Federico Marini
| Snapshot Date: 2022-10-16 13:55:18 -0400 (Sun, 16 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_15 |
| git_last_commit: 19e79ae |
| git_last_commit_date: 2022-08-03 04:42:03 -0400 (Wed, 03 Aug 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-17 13:20:20 -0400 (Mon, 17 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 760/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.0.2 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneTonic |
| Version: 2.0.2 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_2.0.2.tar.gz |
| StartedAt: 2022-10-16 19:44:48 -0400 (Sun, 16 Oct 2022) |
| EndedAt: 2022-10-16 19:53:26 -0400 (Sun, 16 Oct 2022) |
| EllapsedTime: 518.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GeneTonic_2.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘2.0.2’
* 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
GeneTonic 6.540 0.316 6.859
ggs_backbone 6.373 0.132 6.505
signature_volcano 6.390 0.072 6.462
gs_mds 6.307 0.064 6.372
gs_upset 6.153 0.124 6.278
gs_heatmap 6.129 0.109 6.238
summarize_ggs_hubgenes 5.923 0.104 6.027
ggs_graph 5.511 0.072 5.584
gs_scoresheat 4.921 0.096 5.018
* 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-3.15-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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!
---------------------------------
----- 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, 928 found as DE
Upregulated: 329
Downregulated: 599
----- 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 3 | SKIP 0 | PASS 255 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 255 ]
>
> proc.time()
user system elapsed
202.249 8.678 161.281
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.540 | 0.316 | 6.859 | |
| GeneTonicList | 3.703 | 0.204 | 3.907 | |
| check_colors | 0.010 | 0.000 | 0.009 | |
| checkup_GeneTonic | 3.945 | 0.056 | 4.002 | |
| checkup_gtl | 4.094 | 0.132 | 4.226 | |
| cluster_markov | 0.093 | 0.000 | 0.093 | |
| create_jaccard_matrix | 0.800 | 0.028 | 0.828 | |
| create_kappa_matrix | 2.959 | 0.056 | 3.015 | |
| create_upsetdata | 0.023 | 0.072 | 0.095 | |
| deseqresult2df | 0.150 | 0.004 | 0.153 | |
| distill_enrichment | 3.924 | 0.252 | 4.177 | |
| enhance_table | 4.057 | 0.064 | 4.121 | |
| enrichment_map | 3.971 | 0.080 | 4.052 | |
| export_for_iSEE | 3.366 | 0.060 | 3.426 | |
| export_to_sif | 0.018 | 0.000 | 0.018 | |
| gene_plot | 4.250 | 0.148 | 4.398 | |
| geneinfo_2_html | 0.007 | 0.000 | 0.007 | |
| get_aggrscores | 3.661 | 0.052 | 3.713 | |
| get_expression_values | 2.104 | 0.052 | 2.156 | |
| ggs_backbone | 6.373 | 0.132 | 6.505 | |
| ggs_graph | 5.511 | 0.072 | 5.584 | |
| go_2_html | 0.020 | 0.001 | 0.020 | |
| gs_alluvial | 3.882 | 0.140 | 4.023 | |
| gs_dendro | 3.972 | 0.072 | 4.043 | |
| gs_fuzzyclustering | 0.771 | 0.003 | 0.774 | |
| gs_heatmap | 6.129 | 0.109 | 6.238 | |
| gs_horizon | 4.164 | 0.116 | 4.280 | |
| gs_mds | 6.307 | 0.064 | 6.372 | |
| gs_radar | 4.053 | 0.084 | 4.138 | |
| gs_scores | 4.614 | 0.060 | 4.674 | |
| gs_scoresheat | 4.921 | 0.096 | 5.018 | |
| gs_simplify | 0.944 | 0.008 | 0.953 | |
| gs_summary_heat | 3.909 | 0.111 | 4.020 | |
| gs_summary_overview | 3.298 | 0.045 | 3.343 | |
| gs_summary_overview_pair | 3.292 | 0.036 | 3.328 | |
| gs_upset | 6.153 | 0.124 | 6.278 | |
| gs_volcano | 3.565 | 0.029 | 3.593 | |
| happy_hour | 3.179 | 0.095 | 3.275 | |
| map2color | 0.013 | 0.000 | 0.013 | |
| overlap_coefficient | 0.001 | 0.000 | 0.000 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.000 | |
| shake_davidResult | 0.01 | 0.00 | 0.01 | |
| shake_enrichResult | 1.907 | 0.036 | 1.943 | |
| shake_enrichrResult | 0.048 | 0.000 | 0.050 | |
| shake_fgseaResult | 0.134 | 0.000 | 0.134 | |
| shake_gprofilerResult | 0.092 | 0.004 | 0.098 | |
| shake_gsenrichResult | 1.929 | 0.028 | 1.958 | |
| shake_topGOtableResult | 0.01 | 0.00 | 0.01 | |
| signature_volcano | 6.390 | 0.072 | 6.462 | |
| styleColorBar_divergent | 0.205 | 0.012 | 0.216 | |
| summarize_ggs_hubgenes | 5.923 | 0.104 | 6.027 | |