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This page was generated on 2021-10-15 15:06:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GeneTonic package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 730/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneTonic 1.4.1 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GeneTonic |
Version: 1.4.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.4.1.tar.gz |
StartedAt: 2021-10-14 19:23:08 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:34:08 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 660.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneTonic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneTonic.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneTonic/DESCRIPTION’ ... OK * this is package ‘GeneTonic’ version ‘1.4.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 R 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 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 9.849 0.441 10.300 gs_heatmap 9.867 0.184 10.076 ggs_backbone 9.529 0.277 9.826 summarize_ggs_hubgenes 9.213 0.189 9.408 ggs_graph 8.937 0.165 9.112 gs_scoresheat 8.340 0.171 8.530 GeneTonic 7.874 0.281 8.169 gs_scores 7.405 0.167 7.576 gs_dendro 7.282 0.159 7.457 export_for_iSEE 6.710 0.166 6.878 signature_volcano 6.488 0.176 6.672 gs_volcano 6.129 0.113 6.248 gs_horizon 6.066 0.144 6.215 enhance_table 5.404 0.134 5.547 gene_plot 5.407 0.123 5.538 distill_enrichment 5.373 0.134 5.510 gs_alluvial 5.238 0.170 5.411 GeneTonic_list 5.245 0.118 5.367 gs_summary_overview_pair 5.136 0.135 5.279 get_aggrscores 5.087 0.167 5.256 checkup_GeneTonic 4.971 0.143 5.125 gs_radar 4.774 0.247 5.038 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneTonic.Rcheck/00check.log’ for details.
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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... Found 500 gene sets in `topGOtableResult` object. Converting for usage in GeneTonic... - Done! --- Test setup script completed! [ FAIL 0 | WARN 5 | SKIP 0 | PASS 235 ] > > proc.time() user system elapsed 178.131 8.081 186.887
GeneTonic.Rcheck/GeneTonic-Ex.timings
name | user | system | elapsed | |
GeneTonic | 7.874 | 0.281 | 8.169 | |
GeneTonic_list | 5.245 | 0.118 | 5.367 | |
check_colors | 0.018 | 0.003 | 0.021 | |
checkup_GeneTonic | 4.971 | 0.143 | 5.125 | |
checkup_gtl | 4.370 | 0.132 | 4.506 | |
cluster_markov | 0.121 | 0.005 | 0.129 | |
create_jaccard_matrix | 1.348 | 0.048 | 1.400 | |
create_kappa_matrix | 4.176 | 0.310 | 4.494 | |
deseqresult2df | 0.169 | 0.010 | 0.180 | |
distill_enrichment | 5.373 | 0.134 | 5.510 | |
enhance_table | 5.404 | 0.134 | 5.547 | |
enrichment_map | 4.008 | 0.126 | 4.134 | |
export_for_iSEE | 6.710 | 0.166 | 6.878 | |
export_to_sif | 0.027 | 0.002 | 0.028 | |
gene_plot | 5.407 | 0.123 | 5.538 | |
geneinfo_2_html | 0.009 | 0.000 | 0.009 | |
get_aggrscores | 5.087 | 0.167 | 5.256 | |
get_expression_values | 3.381 | 0.090 | 3.475 | |
ggs_backbone | 9.529 | 0.277 | 9.826 | |
ggs_graph | 8.937 | 0.165 | 9.112 | |
go_2_html | 0.044 | 0.001 | 0.045 | |
gs_alluvial | 5.238 | 0.170 | 5.411 | |
gs_dendro | 7.282 | 0.159 | 7.457 | |
gs_fuzzyclustering | 1.103 | 0.078 | 1.185 | |
gs_heatmap | 9.867 | 0.184 | 10.076 | |
gs_horizon | 6.066 | 0.144 | 6.215 | |
gs_mds | 9.849 | 0.441 | 10.300 | |
gs_radar | 4.774 | 0.247 | 5.038 | |
gs_scores | 7.405 | 0.167 | 7.576 | |
gs_scoresheat | 8.340 | 0.171 | 8.530 | |
gs_simplify | 1.949 | 0.063 | 2.024 | |
gs_summary_heat | 4.281 | 0.126 | 4.425 | |
gs_summary_overview | 4.750 | 0.127 | 4.898 | |
gs_summary_overview_pair | 5.136 | 0.135 | 5.279 | |
gs_volcano | 6.129 | 0.113 | 6.248 | |
happy_hour | 4.435 | 0.136 | 4.573 | |
map2color | 0.015 | 0.003 | 0.017 | |
overlap_coefficient | 0.001 | 0.000 | 0.000 | |
overlap_jaccard_index | 0.001 | 0.000 | 0.001 | |
shake_davidResult | 0.012 | 0.001 | 0.013 | |
shake_enrichResult | 3.196 | 0.070 | 3.268 | |
shake_enrichrResult | 0.068 | 0.002 | 0.070 | |
shake_fgseaResult | 0.165 | 0.008 | 0.175 | |
shake_gprofilerResult | 0.12 | 0.01 | 0.13 | |
shake_topGOtableResult | 0.007 | 0.007 | 0.014 | |
signature_volcano | 6.488 | 0.176 | 6.672 | |
styleColorBar_divergent | 0.279 | 0.047 | 0.328 | |
summarize_ggs_hubgenes | 9.213 | 0.189 | 9.408 | |