Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 820/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 2.8.0  (landing page)
Federico Marini
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_19
git_last_commit: dd4c5de
git_last_commit_date: 2024-04-30 11:20:41 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GeneTonic on palomino3

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: 2.8.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GeneTonic_2.8.0.tar.gz
StartedAt: 2024-06-13 04:07:44 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:24:05 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 981.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GeneTonic_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneTonic/DESCRIPTION' ... OK
* this is package 'GeneTonic' version '2.8.0'
* 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 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 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                   7.00   1.74    8.76
GeneTonic                7.02   1.42   13.78
gs_heatmap               5.95   2.20    7.06
summarize_ggs_hubgenes   6.41   1.52    7.92
ggs_backbone             6.17   1.67   11.97
ggs_graph                6.26   1.51    7.81
gs_upset                 5.86   1.28    7.28
signature_volcano        5.81   1.20    7.07
gs_horizon               5.38   1.44    6.66
gs_scores                5.31   1.41    6.82
gs_volcano               5.14   1.28    6.47
gs_dendro                4.88   1.52    6.39
distill_enrichment       5.03   1.17    6.28
gs_summary_overview_pair 4.68   1.41    6.09
gs_summary_heat          4.49   1.25    5.86
export_for_iSEE          4.39   1.20    5.61
enhance_table            4.28   1.27    5.67
gs_radar                 4.12   1.42    5.54
gs_scoresheat            4.13   1.39    5.57
checkup_GeneTonic        4.05   1.42    5.50
gene_plot                4.23   1.19    5.48
gs_summary_overview      3.85   1.38    5.24
get_aggrscores           4.03   1.19    5.28
gs_alluvial              3.33   1.53    6.70
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GeneTonic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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
*** 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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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...
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 1 | SKIP 0 | PASS 264 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
 160.57   22.12  351.57 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic 7.02 1.4213.78
GeneTonicList3.791.084.94
check_colors000
checkup_GeneTonic4.051.425.50
checkup_gtl3.321.354.70
cluster_markov0.130.030.20
create_jaccard_matrix0.840.060.91
create_kappa_matrix3.130.583.69
create_upsetdata0.060.030.09
deseqresult2df0.140.000.14
distill_enrichment5.031.176.28
enhance_table4.281.275.67
enrichment_map3.641.204.91
export_for_iSEE4.391.205.61
export_to_sif0.020.050.06
gene_plot4.231.195.48
geneinfo_2_html000
get_aggrscores4.031.195.28
get_expression_values3.331.254.61
ggs_backbone 6.17 1.6711.97
ggs_graph6.261.517.81
go_2_html0.020.000.02
gs_alluvial3.331.536.70
gs_dendro4.881.526.39
gs_fuzzyclustering0.730.160.89
gs_heatmap5.952.207.06
gs_horizon5.381.446.66
gs_mds7.001.748.76
gs_radar4.121.425.54
gs_scores5.311.416.82
gs_scoresheat4.131.395.57
gs_simplify0.980.071.07
gs_summary_heat4.491.255.86
gs_summary_overview3.851.385.24
gs_summary_overview_pair4.681.416.09
gs_upset5.861.287.28
gs_volcano5.141.286.47
happy_hour3.551.314.92
map2color0.010.000.01
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.030.000.03
shake_enrichResult2.281.193.49
shake_enrichrResult0.080.000.70
shake_fgseaResult0.250.000.25
shake_gprofilerResult0.100.011.05
shake_gsenrichResult1.891.072.97
shake_topGOtableResult000
signature_volcano5.811.207.07
styleColorBar_divergent0.220.140.84
summarize_ggs_hubgenes6.411.527.92