| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:31 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 780/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.5.0 (landing page) Federico Marini
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: GeneTonic |
| Version: 2.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeneTonic_2.5.0.tar.gz |
| StartedAt: 2023-05-09 16:42:59 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 16:55:48 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 769.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeneTonic_2.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.5.0’
* 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 R 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 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 8.729 0.084 8.814
gs_upset 8.331 0.076 8.407
ggs_backbone 8.037 0.152 8.189
GeneTonic 7.811 0.308 8.120
gs_heatmap 7.735 0.136 7.871
ggs_graph 7.660 0.144 7.804
summarize_ggs_hubgenes 7.430 0.136 7.566
signature_volcano 7.102 0.136 7.239
gs_scores 6.860 0.172 7.032
distill_enrichment 5.727 0.143 5.873
gs_scoresheat 5.763 0.088 5.851
gs_volcano 5.419 0.084 5.504
gene_plot 5.210 0.092 5.302
gs_dendro 5.175 0.088 5.264
enhance_table 5.060 0.072 5.135
gs_summary_overview 4.947 0.060 5.008
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GeneTonic_manual.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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, 928 found as DE
Upregulated: 329
Downregulated: 599
----- 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 2 | SKIP 0 | PASS 264 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 264 ]
>
> proc.time()
user system elapsed
238.028 8.704 213.826
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.811 | 0.308 | 8.120 | |
| GeneTonicList | 4.507 | 0.208 | 4.715 | |
| check_colors | 0.008 | 0.004 | 0.012 | |
| checkup_GeneTonic | 4.598 | 0.156 | 4.753 | |
| checkup_gtl | 4.564 | 0.128 | 4.692 | |
| cluster_markov | 0.105 | 0.004 | 0.109 | |
| create_jaccard_matrix | 1.084 | 0.003 | 1.088 | |
| create_kappa_matrix | 3.781 | 0.029 | 3.810 | |
| create_upsetdata | 0.025 | 0.027 | 0.053 | |
| deseqresult2df | 0.160 | 0.001 | 0.161 | |
| distill_enrichment | 5.727 | 0.143 | 5.873 | |
| enhance_table | 5.060 | 0.072 | 5.135 | |
| enrichment_map | 4.664 | 0.108 | 4.773 | |
| export_for_iSEE | 4.218 | 0.076 | 4.295 | |
| export_to_sif | 0.024 | 0.000 | 0.023 | |
| gene_plot | 5.210 | 0.092 | 5.302 | |
| geneinfo_2_html | 0.008 | 0.000 | 0.008 | |
| get_aggrscores | 4.489 | 0.144 | 4.633 | |
| get_expression_values | 2.660 | 0.136 | 2.796 | |
| ggs_backbone | 8.037 | 0.152 | 8.189 | |
| ggs_graph | 7.660 | 0.144 | 7.804 | |
| go_2_html | 0.029 | 0.000 | 0.029 | |
| gs_alluvial | 4.725 | 0.176 | 4.903 | |
| gs_dendro | 5.175 | 0.088 | 5.264 | |
| gs_fuzzyclustering | 1.039 | 0.004 | 1.043 | |
| gs_heatmap | 7.735 | 0.136 | 7.871 | |
| gs_horizon | 4.613 | 0.076 | 4.689 | |
| gs_mds | 8.729 | 0.084 | 8.814 | |
| gs_radar | 3.841 | 0.104 | 3.944 | |
| gs_scores | 6.860 | 0.172 | 7.032 | |
| gs_scoresheat | 5.763 | 0.088 | 5.851 | |
| gs_simplify | 1.503 | 0.000 | 1.504 | |
| gs_summary_heat | 4.810 | 0.084 | 4.894 | |
| gs_summary_overview | 4.947 | 0.060 | 5.008 | |
| gs_summary_overview_pair | 3.962 | 0.052 | 4.014 | |
| gs_upset | 8.331 | 0.076 | 8.407 | |
| gs_volcano | 5.419 | 0.084 | 5.504 | |
| happy_hour | 4.625 | 0.024 | 4.649 | |
| map2color | 0.013 | 0.000 | 0.013 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.012 | 0.000 | 0.013 | |
| shake_enrichResult | 2.009 | 0.044 | 2.053 | |
| shake_enrichrResult | 0.063 | 0.004 | 0.067 | |
| shake_fgseaResult | 0.143 | 0.000 | 0.144 | |
| shake_gprofilerResult | 0.097 | 0.000 | 0.099 | |
| shake_gsenrichResult | 1.914 | 0.032 | 1.946 | |
| shake_topGOtableResult | 0.008 | 0.000 | 0.007 | |
| signature_volcano | 7.102 | 0.136 | 7.239 | |
| styleColorBar_divergent | 0.226 | 0.016 | 0.243 | |
| summarize_ggs_hubgenes | 7.430 | 0.136 | 7.566 | |