Federico Marini
| Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 9473081 |
| git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-30 12:34:37 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 791/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.9.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 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: 2.9.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.9.0.tar.gz |
| StartedAt: 2024-05-29 20:15:27 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 20:25:14 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 587.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneTonic_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.9.0’
* 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 7.347 0.092 7.440
gs_heatmap 7.012 0.080 7.092
gs_upset 6.384 0.120 6.505
signature_volcano 6.345 0.140 6.485
ggs_backbone 6.010 0.120 6.130
ggs_graph 5.940 0.144 6.085
GeneTonic 5.570 0.272 5.843
summarize_ggs_hubgenes 5.265 0.064 5.329
gs_scores 4.938 0.128 5.066
* 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-3.20-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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
182.306 7.623 157.088
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 5.570 | 0.272 | 5.843 | |
| GeneTonicList | 4.216 | 0.180 | 4.395 | |
| check_colors | 0.009 | 0.000 | 0.009 | |
| checkup_GeneTonic | 3.649 | 0.156 | 3.805 | |
| checkup_gtl | 3.472 | 0.140 | 3.611 | |
| cluster_markov | 0.087 | 0.008 | 0.094 | |
| create_jaccard_matrix | 0.817 | 0.036 | 0.854 | |
| create_kappa_matrix | 3.071 | 0.036 | 3.107 | |
| create_upsetdata | 0.025 | 0.016 | 0.040 | |
| deseqresult2df | 0.145 | 0.000 | 0.144 | |
| distill_enrichment | 4.063 | 0.188 | 4.250 | |
| enhance_table | 3.899 | 0.092 | 3.991 | |
| enrichment_map | 3.781 | 0.056 | 3.838 | |
| export_for_iSEE | 3.182 | 0.056 | 3.238 | |
| export_to_sif | 0.023 | 0.000 | 0.022 | |
| gene_plot | 4.328 | 0.156 | 4.484 | |
| geneinfo_2_html | 0.007 | 0.000 | 0.008 | |
| get_aggrscores | 2.862 | 0.052 | 2.913 | |
| get_expression_values | 2.972 | 0.132 | 3.103 | |
| ggs_backbone | 6.01 | 0.12 | 6.13 | |
| ggs_graph | 5.940 | 0.144 | 6.085 | |
| go_2_html | 0.019 | 0.000 | 0.019 | |
| gs_alluvial | 3.781 | 0.120 | 3.901 | |
| gs_dendro | 3.918 | 0.092 | 4.010 | |
| gs_fuzzyclustering | 0.887 | 0.032 | 0.919 | |
| gs_heatmap | 7.012 | 0.080 | 7.092 | |
| gs_horizon | 3.480 | 0.036 | 3.516 | |
| gs_mds | 7.347 | 0.092 | 7.440 | |
| gs_radar | 2.977 | 0.048 | 3.025 | |
| gs_scores | 4.938 | 0.128 | 5.066 | |
| gs_scoresheat | 4.802 | 0.056 | 4.857 | |
| gs_simplify | 0.963 | 0.004 | 0.967 | |
| gs_summary_heat | 3.161 | 0.076 | 3.237 | |
| gs_summary_overview | 3.356 | 0.064 | 3.421 | |
| gs_summary_overview_pair | 3.179 | 0.064 | 3.243 | |
| gs_upset | 6.384 | 0.120 | 6.505 | |
| gs_volcano | 3.967 | 0.068 | 4.035 | |
| happy_hour | 3.384 | 0.052 | 3.436 | |
| 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 | 0.011 | 0.000 | 0.011 | |
| shake_enrichResult | 2.790 | 0.112 | 2.901 | |
| shake_enrichrResult | 0.225 | 0.000 | 0.225 | |
| shake_fgseaResult | 0.208 | 0.000 | 0.208 | |
| shake_gprofilerResult | 0.153 | 0.000 | 0.153 | |
| shake_gsenrichResult | 2.048 | 0.024 | 2.071 | |
| shake_topGOtableResult | 0.008 | 0.000 | 0.007 | |
| signature_volcano | 6.345 | 0.140 | 6.485 | |
| styleColorBar_divergent | 0.209 | 0.000 | 0.210 | |
| summarize_ggs_hubgenes | 5.265 | 0.064 | 5.329 | |