Federico Marini
| Snapshot Date: 2023-03-19 14:00:12 -0400 (Sun, 19 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: master |
| git_last_commit: 4336f49 |
| git_last_commit_date: 2023-03-14 10:34:59 -0400 (Tue, 14 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-20 11:06:33 -0400 (Mon, 20 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4297 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4286 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4150 |
| 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 778/2189 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.3.2 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.1 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: 2.3.2 |
| 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_2.3.2.tar.gz |
| StartedAt: 2023-03-20 01:04:20 -0400 (Mon, 20 Mar 2023) |
| EndedAt: 2023-03-20 01:26:40 -0400 (Mon, 20 Mar 2023) |
| EllapsedTime: 1339.9 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_2.3.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.3.2’
* 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 startup messages can be suppressed ... 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 12.687 0.281 17.425
summarize_ggs_hubgenes 12.256 0.223 17.368
gs_upset 11.756 0.176 15.682
ggs_backbone 11.666 0.265 16.287
gs_heatmap 11.705 0.210 15.132
ggs_graph 11.218 0.193 15.066
GeneTonic 9.500 0.353 12.993
gs_scoresheat 9.291 0.186 12.723
enhance_table 9.280 0.171 12.437
gs_dendro 9.011 0.199 12.318
signature_volcano 8.775 0.193 12.762
gs_scores 8.600 0.200 11.658
gs_volcano 7.630 0.149 10.110
distill_enrichment 7.124 0.188 9.803
export_for_iSEE 7.107 0.122 8.973
get_aggrscores 7.051 0.150 9.416
gs_horizon 6.857 0.128 9.185
gs_radar 6.773 0.196 9.525
gs_summary_overview_pair 6.744 0.128 8.899
gs_alluvial 6.534 0.182 8.703
gene_plot 6.445 0.123 8.913
create_kappa_matrix 6.111 0.381 8.384
gs_summary_overview 6.305 0.144 8.531
enrichment_map 6.296 0.123 8.280
GeneTonicList 6.244 0.174 8.800
checkup_gtl 6.238 0.160 8.512
checkup_GeneTonic 6.167 0.148 8.254
gs_summary_heat 5.814 0.134 8.098
happy_hour 5.471 0.139 7.624
get_expression_values 4.654 0.093 6.482
* 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/4.3/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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 2 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
355.483 12.502 419.692
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 9.500 | 0.353 | 12.993 | |
| GeneTonicList | 6.244 | 0.174 | 8.800 | |
| check_colors | 0.064 | 0.013 | 0.094 | |
| checkup_GeneTonic | 6.167 | 0.148 | 8.254 | |
| checkup_gtl | 6.238 | 0.160 | 8.512 | |
| cluster_markov | 0.176 | 0.003 | 0.225 | |
| create_jaccard_matrix | 2.272 | 0.217 | 3.171 | |
| create_kappa_matrix | 6.111 | 0.381 | 8.384 | |
| create_upsetdata | 0.073 | 0.040 | 0.148 | |
| deseqresult2df | 0.261 | 0.005 | 0.334 | |
| distill_enrichment | 7.124 | 0.188 | 9.803 | |
| enhance_table | 9.280 | 0.171 | 12.437 | |
| enrichment_map | 6.296 | 0.123 | 8.280 | |
| export_for_iSEE | 7.107 | 0.122 | 8.973 | |
| export_to_sif | 0.034 | 0.002 | 0.047 | |
| gene_plot | 6.445 | 0.123 | 8.913 | |
| geneinfo_2_html | 0.013 | 0.000 | 0.016 | |
| get_aggrscores | 7.051 | 0.150 | 9.416 | |
| get_expression_values | 4.654 | 0.093 | 6.482 | |
| ggs_backbone | 11.666 | 0.265 | 16.287 | |
| ggs_graph | 11.218 | 0.193 | 15.066 | |
| go_2_html | 0.045 | 0.000 | 0.059 | |
| gs_alluvial | 6.534 | 0.182 | 8.703 | |
| gs_dendro | 9.011 | 0.199 | 12.318 | |
| gs_fuzzyclustering | 1.693 | 0.046 | 2.266 | |
| gs_heatmap | 11.705 | 0.210 | 15.132 | |
| gs_horizon | 6.857 | 0.128 | 9.185 | |
| gs_mds | 12.687 | 0.281 | 17.425 | |
| gs_radar | 6.773 | 0.196 | 9.525 | |
| gs_scores | 8.600 | 0.200 | 11.658 | |
| gs_scoresheat | 9.291 | 0.186 | 12.723 | |
| gs_simplify | 2.747 | 0.062 | 3.743 | |
| gs_summary_heat | 5.814 | 0.134 | 8.098 | |
| gs_summary_overview | 6.305 | 0.144 | 8.531 | |
| gs_summary_overview_pair | 6.744 | 0.128 | 8.899 | |
| gs_upset | 11.756 | 0.176 | 15.682 | |
| gs_volcano | 7.630 | 0.149 | 10.110 | |
| happy_hour | 5.471 | 0.139 | 7.624 | |
| map2color | 0.018 | 0.003 | 0.024 | |
| overlap_coefficient | 0.000 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.001 | |
| shake_davidResult | 0.019 | 0.001 | 0.029 | |
| shake_enrichResult | 3.080 | 0.076 | 4.241 | |
| shake_enrichrResult | 0.108 | 0.003 | 0.152 | |
| shake_fgseaResult | 0.261 | 0.009 | 0.371 | |
| shake_gprofilerResult | 0.162 | 0.010 | 0.228 | |
| shake_gsenrichResult | 3.063 | 0.075 | 4.541 | |
| shake_topGOtableResult | 0.011 | 0.008 | 0.026 | |
| signature_volcano | 8.775 | 0.193 | 12.762 | |
| styleColorBar_divergent | 0.363 | 0.040 | 0.584 | |
| summarize_ggs_hubgenes | 12.256 | 0.223 | 17.368 | |