Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:17:23 -0500 (Wed, 01 Dec 2021).

CHECK results for CytoGLMM on nebbiolo2

To the developers/maintainers of the CytoGLMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoGLMM.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 439/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoGLMM 1.2.0  (landing page)
Christof Seiler
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/CytoGLMM
git_branch: RELEASE_3_14
git_last_commit: 13036ea
git_last_commit_date: 2021-10-26 13:08:21 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: CytoGLMM
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CytoGLMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CytoGLMM_1.2.0.tar.gz
StartedAt: 2021-11-30 08:44:20 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 08:46:15 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 114.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoGLMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CytoGLMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CytoGLMM_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CytoGLMM.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoGLMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoGLMM’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CytoGLMM’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plot.cytoflexmix     5.414  0.072   5.486
plot_model_selection 4.980  0.072   5.053
* 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


Installation output

CytoGLMM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CytoGLMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘CytoGLMM’ ...
** using staged installation
** R
** 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 (CytoGLMM)

Tests output

CytoGLMM.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(CytoGLMM)
> 
> test_check("CytoGLMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  3.558   0.191   3.743 

Example timings

CytoGLMM.Rcheck/CytoGLMM-Ex.timings

nameusersystemelapsed
cytoflexmix4.6820.1524.834
cytoglm1.2940.1841.478
cytoglmm0.2400.0080.247
cytogroup1.1480.0641.212
cytostab0.5820.0360.618
generate_data0.0860.0000.087
plot.cytoflexmix5.4140.0725.486
plot.cytoglm1.2810.0561.337
plot.cytoglmm0.2860.0000.287
plot.cytogroup1.2390.0311.271
plot_heatmap0.1580.0000.159
plot_lda1.3320.0241.356
plot_mds0.390.000.39
plot_model_selection4.9800.0725.053
plot_prcomp1.8660.0481.914
print.cytoglm0.7600.0040.763
print.cytoglmm0.1970.0030.199
summary.cytoglm0.8540.0200.875
summary.cytoglmm0.2020.0040.206