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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CyTOFpower.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CyTOFpower_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CyTOFpower.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘CyTOFpower/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CyTOFpower’ version ‘1.5.0’
* 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 ‘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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Changes in version 0.99.0 (2021-09-15)
* 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 loading without being on the library search path ... 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   5.         └─limma::duplicateCorrelation(meds, design, block = block_id)
  ── Error ('test_run_models_onesim.R:115:3'): Wrapper to run models ─────────────
  Error in `duplicateCorrelation(meds, design, block = block_id)`: statmod package required but is not installed (or can't be loaded)
  Backtrace:
      ▆
   1. └─CyTOFpower:::function_apply_modelcomputations_modelchoice(...) at test_run_models_onesim.R:115:2
   2.   └─CyTOFpower:::function_to_compute_model_computation_onesimulation_modelchoice(...)
   3.     └─CyTOFpower:::function_run_diffcyt_full_pipeline(...)
   4.       └─CyTOFpower:::function_run_diffcytDSlimma(...)
   5.         └─diffcyt::testDS_limma(...)
   6.           └─limma::duplicateCorrelation(meds, design, block = block_id)
  
  [ FAIL 3 | WARN 33 | SKIP 0 | PASS 54 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘CyTOFpower.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/CyTOFpower.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CyTOFpower
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘CyTOFpower’ ...
** 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 (CyTOFpower)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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(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 with `by = join_by(markers)`
Joining with `by = join_by(markers)`
boundary (singular) fit: see help('isSingular')
Run the limma model with random 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
  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
Run the LMM model with random effect
boundary (singular) fit: see help('isSingular')
[ FAIL 3 | WARN 33 | SKIP 0 | PASS 54 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_run_models.R:328:3'): Run the full diffcyt pipeline ────────────
Error in `duplicateCorrelation(meds, design, block = block_id)`: statmod package required but is not installed (or can't be loaded)
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test_run_models.R:328:2
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. └─CyTOFpower:::function_run_diffcyt_full_pipeline(...)
  8.   └─CyTOFpower:::function_run_diffcytDSlimma(...)
  9.     └─diffcyt::testDS_limma(...)
 10.       └─limma::duplicateCorrelation(meds, design, block = block_id)
── Error ('test_run_models_onesim.R:62:3'): Run models ─────────────────────────
Error in `duplicateCorrelation(meds, design, block = block_id)`: statmod package required but is not installed (or can't be loaded)
Backtrace:
    ▆
 1. └─CyTOFpower:::function_to_compute_model_computation_onesimulation_modelchoice(...) at test_run_models_onesim.R:62:2
 2.   └─CyTOFpower:::function_run_diffcyt_full_pipeline(...)
 3.     └─CyTOFpower:::function_run_diffcytDSlimma(...)
 4.       └─diffcyt::testDS_limma(...)
 5.         └─limma::duplicateCorrelation(meds, design, block = block_id)
── Error ('test_run_models_onesim.R:115:3'): Wrapper to run models ─────────────
Error in `duplicateCorrelation(meds, design, block = block_id)`: statmod package required but is not installed (or can't be loaded)
Backtrace:
    ▆
 1. └─CyTOFpower:::function_apply_modelcomputations_modelchoice(...) at test_run_models_onesim.R:115:2
 2.   └─CyTOFpower:::function_to_compute_model_computation_onesimulation_modelchoice(...)
 3.     └─CyTOFpower:::function_run_diffcyt_full_pipeline(...)
 4.       └─CyTOFpower:::function_run_diffcytDSlimma(...)
 5.         └─diffcyt::testDS_limma(...)
 6.           └─limma::duplicateCorrelation(meds, design, block = block_id)

[ FAIL 3 | WARN 33 | SKIP 0 | PASS 54 ]
Error: Test failures
Execution halted