| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:41 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 763/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.3.0 (landing page) Federico Marini
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: GeneTonic |
| Version: 2.3.0 |
| 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/library --timings GeneTonic_2.3.0.tar.gz |
| StartedAt: 2023-02-28 03:59:09 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 04:11:17 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 728.0 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/library --timings GeneTonic_2.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.3.0’
* 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 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_heatmap 8.591 0.088 8.680
gs_mds 8.080 0.116 8.197
ggs_backbone 8.070 0.120 8.190
ggs_graph 7.779 0.148 7.927
summarize_ggs_hubgenes 7.758 0.043 7.802
GeneTonic 7.557 0.236 7.794
gs_upset 7.423 0.048 7.471
signature_volcano 6.093 0.095 6.189
gs_dendro 5.960 0.076 6.036
gs_scores 5.803 0.048 5.851
gs_scoresheat 5.774 0.044 5.819
gs_horizon 5.279 0.108 5.387
gene_plot 5.286 0.060 5.346
export_for_iSEE 5.066 0.064 5.131
distill_enrichment 4.889 0.196 5.085
enhance_table 4.912 0.112 5.024
gs_summary_overview_pair 4.937 0.080 5.017
* 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/library’ * installing *source* package ‘GeneTonic’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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) (2023-01-14 r83615) -- "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 4 | SKIP 0 | PASS 258 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 258 ]
>
> proc.time()
user system elapsed
241.526 9.031 218.997
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 7.557 | 0.236 | 7.794 | |
| GeneTonicList | 4.450 | 0.092 | 4.543 | |
| check_colors | 0.011 | 0.000 | 0.011 | |
| checkup_GeneTonic | 4.443 | 0.108 | 4.551 | |
| checkup_gtl | 3.781 | 0.076 | 3.858 | |
| cluster_markov | 0.107 | 0.000 | 0.106 | |
| create_jaccard_matrix | 1.118 | 0.000 | 1.118 | |
| create_kappa_matrix | 3.990 | 0.024 | 4.013 | |
| create_upsetdata | 0.019 | 0.036 | 0.055 | |
| deseqresult2df | 0.170 | 0.004 | 0.174 | |
| distill_enrichment | 4.889 | 0.196 | 5.085 | |
| enhance_table | 4.912 | 0.112 | 5.024 | |
| enrichment_map | 4.707 | 0.104 | 4.811 | |
| export_for_iSEE | 5.066 | 0.064 | 5.131 | |
| export_to_sif | 0.024 | 0.000 | 0.024 | |
| gene_plot | 5.286 | 0.060 | 5.346 | |
| geneinfo_2_html | 0.009 | 0.000 | 0.009 | |
| get_aggrscores | 4.441 | 0.152 | 4.593 | |
| get_expression_values | 2.724 | 0.076 | 2.801 | |
| ggs_backbone | 8.07 | 0.12 | 8.19 | |
| ggs_graph | 7.779 | 0.148 | 7.927 | |
| go_2_html | 0.029 | 0.004 | 0.033 | |
| gs_alluvial | 4.606 | 0.168 | 4.774 | |
| gs_dendro | 5.960 | 0.076 | 6.036 | |
| gs_fuzzyclustering | 1.060 | 0.000 | 1.061 | |
| gs_heatmap | 8.591 | 0.088 | 8.680 | |
| gs_horizon | 5.279 | 0.108 | 5.387 | |
| gs_mds | 8.080 | 0.116 | 8.197 | |
| gs_radar | 4.700 | 0.128 | 4.827 | |
| gs_scores | 5.803 | 0.048 | 5.851 | |
| gs_scoresheat | 5.774 | 0.044 | 5.819 | |
| gs_simplify | 1.523 | 0.004 | 1.528 | |
| gs_summary_heat | 4.840 | 0.080 | 4.921 | |
| gs_summary_overview | 4.135 | 0.040 | 4.176 | |
| gs_summary_overview_pair | 4.937 | 0.080 | 5.017 | |
| gs_upset | 7.423 | 0.048 | 7.471 | |
| gs_volcano | 4.441 | 0.092 | 4.533 | |
| happy_hour | 3.827 | 0.028 | 3.856 | |
| map2color | 0.014 | 0.000 | 0.013 | |
| overlap_coefficient | 0.001 | 0.000 | 0.000 | |
| overlap_jaccard_index | 0.001 | 0.000 | 0.000 | |
| shake_davidResult | 0.012 | 0.000 | 0.012 | |
| shake_enrichResult | 2.889 | 0.056 | 2.946 | |
| shake_enrichrResult | 0.062 | 0.000 | 0.063 | |
| shake_fgseaResult | 0.139 | 0.000 | 0.139 | |
| shake_gprofilerResult | 0.094 | 0.000 | 0.094 | |
| shake_gsenrichResult | 1.888 | 0.040 | 1.928 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.007 | |
| signature_volcano | 6.093 | 0.095 | 6.189 | |
| styleColorBar_divergent | 0.234 | 0.013 | 0.246 | |
| summarize_ggs_hubgenes | 7.758 | 0.043 | 7.802 | |