Federico Marini
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 9473081 |
| git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 794/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.9.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 2.9.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneTonic_2.9.0.tar.gz |
| StartedAt: 2024-06-10 03:05:53 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 03:19:50 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 837.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneTonic_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '2.9.0'
* 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 ... 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
summarize_ggs_hubgenes 7.35 1.37 8.77
gs_heatmap 6.44 1.90 7.69
gs_mds 6.61 1.56 8.27
gs_upset 6.71 1.38 8.08
ggs_backbone 6.24 1.49 8.61
GeneTonic 6.39 1.23 7.97
ggs_graph 5.81 1.31 7.13
gs_dendro 5.28 1.54 6.91
gs_volcano 5.28 1.36 6.64
gs_scores 5.15 1.31 6.48
distill_enrichment 5.22 1.20 6.50
signature_volcano 5.25 1.12 6.47
gs_summary_heat 4.84 1.30 6.15
gs_scoresheat 4.85 1.20 6.11
gs_radar 4.28 1.58 5.94
gs_horizon 4.30 1.46 5.67
enrichment_map 4.32 1.36 5.68
export_for_iSEE 4.45 1.21 5.68
gs_summary_overview_pair 4.12 1.22 5.42
get_aggrscores 3.92 1.32 5.27
happy_hour 3.98 1.26 5.28
enhance_table 3.93 1.23 5.27
checkup_GeneTonic 3.94 1.19 5.22
GeneTonicList 3.86 1.17 5.13
gene_plot 3.81 1.18 5.03
gs_alluvial 3.05 1.27 5.78
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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)
>
> 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 264 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
165.26 20.25 233.86
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.39 | 1.23 | 7.97 | |
| GeneTonicList | 3.86 | 1.17 | 5.13 | |
| check_colors | 0.01 | 0.00 | 0.02 | |
| checkup_GeneTonic | 3.94 | 1.19 | 5.22 | |
| checkup_gtl | 3.03 | 1.13 | 4.17 | |
| cluster_markov | 0.11 | 0.03 | 0.16 | |
| create_jaccard_matrix | 0.89 | 0.03 | 0.92 | |
| create_kappa_matrix | 3.64 | 0.33 | 3.97 | |
| create_upsetdata | 0.06 | 0.06 | 0.13 | |
| deseqresult2df | 0.17 | 0.02 | 0.18 | |
| distill_enrichment | 5.22 | 1.20 | 6.50 | |
| enhance_table | 3.93 | 1.23 | 5.27 | |
| enrichment_map | 4.32 | 1.36 | 5.68 | |
| export_for_iSEE | 4.45 | 1.21 | 5.68 | |
| export_to_sif | 0.02 | 0.03 | 0.05 | |
| gene_plot | 3.81 | 1.18 | 5.03 | |
| geneinfo_2_html | 0 | 0 | 0 | |
| get_aggrscores | 3.92 | 1.32 | 5.27 | |
| get_expression_values | 3.47 | 1.15 | 4.69 | |
| ggs_backbone | 6.24 | 1.49 | 8.61 | |
| ggs_graph | 5.81 | 1.31 | 7.13 | |
| go_2_html | 0.03 | 0.00 | 0.03 | |
| gs_alluvial | 3.05 | 1.27 | 5.78 | |
| gs_dendro | 5.28 | 1.54 | 6.91 | |
| gs_fuzzyclustering | 0.78 | 0.13 | 0.90 | |
| gs_heatmap | 6.44 | 1.90 | 7.69 | |
| gs_horizon | 4.30 | 1.46 | 5.67 | |
| gs_mds | 6.61 | 1.56 | 8.27 | |
| gs_radar | 4.28 | 1.58 | 5.94 | |
| gs_scores | 5.15 | 1.31 | 6.48 | |
| gs_scoresheat | 4.85 | 1.20 | 6.11 | |
| gs_simplify | 1.07 | 0.03 | 1.10 | |
| gs_summary_heat | 4.84 | 1.30 | 6.15 | |
| gs_summary_overview | 3.47 | 1.45 | 4.94 | |
| gs_summary_overview_pair | 4.12 | 1.22 | 5.42 | |
| gs_upset | 6.71 | 1.38 | 8.08 | |
| gs_volcano | 5.28 | 1.36 | 6.64 | |
| happy_hour | 3.98 | 1.26 | 5.28 | |
| map2color | 0.01 | 0.00 | 0.02 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.02 | 0.00 | 0.03 | |
| shake_enrichResult | 1.87 | 1.00 | 2.93 | |
| shake_enrichrResult | 0.05 | 0.03 | 0.10 | |
| shake_fgseaResult | 0.2 | 0.0 | 0.2 | |
| shake_gprofilerResult | 0.10 | 0.04 | 0.17 | |
| shake_gsenrichResult | 1.84 | 1.01 | 2.91 | |
| shake_topGOtableResult | 0.00 | 0.02 | 0.01 | |
| signature_volcano | 5.25 | 1.12 | 6.47 | |
| styleColorBar_divergent | 0.22 | 0.10 | 0.67 | |
| summarize_ggs_hubgenes | 7.35 | 1.37 | 8.77 | |