| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 760/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneTonic 2.3.0 (landing page) Federico Marini
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: GeneTonic |
| Version: 2.3.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GeneTonic_2.3.0.tar.gz |
| StartedAt: 2022-12-29 00:03:06 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:11:03 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 477.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneTonic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GeneTonic_2.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GeneTonic.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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_mds 6.16 0.33 6.48
summarize_ggs_hubgenes 5.83 0.17 6.02
GeneTonic 5.31 0.20 5.78
gs_upset 5.22 0.15 5.37
ggs_backbone 5.00 0.34 5.72
gs_heatmap 4.99 0.11 5.10
ggs_graph 4.92 0.16 5.08
signature_volcano 4.86 0.20 5.07
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
GeneTonic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GeneTonic ### ############################################################################## ############################################################################## * installing to library 'F:/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 5 | SKIP 0 | PASS 258 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 258 ]
>
> proc.time()
user system elapsed
118.59 9.39 157.76
GeneTonic.Rcheck/GeneTonic-Ex.timings
| name | user | system | elapsed | |
| GeneTonic | 5.31 | 0.20 | 5.78 | |
| GeneTonicList | 3.72 | 0.14 | 3.86 | |
| check_colors | 0.00 | 0.02 | 0.02 | |
| checkup_GeneTonic | 3.15 | 0.16 | 3.31 | |
| checkup_gtl | 3.19 | 0.09 | 3.28 | |
| cluster_markov | 0.08 | 0.00 | 0.08 | |
| create_jaccard_matrix | 0.67 | 0.05 | 0.72 | |
| create_kappa_matrix | 1.83 | 0.34 | 2.17 | |
| create_upsetdata | 0.04 | 0.02 | 0.07 | |
| deseqresult2df | 0.13 | 0.00 | 0.12 | |
| distill_enrichment | 3.44 | 0.09 | 3.53 | |
| enhance_table | 3.51 | 0.11 | 3.63 | |
| enrichment_map | 3.39 | 0.19 | 3.57 | |
| export_for_iSEE | 3.36 | 0.09 | 3.46 | |
| export_to_sif | 0.02 | 0.00 | 0.01 | |
| gene_plot | 3.40 | 0.14 | 3.55 | |
| geneinfo_2_html | 0 | 0 | 0 | |
| get_aggrscores | 3.60 | 0.03 | 3.63 | |
| get_expression_values | 2.53 | 0.08 | 2.60 | |
| ggs_backbone | 5.00 | 0.34 | 5.72 | |
| ggs_graph | 4.92 | 0.16 | 5.08 | |
| go_2_html | 0.02 | 0.00 | 0.02 | |
| gs_alluvial | 3.31 | 0.22 | 4.56 | |
| gs_dendro | 4.12 | 0.12 | 4.25 | |
| gs_fuzzyclustering | 0.54 | 0.02 | 0.55 | |
| gs_heatmap | 4.99 | 0.11 | 5.10 | |
| gs_horizon | 3.90 | 0.08 | 3.98 | |
| gs_mds | 6.16 | 0.33 | 6.48 | |
| gs_radar | 2.77 | 0.20 | 2.96 | |
| gs_scores | 3.72 | 0.18 | 3.90 | |
| gs_scoresheat | 4.53 | 0.11 | 4.64 | |
| gs_simplify | 0.84 | 0.02 | 0.86 | |
| gs_summary_heat | 3.38 | 0.12 | 3.50 | |
| gs_summary_overview | 3.06 | 0.16 | 3.22 | |
| gs_summary_overview_pair | 3.91 | 0.11 | 4.02 | |
| gs_upset | 5.22 | 0.15 | 5.37 | |
| gs_volcano | 3.81 | 0.11 | 3.92 | |
| happy_hour | 3.25 | 0.07 | 3.31 | |
| map2color | 0.01 | 0.00 | 0.02 | |
| overlap_coefficient | 0 | 0 | 0 | |
| overlap_jaccard_index | 0 | 0 | 0 | |
| shake_davidResult | 0.02 | 0.00 | 0.02 | |
| shake_enrichResult | 1.47 | 0.06 | 1.53 | |
| shake_enrichrResult | 0.03 | 0.01 | 0.04 | |
| shake_fgseaResult | 0.08 | 0.03 | 0.11 | |
| shake_gprofilerResult | 0.09 | 0.00 | 0.11 | |
| shake_gsenrichResult | 1.47 | 0.05 | 1.52 | |
| shake_topGOtableResult | 0 | 0 | 0 | |
| signature_volcano | 4.86 | 0.20 | 5.07 | |
| styleColorBar_divergent | 0.17 | 0.08 | 0.50 | |
| summarize_ggs_hubgenes | 5.83 | 0.17 | 6.02 | |