Federico Marini
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_14 |
| git_last_commit: c9ee95b |
| git_last_commit_date: 2022-03-24 08:30:47 -0400 (Thu, 24 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:03 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 739/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 1.6.4 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneTonic |
| Version: 1.6.4 |
| 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_1.6.4.tar.gz |
| StartedAt: 2022-04-12 13:37:34 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 13:51:20 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 825.9 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_1.6.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.6.4’
* 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 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 10.983 0.452 11.446
gs_heatmap 10.865 0.194 11.071
summarize_ggs_hubgenes 10.606 0.237 10.884
ggs_graph 10.428 0.190 10.663
ggs_backbone 10.326 0.257 10.595
gs_scores 9.972 0.218 10.240
GeneTonic 9.316 0.344 9.669
gs_scoresheat 8.519 0.158 8.695
gs_dendro 7.745 0.182 7.948
signature_volcano 7.648 0.219 7.912
export_for_iSEE 7.656 0.150 7.813
gene_plot 6.927 0.255 7.230
gs_summary_overview 6.887 0.183 7.094
checkup_GeneTonic 6.606 0.225 6.837
get_aggrscores 6.533 0.220 6.832
gs_horizon 6.558 0.163 6.728
gs_summary_overview_pair 6.373 0.120 6.498
enhance_table 6.335 0.143 6.494
GeneTonic_list 6.253 0.221 6.479
gs_summary_heat 6.139 0.131 6.285
gs_alluvial 5.899 0.179 6.096
enrichment_map 5.887 0.107 5.997
happy_hour 5.742 0.125 5.870
distill_enrichment 5.628 0.184 5.845
gs_volcano 5.589 0.089 5.685
gs_radar 5.383 0.268 6.030
checkup_gtl 5.163 0.158 5.324
* 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: 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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 243 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 243 ]
>
> proc.time()
user system elapsed
327.385 16.741 271.175
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.316 | 0.344 | 9.669 | |
| GeneTonic_list | 6.253 | 0.221 | 6.479 | |
| check_colors | 0.015 | 0.002 | 0.017 | |
| checkup_GeneTonic | 6.606 | 0.225 | 6.837 | |
| checkup_gtl | 5.163 | 0.158 | 5.324 | |
| cluster_markov | 0.145 | 0.004 | 0.149 | |
| create_jaccard_matrix | 2.480 | 0.082 | 2.564 | |
| create_kappa_matrix | 4.366 | 0.605 | 4.973 | |
| deseqresult2df | 0.206 | 0.003 | 0.210 | |
| distill_enrichment | 5.628 | 0.184 | 5.845 | |
| enhance_table | 6.335 | 0.143 | 6.494 | |
| enrichment_map | 5.887 | 0.107 | 5.997 | |
| export_for_iSEE | 7.656 | 0.150 | 7.813 | |
| export_to_sif | 0.029 | 0.002 | 0.031 | |
| gene_plot | 6.927 | 0.255 | 7.230 | |
| geneinfo_2_html | 0.009 | 0.000 | 0.010 | |
| get_aggrscores | 6.533 | 0.220 | 6.832 | |
| get_expression_values | 4.454 | 0.141 | 4.605 | |
| ggs_backbone | 10.326 | 0.257 | 10.595 | |
| ggs_graph | 10.428 | 0.190 | 10.663 | |
| go_2_html | 0.043 | 0.001 | 0.044 | |
| gs_alluvial | 5.899 | 0.179 | 6.096 | |
| gs_dendro | 7.745 | 0.182 | 7.948 | |
| gs_fuzzyclustering | 1.271 | 0.065 | 1.341 | |
| gs_heatmap | 10.865 | 0.194 | 11.071 | |
| gs_horizon | 6.558 | 0.163 | 6.728 | |
| gs_mds | 10.983 | 0.452 | 11.446 | |
| gs_radar | 5.383 | 0.268 | 6.030 | |
| gs_scores | 9.972 | 0.218 | 10.240 | |
| gs_scoresheat | 8.519 | 0.158 | 8.695 | |
| gs_simplify | 1.953 | 0.046 | 2.001 | |
| gs_summary_heat | 6.139 | 0.131 | 6.285 | |
| gs_summary_overview | 6.887 | 0.183 | 7.094 | |
| gs_summary_overview_pair | 6.373 | 0.120 | 6.498 | |
| gs_volcano | 5.589 | 0.089 | 5.685 | |
| happy_hour | 5.742 | 0.125 | 5.870 | |
| map2color | 0.015 | 0.002 | 0.017 | |
| overlap_coefficient | 0.000 | 0.001 | 0.002 | |
| overlap_jaccard_index | 0.001 | 0.001 | 0.001 | |
| shake_davidResult | 0.017 | 0.002 | 0.019 | |
| shake_enrichResult | 2.735 | 0.056 | 2.801 | |
| shake_enrichrResult | 0.081 | 0.004 | 0.086 | |
| shake_fgseaResult | 0.190 | 0.003 | 0.194 | |
| shake_gprofilerResult | 0.133 | 0.005 | 0.139 | |
| shake_gsenrichResult | 2.731 | 0.100 | 2.848 | |
| shake_topGOtableResult | 0.010 | 0.007 | 0.017 | |
| signature_volcano | 7.648 | 0.219 | 7.912 | |
| styleColorBar_divergent | 0.284 | 0.049 | 0.342 | |
| summarize_ggs_hubgenes | 10.606 | 0.237 | 10.884 | |