Federico Marini
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/GeneTonic |
| git_branch: devel |
| git_last_commit: 6e69529 |
| git_last_commit_date: 2024-03-24 09:43:09 -0400 (Sun, 24 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:45 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 812/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.7.3 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: GeneTonic |
| Version: 2.7.3 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings GeneTonic_2.7.3.tar.gz |
| StartedAt: 2024-03-28 05:37:05 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:48:54 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 709.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings GeneTonic_2.7.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.7.3’
* 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 9.040 0.048 9.106
ggs_backbone 8.543 0.131 8.693
ggs_graph 8.397 0.116 8.531
gs_heatmap 8.251 0.088 8.355
GeneTonic 7.978 0.256 8.256
gs_upset 7.926 0.052 7.997
summarize_ggs_hubgenes 7.817 0.060 7.894
enhance_table 7.469 0.079 7.565
gs_scoresheat 7.023 0.052 7.089
signature_volcano 6.479 0.032 6.525
gs_dendro 6.204 0.064 6.281
gs_scores 5.980 0.016 6.007
gene_plot 5.813 0.096 5.921
gs_volcano 5.752 0.040 5.804
gs_summary_overview_pair 5.363 0.072 5.447
export_for_iSEE 5.228 0.112 5.350
gs_horizon 5.122 0.052 5.185
distill_enrichment 5.004 0.108 5.120
* 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 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/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...
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
237.692 5.790 212.501
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.978 | 0.256 | 8.256 | |
| GeneTonicList | 4.686 | 0.148 | 4.843 | |
| check_colors | 0.012 | 0.000 | 0.013 | |
| checkup_GeneTonic | 4.663 | 0.067 | 4.741 | |
| checkup_gtl | 4.726 | 0.140 | 4.876 | |
| cluster_markov | 0.109 | 0.000 | 0.109 | |
| create_jaccard_matrix | 1.103 | 0.036 | 1.142 | |
| create_kappa_matrix | 3.960 | 0.024 | 3.992 | |
| create_upsetdata | 0.033 | 0.008 | 0.042 | |
| deseqresult2df | 0.157 | 0.004 | 0.162 | |
| distill_enrichment | 5.004 | 0.108 | 5.120 | |
| enhance_table | 7.469 | 0.079 | 7.565 | |
| enrichment_map | 4.655 | 0.032 | 4.696 | |
| export_for_iSEE | 5.228 | 0.112 | 5.350 | |
| export_to_sif | 0.026 | 0.000 | 0.027 | |
| gene_plot | 5.813 | 0.096 | 5.921 | |
| geneinfo_2_html | 0.009 | 0.000 | 0.009 | |
| get_aggrscores | 4.627 | 0.048 | 4.685 | |
| get_expression_values | 2.721 | 0.020 | 2.746 | |
| ggs_backbone | 8.543 | 0.131 | 8.693 | |
| ggs_graph | 8.397 | 0.116 | 8.531 | |
| go_2_html | 0.031 | 0.000 | 0.031 | |
| gs_alluvial | 4.807 | 0.032 | 4.848 | |
| gs_dendro | 6.204 | 0.064 | 6.281 | |
| gs_fuzzyclustering | 1.006 | 0.000 | 1.008 | |
| gs_heatmap | 8.251 | 0.088 | 8.355 | |
| gs_horizon | 5.122 | 0.052 | 5.185 | |
| gs_mds | 9.040 | 0.048 | 9.106 | |
| gs_radar | 3.811 | 0.040 | 3.858 | |
| gs_scores | 5.980 | 0.016 | 6.007 | |
| gs_scoresheat | 7.023 | 0.052 | 7.089 | |
| gs_simplify | 1.514 | 0.003 | 1.521 | |
| gs_summary_heat | 4.037 | 0.072 | 4.117 | |
| gs_summary_overview | 4.533 | 0.020 | 4.564 | |
| gs_summary_overview_pair | 5.363 | 0.072 | 5.447 | |
| gs_upset | 7.926 | 0.052 | 7.997 | |
| gs_volcano | 5.752 | 0.040 | 5.804 | |
| happy_hour | 3.725 | 0.040 | 3.772 | |
| map2color | 0.011 | 0.000 | 0.011 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.012 | 0.000 | 0.013 | |
| shake_enrichResult | 3.078 | 0.016 | 3.100 | |
| shake_enrichrResult | 0.065 | 0.000 | 0.066 | |
| shake_fgseaResult | 0.136 | 0.000 | 0.136 | |
| shake_gprofilerResult | 0.094 | 0.000 | 0.097 | |
| shake_gsenrichResult | 1.891 | 0.008 | 1.904 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.007 | |
| signature_volcano | 6.479 | 0.032 | 6.525 | |
| styleColorBar_divergent | 0.324 | 0.012 | 0.336 | |
| summarize_ggs_hubgenes | 7.817 | 0.060 | 7.894 | |