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 13:23:01 -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: /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_2.0.2.tar.gz |
| StartedAt: 2022-10-17 02:39:13 -0400 (Mon, 17 Oct 2022) |
| EndedAt: 2022-10-17 02:54:37 -0400 (Mon, 17 Oct 2022) |
| EllapsedTime: 923.3 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_2.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘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
gs_mds 11.933 0.389 12.401
summarize_ggs_hubgenes 11.777 0.232 12.043
gs_upset 11.044 0.210 11.290
ggs_backbone 10.999 0.210 11.242
gs_heatmap 10.634 0.191 10.843
ggs_graph 10.477 0.184 10.693
GeneTonic 9.346 0.338 9.701
gs_scoresheat 8.671 0.191 8.894
gs_scores 8.601 0.191 8.822
gs_dendro 8.140 0.227 8.382
signature_volcano 8.111 0.190 8.324
gs_horizon 7.482 0.133 7.687
gene_plot 6.866 0.165 7.050
export_for_iSEE 6.887 0.109 7.004
gs_summary_overview 6.526 0.140 6.682
gs_radar 6.424 0.216 6.661
distill_enrichment 6.426 0.137 6.577
GeneTonicList 6.040 0.163 6.214
checkup_gtl 5.960 0.165 6.144
enrichment_map 5.979 0.142 6.133
checkup_GeneTonic 5.942 0.153 6.108
gs_volcano 5.951 0.132 6.111
create_kappa_matrix 5.663 0.377 6.050
happy_hour 5.792 0.134 5.938
get_aggrscores 5.788 0.086 5.880
gs_alluvial 5.575 0.190 5.783
gs_summary_heat 5.429 0.140 5.575
gs_summary_overview_pair 5.394 0.133 5.587
enhance_table 5.341 0.107 5.456
* 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/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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!
---------------------------------
----- 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
345.499 11.538 288.020
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.346 | 0.338 | 9.701 | |
| GeneTonicList | 6.040 | 0.163 | 6.214 | |
| check_colors | 0.018 | 0.001 | 0.019 | |
| checkup_GeneTonic | 5.942 | 0.153 | 6.108 | |
| checkup_gtl | 5.960 | 0.165 | 6.144 | |
| cluster_markov | 0.156 | 0.004 | 0.160 | |
| create_jaccard_matrix | 2.026 | 0.098 | 2.131 | |
| create_kappa_matrix | 5.663 | 0.377 | 6.050 | |
| create_upsetdata | 0.063 | 0.027 | 0.091 | |
| deseqresult2df | 0.247 | 0.003 | 0.252 | |
| distill_enrichment | 6.426 | 0.137 | 6.577 | |
| enhance_table | 5.341 | 0.107 | 5.456 | |
| enrichment_map | 5.979 | 0.142 | 6.133 | |
| export_for_iSEE | 6.887 | 0.109 | 7.004 | |
| export_to_sif | 0.034 | 0.002 | 0.036 | |
| gene_plot | 6.866 | 0.165 | 7.050 | |
| geneinfo_2_html | 0.013 | 0.000 | 0.014 | |
| get_aggrscores | 5.788 | 0.086 | 5.880 | |
| get_expression_values | 4.543 | 0.109 | 4.659 | |
| ggs_backbone | 10.999 | 0.210 | 11.242 | |
| ggs_graph | 10.477 | 0.184 | 10.693 | |
| go_2_html | 0.048 | 0.001 | 0.048 | |
| gs_alluvial | 5.575 | 0.190 | 5.783 | |
| gs_dendro | 8.140 | 0.227 | 8.382 | |
| gs_fuzzyclustering | 1.471 | 0.101 | 1.574 | |
| gs_heatmap | 10.634 | 0.191 | 10.843 | |
| gs_horizon | 7.482 | 0.133 | 7.687 | |
| gs_mds | 11.933 | 0.389 | 12.401 | |
| gs_radar | 6.424 | 0.216 | 6.661 | |
| gs_scores | 8.601 | 0.191 | 8.822 | |
| gs_scoresheat | 8.671 | 0.191 | 8.894 | |
| gs_simplify | 2.436 | 0.046 | 2.487 | |
| gs_summary_heat | 5.429 | 0.140 | 5.575 | |
| gs_summary_overview | 6.526 | 0.140 | 6.682 | |
| gs_summary_overview_pair | 5.394 | 0.133 | 5.587 | |
| gs_upset | 11.044 | 0.210 | 11.290 | |
| gs_volcano | 5.951 | 0.132 | 6.111 | |
| happy_hour | 5.792 | 0.134 | 5.938 | |
| map2color | 0.016 | 0.001 | 0.017 | |
| overlap_coefficient | 0.000 | 0.001 | 0.000 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.000 | |
| shake_davidResult | 0.018 | 0.001 | 0.019 | |
| shake_enrichResult | 2.727 | 0.059 | 2.791 | |
| shake_enrichrResult | 0.090 | 0.001 | 0.092 | |
| shake_fgseaResult | 0.191 | 0.008 | 0.199 | |
| shake_gprofilerResult | 0.152 | 0.010 | 0.162 | |
| shake_gsenrichResult | 2.685 | 0.061 | 2.749 | |
| shake_topGOtableResult | 0.011 | 0.007 | 0.017 | |
| signature_volcano | 8.111 | 0.190 | 8.324 | |
| styleColorBar_divergent | 0.352 | 0.040 | 0.398 | |
| summarize_ggs_hubgenes | 11.777 | 0.232 | 12.043 | |