Federico Marini
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: RELEASE_3_19 |
| git_last_commit: dd4c5de |
| git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | ||||
| Package 820/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.8.0 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the GeneTonic package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GeneTonic |
| Version: 2.8.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneTonic_2.8.0.tar.gz |
| StartedAt: 2024-10-17 00:44:16 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 00:54:05 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 589.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeneTonic_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.8.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether 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 6.250 0.064 6.314
gs_upset 6.272 0.040 6.312
gs_heatmap 5.752 0.112 5.864
ggs_backbone 5.683 0.100 5.783
ggs_graph 5.421 0.164 5.585
GeneTonic 5.266 0.296 5.564
summarize_ggs_hubgenes 5.170 0.132 5.302
signature_volcano 4.981 0.096 5.077
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).
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, 1024 found as DE
Upregulated: 652
Downregulated: 372
----- 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 0 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
183.998 8.366 161.823
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 5.266 | 0.296 | 5.564 | |
| GeneTonicList | 4.380 | 0.204 | 4.585 | |
| check_colors | 0.01 | 0.00 | 0.01 | |
| checkup_GeneTonic | 3.668 | 0.108 | 3.777 | |
| checkup_gtl | 3.606 | 0.116 | 3.722 | |
| cluster_markov | 0.089 | 0.000 | 0.089 | |
| create_jaccard_matrix | 0.810 | 0.044 | 0.854 | |
| create_kappa_matrix | 3.193 | 0.060 | 3.254 | |
| create_upsetdata | 0.028 | 0.052 | 0.079 | |
| deseqresult2df | 0.138 | 0.008 | 0.146 | |
| distill_enrichment | 3.827 | 0.140 | 3.967 | |
| enhance_table | 3.516 | 0.104 | 3.620 | |
| enrichment_map | 3.374 | 0.104 | 3.478 | |
| export_for_iSEE | 3.133 | 0.076 | 3.208 | |
| export_to_sif | 0.019 | 0.000 | 0.018 | |
| gene_plot | 4.129 | 0.148 | 4.278 | |
| geneinfo_2_html | 0.000 | 0.008 | 0.008 | |
| get_aggrscores | 2.853 | 0.152 | 3.006 | |
| get_expression_values | 2.829 | 0.100 | 2.929 | |
| ggs_backbone | 5.683 | 0.100 | 5.783 | |
| ggs_graph | 5.421 | 0.164 | 5.585 | |
| go_2_html | 0.019 | 0.000 | 0.018 | |
| gs_alluvial | 2.860 | 0.152 | 3.012 | |
| gs_dendro | 4.501 | 0.124 | 4.626 | |
| gs_fuzzyclustering | 0.770 | 0.000 | 0.771 | |
| gs_heatmap | 5.752 | 0.112 | 5.864 | |
| gs_horizon | 4.197 | 0.048 | 4.248 | |
| gs_mds | 6.250 | 0.064 | 6.314 | |
| gs_radar | 3.568 | 0.088 | 3.655 | |
| gs_scores | 3.980 | 0.065 | 4.044 | |
| gs_scoresheat | 4.798 | 0.132 | 4.930 | |
| gs_simplify | 1.069 | 0.000 | 1.069 | |
| gs_summary_heat | 3.200 | 0.096 | 3.295 | |
| gs_summary_overview | 3.923 | 0.116 | 4.039 | |
| gs_summary_overview_pair | 2.962 | 0.080 | 3.043 | |
| gs_upset | 6.272 | 0.040 | 6.312 | |
| gs_volcano | 3.229 | 0.040 | 3.269 | |
| happy_hour | 2.902 | 0.076 | 2.979 | |
| map2color | 0.013 | 0.000 | 0.012 | |
| overlap_coefficient | 0.001 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.001 | |
| shake_davidResult | 0.009 | 0.000 | 0.009 | |
| shake_enrichResult | 2.443 | 0.060 | 2.503 | |
| shake_enrichrResult | 0.046 | 0.000 | 0.047 | |
| shake_fgseaResult | 0.119 | 0.000 | 0.118 | |
| shake_gprofilerResult | 0.086 | 0.000 | 0.088 | |
| shake_gsenrichResult | 1.562 | 0.048 | 1.610 | |
| shake_topGOtableResult | 0.006 | 0.000 | 0.007 | |
| signature_volcano | 4.981 | 0.096 | 5.077 | |
| styleColorBar_divergent | 0.183 | 0.012 | 0.198 | |
| summarize_ggs_hubgenes | 5.170 | 0.132 | 5.302 | |