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 12:05:24 -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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneTonic_1.6.4.tar.gz |
| StartedAt: 2022-04-12 07:33:22 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:41:53 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 510.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneTonic_1.6.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 7.368 0.036 7.405
GeneTonic 6.984 0.296 7.280
gs_scores 6.543 0.132 6.675
summarize_ggs_hubgenes 6.532 0.048 6.580
gs_heatmap 6.381 0.136 6.517
ggs_graph 6.075 0.153 6.227
ggs_backbone 5.810 0.076 5.888
gs_scoresheat 5.201 0.120 5.322
signature_volcano 5.172 0.040 5.212
* 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: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-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 ** 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-pc-linux-gnu (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
194.873 8.985 159.147
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.984 | 0.296 | 7.280 | |
| GeneTonic_list | 4.027 | 0.120 | 4.147 | |
| check_colors | 0.008 | 0.000 | 0.008 | |
| checkup_GeneTonic | 4.067 | 0.092 | 4.158 | |
| checkup_gtl | 3.217 | 0.044 | 3.260 | |
| cluster_markov | 0.079 | 0.000 | 0.078 | |
| create_jaccard_matrix | 1.546 | 0.060 | 1.607 | |
| create_kappa_matrix | 2.490 | 0.071 | 2.562 | |
| deseqresult2df | 0.131 | 0.002 | 0.133 | |
| distill_enrichment | 3.306 | 0.078 | 3.384 | |
| enhance_table | 4.030 | 0.115 | 4.146 | |
| enrichment_map | 3.908 | 0.105 | 4.012 | |
| export_for_iSEE | 4.797 | 0.091 | 4.889 | |
| export_to_sif | 0.025 | 0.001 | 0.025 | |
| gene_plot | 4.173 | 0.135 | 4.309 | |
| geneinfo_2_html | 0.007 | 0.001 | 0.007 | |
| get_aggrscores | 3.865 | 0.111 | 3.977 | |
| get_expression_values | 3.144 | 0.045 | 3.189 | |
| ggs_backbone | 5.810 | 0.076 | 5.888 | |
| ggs_graph | 6.075 | 0.153 | 6.227 | |
| go_2_html | 0.019 | 0.001 | 0.020 | |
| gs_alluvial | 4.262 | 0.136 | 4.398 | |
| gs_dendro | 4.886 | 0.100 | 4.986 | |
| gs_fuzzyclustering | 0.72 | 0.00 | 0.72 | |
| gs_heatmap | 6.381 | 0.136 | 6.517 | |
| gs_horizon | 4.715 | 0.044 | 4.759 | |
| gs_mds | 7.368 | 0.036 | 7.405 | |
| gs_radar | 3.360 | 0.076 | 3.437 | |
| gs_scores | 6.543 | 0.132 | 6.675 | |
| gs_scoresheat | 5.201 | 0.120 | 5.322 | |
| gs_simplify | 0.993 | 0.000 | 0.994 | |
| gs_summary_heat | 3.894 | 0.076 | 3.970 | |
| gs_summary_overview | 3.541 | 0.040 | 3.581 | |
| gs_summary_overview_pair | 4.099 | 0.032 | 4.131 | |
| gs_volcano | 3.945 | 0.028 | 3.973 | |
| happy_hour | 3.177 | 0.032 | 3.209 | |
| map2color | 0.013 | 0.000 | 0.013 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.001 | |
| shake_davidResult | 0.011 | 0.000 | 0.011 | |
| shake_enrichResult | 2.712 | 0.103 | 2.816 | |
| shake_enrichrResult | 0.042 | 0.000 | 0.043 | |
| shake_fgseaResult | 0.117 | 0.000 | 0.116 | |
| shake_gprofilerResult | 0.075 | 0.003 | 0.079 | |
| shake_gsenrichResult | 1.789 | 0.004 | 1.794 | |
| shake_topGOtableResult | 0.006 | 0.000 | 0.005 | |
| signature_volcano | 5.172 | 0.040 | 5.212 | |
| styleColorBar_divergent | 0.199 | 0.011 | 0.211 | |
| summarize_ggs_hubgenes | 6.532 | 0.048 | 6.580 | |