.02 | 0.16 | |
| distill_enrichment | 3.66 | 0.28 | 3.94 | |
| enhance_table | 6.03 | 0.23 | 6.31 | |
| enrichment_map | 4.72 | 0.18 | 4.89 | |
| export_for_iSEE | 4.02 | 0.15 | 4.17 | |
| export_to_sif | 0.03 | 0.00 | 0.03 | |
| gene_plot | 5.70 | 0.28 | 5.97 | |
| geneinfo_2_html | 0.01 | 0.00 | 0.01 | |
| get_aggrscores | 5.02 | 0.27 | 5.29 | |
| get_expression_values | 2.81 | 0.25 | 3.06 | |
| ggs_backbone | 6.48 | 0.43 | 7.86 | |
| ggs_graph | 7.08 | 0.30 | 7.37 | |
| go_2_html | 0.02 | 0.00 | 0.02 | |
| gs_alluvial | 5.48 | 0.47 | 8.10 | |
| gs_dendro | 6.70 | 0.44 | 7.16 | |
| gs_fuzzyclustering | 1.25 | 0.17 | 1.42 | |
| gs_heatmap | 7.16 | 0.82 | 7.25 | |
| gs_horizon | 6.08 | 0.21 | 6.31 | |
| gs_mds | 8.76 | 0.90 | 9.64 | |
| gs_radar | 5.55 | 0.34 | 5.92 | |
| gs_scores | 5.55 | 0.31 | 5.86 | |
| gs_scoresheat | 7.23 | 0.25 | 7.49 | |
| gs_simplify | 1.37 | 0.02 | 1.39 | |
| gs_summary_heat | 4.14 | 0.26 | 4.41 | |
| gs_summary_overview | 4.37 | 0.30 | 4.67 | |
| gs_summary_overview_pair | 4.19 | 0.22 | 4.40 | |
| gs_upset | 9.39 | 0.30 | 9.71 | |
| gs_volcano | 4.46 | 0.14 | 4.59 | |
| happy_hour | 5.09 | 0.29 | 5.39 | |
| map2color | 0.02 | 0.02 | 0.03 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.01 | 0.00 | 0.03 | |
| shake_enrichResult | 2.13 | 0.15 | 2.28 | |
| shake_enrichrResult | 0.11 | 0.00 | 0.16 | |
| shake_fgseaResult | 0.17 | 0.02 | 0.19 | |
| shake_gprofilerResult | 0.09 | 0.02 | 0.61 | |
| shake_gsenrichResult | 2.00 | 0.09 | 2.09 | |
| shake_topGOtableResult | 0 | 0 | 0 | |
| signature_volcano | 6.88 | 0.37 | 7.25 | |
| styleColorBar_divergent | 0.28 | 0.00 | 0.88 | |
| summarize_ggs_hubgenes | 9.00 | 0.35 | 9.37 | |