Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 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: 3.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.0.0.tar.gz |
StartedAt: 2024-12-20 20:22:36 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 20:35:26 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 770.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneTonic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_3.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * 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 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_mds 8.265 0.528 8.816 gs_upset 7.785 0.219 8.019 GeneTonic 7.287 0.244 7.546 enhance_table 7.065 0.220 7.307 ggs_backbone 6.848 0.247 7.123 summarize_ggs_hubgenes 6.495 0.273 6.781 gs_heatmap 6.084 0.234 6.328 gs_dendro 6.034 0.226 6.281 gs_scoresheat 5.980 0.256 6.250 ggs_graph 5.962 0.266 6.230 signature_volcano 5.662 0.202 5.890 distill_enrichment 5.513 0.197 5.715 gs_summary_overview 5.471 0.168 5.654 gs_scores 5.323 0.282 5.608 checkup_gtl 5.122 0.160 5.310 gs_alluvial 5.040 0.234 5.311 checkup_GeneTonic 5.074 0.181 5.257 get_aggrscores 5.099 0.156 5.273 enrichment_map 5.076 0.153 5.248 gs_volcano 4.991 0.173 5.177 export_for_iSEE 5.011 0.145 5.174 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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! | | | 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% | 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GeneTonic.Rcheck/GeneTonic-Ex.timings
name | user | system | elapsed | |
GeneTonic | 7.287 | 0.244 | 7.546 | |
GeneTonicList | 4.418 | 0.147 | 4.598 | |
check_colors | 0.010 | 0.002 | 0.012 | |
checkup_GeneTonic | 5.074 | 0.181 | 5.257 | |
checkup_gtl | 5.122 | 0.160 | 5.310 | |
cluster_markov | 0.115 | 0.005 | 0.120 | |
create_jaccard_matrix | 0.884 | 0.043 | 0.933 | |
create_kappa_matrix | 2.945 | 0.352 | 3.348 | |
create_upsetdata | 0.043 | 0.038 | 0.082 | |
deprecated | 0 | 0 | 0 | |
deseqresult2df | 0.203 | 0.003 | 0.209 | |
distill_enrichment | 5.513 | 0.197 | 5.715 | |
enhance_table | 7.065 | 0.220 | 7.307 | |
enrichment_map | 5.076 | 0.153 | 5.248 | |
export_for_iSEE | 5.011 | 0.145 | 5.174 | |
export_to_sif | 0.020 | 0.002 | 0.023 | |
gene_plot | 4.347 | 0.192 | 4.547 | |
geneinfo_2_html | 0.009 | 0.001 | 0.010 | |
get_aggrscores | 5.099 | 0.156 | 5.273 | |
get_expression_values | 3.660 | 0.132 | 3.815 | |
ggs_backbone | 6.848 | 0.247 | 7.123 | |
ggs_graph | 5.962 | 0.266 | 6.230 | |
go_2_html | 0.021 | 0.001 | 0.022 | |
gs_alluvial | 5.040 | 0.234 | 5.311 | |
gs_dendro | 6.034 | 0.226 | 6.281 | |
gs_fuzzyclustering | 2.162 | 0.075 | 2.237 | |
gs_heatmap | 6.084 | 0.234 | 6.328 | |
gs_horizon | 4.479 | 0.158 | 4.643 | |
gs_mds | 8.265 | 0.528 | 8.816 | |
gs_radar | 3.421 | 0.236 | 3.713 | |
gs_scores | 5.323 | 0.282 | 5.608 | |
gs_scoresheat | 5.980 | 0.256 | 6.250 | |
gs_simplify | 1.097 | 0.054 | 1.151 | |
gs_summary_heat | 4.113 | 0.185 | 4.332 | |
gs_summary_overview | 5.471 | 0.168 | 5.654 | |
gs_summary_overview_pair | 3.417 | 0.141 | 3.575 | |
gs_upset | 7.785 | 0.219 | 8.019 | |
gs_volcano | 4.991 | 0.173 | 5.177 | |
happy_hour | 3.894 | 0.138 | 4.042 | |
map2color | 0.020 | 0.007 | 0.027 | |
overlap_coefficient | 0.000 | 0.000 | 0.001 | |
overlap_jaccard_index | 0.001 | 0.000 | 0.001 | |
shake_davidResult | 0.013 | 0.001 | 0.014 | |
shake_enrichResult | 2.329 | 0.053 | 2.387 | |
shake_enrichrResult | 0.038 | 0.002 | 0.040 | |
shake_fgseaResult | 0.110 | 0.001 | 0.113 | |
shake_gprofilerResult | 0.076 | 0.003 | 0.079 | |
shake_gsenrichResult | 2.648 | 0.081 | 2.731 | |
shake_topGOtableResult | 0.005 | 0.004 | 0.009 | |
signature_volcano | 5.662 | 0.202 | 5.890 | |
styleColorBar_divergent | 0.279 | 0.029 | 0.310 | |
summarize_ggs_hubgenes | 6.495 | 0.273 | 6.781 | |