Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:18 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for CyTOFpower on riesling1


To the developers/maintainers of the CyTOFpower package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CyTOFpower.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 444/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CyTOFpower 1.1.0  (landing page)
Anne-Maud Ferreira
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/CyTOFpower
git_branch: master
git_last_commit: 6024ae9
git_last_commit_date: 2021-10-26 13:13:28 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'diffcyt' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CyTOFpower
Version: 1.1.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CyTOFpower.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CyTOFpower_1.1.0.tar.gz
StartedAt: 2022-03-17 18:51:28 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:52:38 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CyTOFpower.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CyTOFpower.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CyTOFpower_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CyTOFpower.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CyTOFpower/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CyTOFpower' version '1.1.0'
* 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 'CyTOFpower' 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
* 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

CyTOFpower.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CyTOFpower
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CyTOFpower' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CyTOFpower'
    finding HTML links ... done
    CyTOFpower                              html  
    compute_effectsize                      html  
    compute_pwr                             html  
    compute_variance                        html  
    function_DEmarkers_sup_nbmarkers        html  
    function_apply_modelcomputations_modelchoice
                                            html  
    function_apply_onesimulation_withmarkerinfo
                                            html  
    function_check_nbDEmarkers              html  
    function_check_nbmarkers                html  
    function_compute_diffcyt_features       html  
    function_create_mock_dataset_withmarkerinfo
                                            html  
    function_desigmat_contrast_diffcytDSlimma_fixedeffect
                                            html  
    function_desigmat_contrast_diffcytDSlimma_randomeffect
                                            html  
    function_extract_marker_names           html  
    function_formula_contrast_diffcytDSLMM_randomeffect
                                            html  
    function_is_data_paired                 html  
    function_names_DE_markers               html  
    function_run_bootstrapcytoGLMM          html  
    function_run_cytoGLMM                   html  
    function_run_diffcytDSLMM               html  
    function_run_diffcytDSlimma             html  
    function_run_diffcyt_full_pipeline      html  
    function_summary_results_models         html  
    function_to_compute_model_computation_onesimulation_modelchoice
                                            html  
    function_to_transform_data              html  
    function_value_onemarker                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
* DONE (CyTOFpower)
Making 'packages.html' ... done

Tests output

CyTOFpower.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(CyTOFpower)
> 
> test_check("CyTOFpower")
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  1

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  1

  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

[[1]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3   1            0.1  10          3                  3

[[2]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m2        3 1.1            0.1  10          3                  3

[[3]]
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m3        3   1            0.1  10          3                  3

Joining, by = "markers"
Joining, by = "markers"
boundary (singular) fit: see help('isSingular')
Fitting linear models with random effects term for 'block_id'.
boundary (singular) fit: see help('isSingular')
Run the limma model with random effect
Fitting linear models with random effects term for 'block_id'.
Run the limma model with fixed effect
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the limma model with random effect
Fitting linear models with random effects term for 'block_id'.
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the limma model with fixed effect
  marker_name nb_donor rho subject_effect mu0 dispersion nb_cell_per_sample
1          m1        3 1.0            0.1  10          3                  3
2          m2        3 1.1            0.1  10          3                  3
3          m3        3 1.0            0.1  10          3                  3
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 69 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 69 ]
> 
> proc.time()
   user  system elapsed 
  17.87    1.81   19.68

Example timings

CyTOFpower.Rcheck/CyTOFpower-Ex.timings

nameusersystemelapsed
CyTOFpower000