Federico Marini
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 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 2024-05-31 17:02:58 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-05-31 04:01:01 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 04:10:57 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 595.4 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 4.4.0 (2024-04-24)
* 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 ‘2.8.0’
* 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
signature_volcano 8.424 0.168 8.592
gs_mds 7.056 0.100 7.156
gs_heatmap 6.467 0.132 6.598
gs_upset 6.264 0.132 6.396
GeneTonic 5.535 0.312 5.848
ggs_backbone 5.570 0.156 5.726
ggs_graph 5.444 0.196 5.640
summarize_ggs_hubgenes 5.095 0.092 5.187
* 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 4.4.0 (2024-04-24) -- "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!
|
| | 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
182.034 9.928 159.648
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 5.535 | 0.312 | 5.848 | |
| GeneTonicList | 4.469 | 0.168 | 4.638 | |
| check_colors | 0.01 | 0.00 | 0.01 | |
| checkup_GeneTonic | 3.577 | 0.128 | 3.704 | |
| checkup_gtl | 3.475 | 0.108 | 3.583 | |
| cluster_markov | 0.084 | 0.012 | 0.096 | |
| create_jaccard_matrix | 0.794 | 0.071 | 0.866 | |
| create_kappa_matrix | 3.064 | 0.040 | 3.104 | |
| create_upsetdata | 0.023 | 0.056 | 0.079 | |
| deseqresult2df | 0.144 | 0.000 | 0.143 | |
| distill_enrichment | 3.930 | 0.180 | 4.109 | |
| enhance_table | 3.745 | 0.088 | 3.833 | |
| enrichment_map | 3.497 | 0.072 | 3.569 | |
| export_for_iSEE | 3.127 | 0.072 | 3.200 | |
| export_to_sif | 0.021 | 0.000 | 0.021 | |
| gene_plot | 4.200 | 0.124 | 4.324 | |
| geneinfo_2_html | 0.008 | 0.000 | 0.008 | |
| get_aggrscores | 2.826 | 0.072 | 2.899 | |
| get_expression_values | 2.851 | 0.108 | 2.959 | |
| ggs_backbone | 5.570 | 0.156 | 5.726 | |
| ggs_graph | 5.444 | 0.196 | 5.640 | |
| go_2_html | 0.018 | 0.000 | 0.019 | |
| gs_alluvial | 3.833 | 0.104 | 3.937 | |
| gs_dendro | 3.864 | 0.164 | 4.028 | |
| gs_fuzzyclustering | 0.843 | 0.000 | 0.844 | |
| gs_heatmap | 6.467 | 0.132 | 6.598 | |
| gs_horizon | 3.386 | 0.076 | 3.462 | |
| gs_mds | 7.056 | 0.100 | 7.156 | |
| gs_radar | 2.917 | 0.088 | 3.005 | |
| gs_scores | 4.831 | 0.112 | 4.943 | |
| gs_scoresheat | 4.624 | 0.032 | 4.656 | |
| gs_simplify | 0.984 | 0.036 | 1.020 | |
| gs_summary_heat | 3.011 | 0.051 | 3.062 | |
| gs_summary_overview | 3.152 | 0.076 | 3.227 | |
| gs_summary_overview_pair | 3.089 | 0.048 | 3.137 | |
| gs_upset | 6.264 | 0.132 | 6.396 | |
| gs_volcano | 3.212 | 0.044 | 3.255 | |
| happy_hour | 2.825 | 0.044 | 2.869 | |
| map2color | 0.012 | 0.000 | 0.012 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.005 | 0.004 | 0.009 | |
| shake_enrichResult | 2.256 | 0.052 | 2.308 | |
| shake_enrichrResult | 0.205 | 0.000 | 0.206 | |
| shake_fgseaResult | 0.212 | 0.000 | 0.213 | |
| shake_gprofilerResult | 0.150 | 0.011 | 0.163 | |
| shake_gsenrichResult | 2.785 | 0.084 | 2.869 | |
| shake_topGOtableResult | 0.01 | 0.00 | 0.01 | |
| signature_volcano | 8.424 | 0.168 | 8.592 | |
| styleColorBar_divergent | 0.201 | 0.012 | 0.213 | |
| summarize_ggs_hubgenes | 5.095 | 0.092 | 5.187 | |