Federico Marini
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 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 2024-07-06 11:43 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 795/2243 | 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 | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | ERROR | skipped | ||||||||||
|
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: /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_2.9.0.tar.gz |
| StartedAt: 2024-07-06 00:40:57 -0400 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 00:46:34 -0400 (Sat, 06 Jul 2024) |
| EllapsedTime: 337.1 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_2.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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: aarch64-apple-darwin20
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!
|
| | 0%
|
| | 1%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|== | 4%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======= | 11%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========= | 14%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================ | 24%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|===================== | 31%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 32%
|
|======================= | 33%
|
|======================= | 34%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|============================== | 44%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 49%
|
|=================================== | 50%
|
|=================================== | 51%
|
|==================================== | 51%
|
|==================================== | 52%
|
|===================================== | 52%
|
|===================================== | 53%
|
|===================================== | 54%
|
|====================================== | 54%
|
|====================================== | 55%
|
|======================================= | 55%
|
|======================================= | 56%
|
|======================================== | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 59%
|
|========================================== | 60%
|
|========================================== | 61%
|
|=========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================ | 64%
|
|============================================= | 64%
|
|============================================= | 65%
|
|============================================== | 65%
|
|============================================== | 66%
|
|=============================================== | 66%
|
|=============================================== | 67%
|
|=============================================== | 68%
|
|================================================ | 68%
|
|================================================ | 69%
|
|================================================= | 69%
|
|================================================= | 70%
|
|================================================= | 71%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|=================================================== | 74%
|
|==================================================== | 74%
|
|==================================================== | 75%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 79%
|
|======================================================== | 80%
|
|======================================================== | 81%
|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|========================================================== | 84%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================= | 94%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 99%
|
|======================================================================| 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
99.047 6.276 107.677
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 3.272 | 0.091 | 4.170 | |
| GeneTonicList | 2.248 | 0.073 | 2.868 | |
| check_colors | 0.006 | 0.001 | 0.008 | |
| checkup_GeneTonic | 1.779 | 0.073 | 2.270 | |
| checkup_gtl | 1.834 | 0.070 | 2.278 | |
| cluster_markov | 0.041 | 0.002 | 0.057 | |
| create_jaccard_matrix | 0.352 | 0.037 | 0.451 | |
| create_kappa_matrix | 1.339 | 0.201 | 1.948 | |
| create_upsetdata | 0.015 | 0.013 | 0.034 | |
| deseqresult2df | 0.078 | 0.003 | 0.105 | |
| distill_enrichment | 1.999 | 0.132 | 2.655 | |
| enhance_table | 2.253 | 0.122 | 2.953 | |
| enrichment_map | 1.814 | 0.083 | 2.407 | |
| export_for_iSEE | 1.917 | 0.068 | 2.353 | |
| export_to_sif | 0.008 | 0.000 | 0.009 | |
| gene_plot | 2.004 | 0.072 | 2.494 | |
| geneinfo_2_html | 0.002 | 0.000 | 0.002 | |
| get_aggrscores | 1.804 | 0.059 | 2.252 | |
| get_expression_values | 1.015 | 0.034 | 1.280 | |
| ggs_backbone | 2.639 | 0.119 | 3.559 | |
| ggs_graph | 2.534 | 0.096 | 3.415 | |
| go_2_html | 0.011 | 0.001 | 0.012 | |
| gs_alluvial | 2.056 | 0.085 | 2.730 | |
| gs_dendro | 2.263 | 0.094 | 2.959 | |
| gs_fuzzyclustering | 0.320 | 0.041 | 0.465 | |
| gs_heatmap | 2.751 | 0.098 | 3.581 | |
| gs_horizon | 2.127 | 0.062 | 2.740 | |
| gs_mds | 3.135 | 0.297 | 4.349 | |
| gs_radar | 1.415 | 0.076 | 1.914 | |
| gs_scores | 1.913 | 0.121 | 2.613 | |
| gs_scoresheat | 1.981 | 0.090 | 2.570 | |
| gs_simplify | 0.415 | 0.024 | 0.530 | |
| gs_summary_heat | 1.961 | 0.082 | 2.544 | |
| gs_summary_overview | 1.485 | 0.074 | 1.986 | |
| gs_summary_overview_pair | 1.407 | 0.073 | 1.878 | |
| gs_upset | 2.398 | 0.076 | 3.086 | |
| gs_volcano | 1.594 | 0.062 | 2.060 | |
| happy_hour | 1.870 | 0.090 | 2.444 | |
| map2color | 0.007 | 0.005 | 0.013 | |
| overlap_coefficient | 0.001 | 0.000 | 0.000 | |
| overlap_jaccard_index | 0.000 | 0.000 | 0.001 | |
| shake_davidResult | 0.005 | 0.001 | 0.005 | |
| shake_enrichResult | 0.896 | 0.028 | 1.197 | |
| shake_enrichrResult | 0.031 | 0.001 | 0.044 | |
| shake_fgseaResult | 0.057 | 0.001 | 0.065 | |
| shake_gprofilerResult | 0.097 | 0.009 | 0.133 | |
| shake_gsenrichResult | 0.821 | 0.026 | 1.056 | |
| shake_topGOtableResult | 0.003 | 0.001 | 0.003 | |
| signature_volcano | 2.290 | 0.094 | 3.020 | |
| styleColorBar_divergent | 0.152 | 0.018 | 0.201 | |
| summarize_ggs_hubgenes | 2.445 | 0.114 | 3.294 | |