Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 804/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 3.1.1  (landing page)
Federico Marini
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: devel
git_last_commit: fe808f5
git_last_commit_date: 2024-12-19 15:34:51 -0500 (Thu, 19 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for GeneTonic on nebbiolo1

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.

raw results


Summary

Package: GeneTonic
Version: 3.1.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneTonic_3.1.1.tar.gz
StartedAt: 2024-12-22 22:23:36 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 22:35:15 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 698.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneTonic_3.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneTonic.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘3.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
gs_mds                 7.462  0.058   7.521
GeneTonic              6.723  0.338   7.062
ggs_graph              6.120  0.139   6.261
gs_heatmap             6.115  0.105   6.221
gs_upset               5.516  0.050   5.567
ggs_backbone           5.208  0.118   5.327
summarize_ggs_hubgenes 5.087  0.072   5.160
gs_dendro              5.029  0.108   5.137
gs_scoresheat          5.041  0.043   5.084
* 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


Installation output

GeneTonic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-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)

Tests output

GeneTonic.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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)

Welcome to GeneTonic v3.1.1

If you use GeneTonic in your work, please cite:

  GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
  Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
  BMC Bioinformatics, 2021 - https://doi.org/10.1186/s12859-021-04461-5
and/or (if adopting the series of protocols as a whole)
  Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, ideal, and GeneTonic
  Annekathrin Ludt, Arsenij Ustjanzew, Harald Binder, Konstantin Strauch, Federico Marini
  Current Protocols, 2022 - https://doi.org/10.1002/cpz1.411

> 
> 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!

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
195.020   6.918 168.741 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic6.7230.3387.062
GeneTonicList3.8720.0823.954
check_colors0.0070.0000.008
checkup_GeneTonic3.8150.1353.951
checkup_gtl2.7810.0842.866
cluster_markov0.0810.0000.081
create_jaccard_matrix0.9610.0401.001
create_kappa_matrix4.4520.1264.580
create_upsetdata0.0260.0510.077
deprecated0.0000.0000.001
deseqresult2df0.1350.0040.139
distill_enrichment3.3320.0513.388
enhance_table3.9000.1244.025
enrichment_map3.9950.1444.139
export_for_iSEE4.2060.0454.252
export_to_sif0.0220.0000.022
gene_plot3.4240.0783.503
geneinfo_2_html0.0080.0000.008
get_aggrscores3.8850.0633.948
get_expression_values2.9960.0543.050
ggs_backbone5.2080.1185.327
ggs_graph6.1200.1396.261
go_2_html0.0230.0000.022
gs_alluvial3.0980.0883.186
gs_dendro5.0290.1085.137
gs_fuzzyclustering0.8850.0040.889
gs_heatmap6.1150.1056.221
gs_horizon3.4180.0853.503
gs_mds7.4620.0587.521
gs_radar2.9520.0743.026
gs_scores4.2610.0814.359
gs_scoresheat5.0410.0435.084
gs_simplify1.0020.0011.004
gs_summary_heat3.0310.0413.074
gs_summary_overview4.2500.0584.309
gs_summary_overview_pair2.9400.0392.980
gs_upset5.5160.0505.567
gs_volcano4.3250.0484.374
happy_hour2.7450.0462.791
map2color0.0120.0000.012
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.0090.0000.009
shake_enrichResult1.6740.0351.708
shake_enrichrResult0.0450.0000.049
shake_fgseaResult0.1140.0010.115
shake_gprofilerResult0.0820.0030.085
shake_gsenrichResult2.7870.0392.826
shake_topGOtableResult0.0060.0010.007
signature_volcano4.6970.0904.787
styleColorBar_divergent0.2110.0120.223
summarize_ggs_hubgenes5.0870.0725.160