| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:36 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 786/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.3.2 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: GeneTonic |
| Version: 2.3.2 |
| 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_2.3.2.tar.gz |
| StartedAt: 2023-04-12 06:27:34 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 06:37:25 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 590.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_2.3.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.3.2’
* 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 loading without being on the library search path ... 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 7.005 0.032 7.036
summarize_ggs_hubgenes 6.844 0.100 6.944
GeneTonic 6.332 0.276 6.609
gs_upset 6.107 0.092 6.199
signature_volcano 6.095 0.076 6.171
ggs_graph 5.983 0.100 6.084
gs_scoresheat 5.935 0.076 6.013
gs_heatmap 5.641 0.080 5.722
ggs_backbone 5.610 0.076 5.686
* 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/site-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) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
182.574 6.164 158.904
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 6.332 | 0.276 | 6.609 | |
| GeneTonicList | 3.943 | 0.116 | 4.059 | |
| check_colors | 0.008 | 0.000 | 0.008 | |
| checkup_GeneTonic | 4.007 | 0.088 | 4.094 | |
| checkup_gtl | 3.102 | 0.056 | 3.159 | |
| cluster_markov | 0.089 | 0.000 | 0.090 | |
| create_jaccard_matrix | 1.531 | 0.060 | 1.591 | |
| create_kappa_matrix | 2.708 | 0.104 | 2.813 | |
| create_upsetdata | 0.025 | 0.015 | 0.040 | |
| deseqresult2df | 0.141 | 0.004 | 0.146 | |
| distill_enrichment | 3.468 | 0.148 | 3.617 | |
| enhance_table | 4.204 | 0.088 | 4.292 | |
| enrichment_map | 4.203 | 0.104 | 4.307 | |
| export_for_iSEE | 4.182 | 0.048 | 4.230 | |
| export_to_sif | 0.02 | 0.00 | 0.02 | |
| gene_plot | 4.590 | 0.276 | 4.867 | |
| geneinfo_2_html | 0.008 | 0.000 | 0.009 | |
| get_aggrscores | 4.051 | 0.104 | 4.163 | |
| get_expression_values | 2.936 | 0.072 | 3.008 | |
| ggs_backbone | 5.610 | 0.076 | 5.686 | |
| ggs_graph | 5.983 | 0.100 | 6.084 | |
| go_2_html | 0.019 | 0.000 | 0.019 | |
| gs_alluvial | 2.936 | 0.116 | 3.053 | |
| gs_dendro | 4.697 | 0.120 | 4.817 | |
| gs_fuzzyclustering | 0.753 | 0.000 | 0.753 | |
| gs_heatmap | 5.641 | 0.080 | 5.722 | |
| gs_horizon | 3.377 | 0.096 | 3.474 | |
| gs_mds | 7.005 | 0.032 | 7.036 | |
| gs_radar | 4.045 | 0.136 | 4.181 | |
| gs_scores | 4.807 | 0.032 | 4.839 | |
| gs_scoresheat | 5.935 | 0.076 | 6.013 | |
| gs_simplify | 1.145 | 0.028 | 1.174 | |
| gs_summary_heat | 4.143 | 0.052 | 4.195 | |
| gs_summary_overview | 3.251 | 0.076 | 3.326 | |
| gs_summary_overview_pair | 4.149 | 0.032 | 4.181 | |
| gs_upset | 6.107 | 0.092 | 6.199 | |
| gs_volcano | 4.759 | 0.048 | 4.807 | |
| happy_hour | 3.805 | 0.060 | 3.865 | |
| map2color | 0.012 | 0.000 | 0.012 | |
| overlap_coefficient | 0.001 | 0.000 | 0.001 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.009 | 0.000 | 0.009 | |
| shake_enrichResult | 1.721 | 0.024 | 1.744 | |
| shake_enrichrResult | 0.045 | 0.000 | 0.045 | |
| shake_fgseaResult | 0.122 | 0.000 | 0.122 | |
| shake_gprofilerResult | 0.078 | 0.004 | 0.083 | |
| shake_gsenrichResult | 1.716 | 0.032 | 1.748 | |
| shake_topGOtableResult | 0.007 | 0.000 | 0.007 | |
| signature_volcano | 6.095 | 0.076 | 6.171 | |
| styleColorBar_divergent | 0.231 | 0.004 | 0.235 | |
| summarize_ggs_hubgenes | 6.844 | 0.100 | 6.944 | |