Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).

CHECK results for CytoGLMM on tokay2

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 432/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoGLMM 1.0.0  (landing page)
Christof Seiler
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CytoGLMM
git_branch: RELEASE_3_13
git_last_commit: 6da96d2
git_last_commit_date: 2021-05-19 13:01:29 -0400 (Wed, 19 May 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: CytoGLMM
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoGLMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CytoGLMM_1.0.0.tar.gz
StartedAt: 2021-10-14 21:50:33 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:54:00 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 207.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoGLMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoGLMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CytoGLMM_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoGLMM.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoGLMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoGLMM' version '1.0.0'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plot_model_selection 7.35   0.06    7.41
cytoflexmix          5.52   0.13    5.64
plot.cytoflexmix     5.32   0.06    5.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
plot_model_selection 6.25   0.01    6.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CytoGLMM_1.0.0.tar.gz && rm -rf CytoGLMM.buildbin-libdir && mkdir CytoGLMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoGLMM.buildbin-libdir CytoGLMM_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CytoGLMM_1.0.0.zip && rm CytoGLMM_1.0.0.tar.gz CytoGLMM_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 35343  100 35343    0     0   300k      0 --:--:-- --:--:-- --:--:--  302k

install for i386

* installing *source* package 'CytoGLMM' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CytoGLMM'
    finding HTML links ... done
    cyto_check                              html  
    cytoflexmix                             html  
    cytoglm                                 html  
    cytoglmm                                html  
    cytogroup                               html  
    cytostab                                html  
    generate_data                           html  
    glmm_moment                             html  
    is_unpaired                             html  
    plot.cytoflexmix                        html  
    plot.cytoglm                            html  
    plot.cytoglmm                           html  
    plot.cytogroup                          html  
    plot_coeff                              html  
    plot_heatmap                            html  
    plot_lda                                html  
    plot_mds                                html  
    plot_model_selection                    html  
    plot_prcomp                             html  
    print.cytoglm                           html  
    print.cytoglmm                          html  
    remove_samples                          html  
    summary.cytoglm                         html  
    summary.cytoglmm                        html  
** 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

install for x64

* installing *source* package 'CytoGLMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoGLMM' as CytoGLMM_1.0.0.zip
* DONE (CytoGLMM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CytoGLMM' successfully unpacked and MD5 sums checked

Tests output

CytoGLMM.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   3.79    0.57    4.35 

CytoGLMM.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(CytoGLMM)
> 
> test_check("CytoGLMM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   3.93    0.31    4.21 

Example timings

CytoGLMM.Rcheck/examples_i386/CytoGLMM-Ex.timings

nameusersystemelapsed
cytoflexmix5.520.135.64
cytoglm1.170.001.17
cytoglmm0.250.000.25
cytogroup0.820.030.84
cytostab0.220.000.22
generate_data0.100.000.09
plot.cytoflexmix5.320.065.39
plot.cytoglm1.410.021.42
plot.cytoglmm0.310.010.33
plot.cytogroup0.860.030.89
plot_heatmap0.420.010.44
plot_lda1.580.071.64
plot_mds0.450.030.48
plot_model_selection7.350.067.41
plot_prcomp1.920.082.00
print.cytoglm1.310.001.31
print.cytoglmm0.220.000.22
summary.cytoglm1.220.001.22
summary.cytoglmm0.220.000.22

CytoGLMM.Rcheck/examples_x64/CytoGLMM-Ex.timings

nameusersystemelapsed
cytoflexmix4.500.034.54
cytoglm1.010.001.01
cytoglmm0.170.020.18
cytogroup0.480.040.54
cytostab0.380.020.39
generate_data0.090.000.09
plot.cytoflexmix4.560.054.61
plot.cytoglm1.220.011.23
plot.cytoglmm0.30.00.3
plot.cytogroup0.950.030.99
plot_heatmap0.140.000.14
plot_lda1.570.051.61
plot_mds0.390.020.40
plot_model_selection6.250.016.27
plot_prcomp1.720.081.79
print.cytoglm1.120.001.13
print.cytoglmm0.190.030.22
summary.cytoglm0.890.000.89
summary.cytoglmm0.470.020.48