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This page was generated on 2021-09-24 15:06:42 -0400 (Fri, 24 Sep 2021).

CHECK results for GeneTonic on machv2

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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 730/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.4.1  (landing page)
Federico Marini
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_13
git_last_commit: 32c4e77
git_last_commit_date: 2021-06-04 17:41:55 -0400 (Fri, 04 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneTonic
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.4.1.tar.gz
StartedAt: 2021-09-23 19:11:17 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 19:22:28 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 670.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneTonic_1.4.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneTonic.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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_mds                   9.958  0.492  10.458
ggs_backbone             9.983  0.223  10.220
gs_heatmap               9.268  0.180   9.465
gs_scoresheat            8.863  0.198   9.067
ggs_graph                8.618  0.166   8.802
summarize_ggs_hubgenes   8.342  0.221   8.572
signature_volcano        8.232  0.217   8.458
gs_scores                8.222  0.168   8.406
GeneTonic                7.756  0.298   8.070
gs_dendro                7.182  0.180   7.371
export_for_iSEE          6.735  0.176   6.922
gene_plot                5.934  0.171   6.127
gs_horizon               5.950  0.110   6.069
distill_enrichment       5.727  0.161   5.891
gs_alluvial              5.547  0.261   5.816
get_aggrscores           5.478  0.144   5.632
enhance_table            5.426  0.149   5.582
gs_summary_overview_pair 5.298  0.141   5.443
GeneTonic_list           5.267  0.139   5.409
checkup_GeneTonic        4.936  0.134   5.072
gs_summary_heat          4.902  0.154   5.113
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneTonic.Rcheck/00check.log’
for details.



Installation output

GeneTonic.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneTonic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

GeneTonic.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 235 ]
> 
> proc.time()
   user  system elapsed 
182.912   8.221 192.079 

Example timings

GeneTonic.Rcheck/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.7560.2988.070
GeneTonic_list5.2670.1395.409
check_colors0.0130.0020.016
checkup_GeneTonic4.9360.1345.072
checkup_gtl4.4170.1524.575
cluster_markov0.1180.0030.121
create_jaccard_matrix1.2240.0411.265
create_kappa_matrix4.0460.3194.382
deseqresult2df0.1850.0110.197
distill_enrichment5.7270.1615.891
enhance_table5.4260.1495.582
enrichment_map4.8750.1245.000
export_for_iSEE6.7350.1766.922
export_to_sif0.0230.0010.025
gene_plot5.9340.1716.127
geneinfo_2_html0.0130.0010.014
get_aggrscores5.4780.1445.632
get_expression_values3.7460.1323.879
ggs_backbone 9.983 0.22310.220
ggs_graph8.6180.1668.802
go_2_html0.0310.0000.031
gs_alluvial5.5470.2615.816
gs_dendro7.1820.1807.371
gs_fuzzyclustering1.1610.0771.239
gs_heatmap9.2680.1809.465
gs_horizon5.9500.1106.069
gs_mds 9.958 0.49210.458
gs_radar4.3840.2304.638
gs_scores8.2220.1688.406
gs_scoresheat8.8630.1989.067
gs_simplify2.0180.0532.072
gs_summary_heat4.9020.1545.113
gs_summary_overview4.6790.1084.793
gs_summary_overview_pair5.2980.1415.443
gs_volcano4.8400.0904.932
happy_hour4.6060.1534.765
map2color0.0150.0020.017
overlap_coefficient0.0000.0000.001
overlap_jaccard_index0.0000.0000.001
shake_davidResult0.0190.0020.020
shake_enrichResult2.8250.0542.892
shake_enrichrResult0.0840.0040.088
shake_fgseaResult0.2340.0260.263
shake_gprofilerResult0.1350.0030.139
shake_topGOtableResult0.0110.0010.012
signature_volcano8.2320.2178.458
styleColorBar_divergent0.2870.0350.324
summarize_ggs_hubgenes8.3420.2218.572