##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDesign3.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings scDesign3_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/scDesign3.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scDesign3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scDesign3' 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 whether package 'scDesign3' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... ERROR
Running examples in 'scDesign3-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perform_lrt
> ### Title: Perform the likelihood ratio test
> ### Aliases: perform_lrt
> 
> ### ** Examples
> 
> data(example_sce)
> my_data <- construct_data(
+ sce = example_sce,
+ assay_use = "counts",
+ celltype = "cell_type",
+ pseudotime = "pseudotime",
+ spatial = NULL,
+ other_covariates = NULL,
+ corr_by = "cell_type"
+ )
> 
> my_data2 <- construct_data(
+   sce = example_sce,
+   assay_use = "counts",
+   celltype = "cell_type",
+   pseudotime = "pseudotime",
+   spatial = NULL,
+   other_covariates = NULL,
+   corr_by = "pseudotime",
+   ncell = 10000
+ )
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Error: BiocParallel errors
  3 remote errors, element index: 1, 3, 5
  2 unevaluated and other errors
  first remote error:
Error in eval(expr, p): Index out of bounds: [index='prob0'].
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
construct_data 6.42   0.26    6.69
extract_para   6.45   0.16    6.63
* 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:
  
  Backtrace:
      ▆
   1. └─scDesign3::construct_data(...) at test-scDesign3.R:16:3
   2.   ├─base::as.data.frame(...)
   3.   └─scDesign3:::simuCovariateMat(dat, ncell, parallelization, BPPARAM)
   4.     ├─BiocParallel (local) paraFunc(...)
   5.     └─BiocParallel (local) paraFunc(...)
   6.       ├─BiocParallel::bplapply(...)
   7.       └─BiocParallel::bplapply(...)
   8.         └─BiocParallel:::.bpinit(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/scDesign3.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL scDesign3
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'scDesign3' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (scDesign3)

R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(scDesign3)
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
> 
> test_check("scDesign3")
Loading required namespace: SingleCellExperiment
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-scDesign3.R:16:3'): Run scDesign3 ──────────────────────────────
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  3 remote errors, element index: 1, 3, 5
  2 unevaluated and other errors
  first remote error:
Error in eval(expr, p): Index out of bounds: [index='prob0'].

Backtrace:
    ▆
 1. └─scDesign3::construct_data(...) at test-scDesign3.R:16:3
 2.   ├─base::as.data.frame(...)
 3.   └─scDesign3:::simuCovariateMat(dat, ncell, parallelization, BPPARAM)
 4.     ├─BiocParallel (local) paraFunc(...)
 5.     └─BiocParallel (local) paraFunc(...)
 6.       ├─BiocParallel::bplapply(...)
 7.       └─BiocParallel::bplapply(...)
 8.         └─BiocParallel:::.bpinit(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted