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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSPrep_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSPrep.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSPrep/DESCRIPTION’ ... OK
* this is package ‘MSPrep’ version ‘1.20.0’
* 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 ‘MSPrep’ 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 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MSPrep      18.348  0.336  18.685
msImpute    17.461  0.248  17.711
msNormalize 13.580  0.114  13.696
msPrepare   12.644  0.085  12.731
msSummarize 12.576  0.028  12.604
msFilter    12.331  0.085  12.417
* 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.         └─ranger::ranger(...)
  ── Error ('test_sedf_equality.R:78:1'): (code run outside of `test_that()`) ────
  Error in `ranger::ranger(x = obsX, y = obsY, num.trees = ntree, mtry = mtry, replace = replace, sample.fraction = sf, min.bucket = if (!is.null(nodesize)) nodesize[1] else 5, write.forest = TRUE, oob.error = TRUE, num.threads = if (!is.null(num.threads)) num.threads else if (parallelize == "forests") foreach::getDoParWorkers() else NULL, verbose = FALSE)`: Error: No covariates found.
  Backtrace:
      ▆
   1. └─MSPrep::msImpute(...) at test_sedf_equality.R:78:1
   2.   └─MSPrep:::.dfImpute(...)
   3.     └─MSPrep:::.imputeRf(abundanceColumns, maxIterRf, nTreeRf)
   4.       └─missForest::missForest(...)
   5.         └─ranger::ranger(...)
  
  [ FAIL 2 | WARN 6 | SKIP 0 | PASS 32 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MSPrep.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MSPrep
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MSPrep’ ...
** this is package ‘MSPrep’ version ‘1.20.0’
** using staged installation
** R
** data
** 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 (MSPrep)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(MSPrep)
> 
> test_check("MSPrep")
Saving _problems/test_msImpute-46.R
Saving _problems/test_sedf_equality-83.R
[ FAIL 2 | WARN 6 | SKIP 0 | PASS 32 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_msImpute.R:41:1'): (code run outside of `test_that()`) ─────────
Error in `ranger::ranger(x = obsX, y = obsY, num.trees = ntree, mtry = mtry, replace = replace, sample.fraction = sf, min.bucket = if (!is.null(nodesize)) nodesize[1] else 5, write.forest = TRUE, oob.error = TRUE, num.threads = if (!is.null(num.threads)) num.threads else if (parallelize == "forests") foreach::getDoParWorkers() else NULL, verbose = FALSE)`: Error: No covariates found.
Backtrace:
    ▆
 1. └─MSPrep::msImpute(...) at test_msImpute.R:41:1
 2.   └─MSPrep:::.dfImpute(...)
 3.     └─MSPrep:::.imputeRf(abundanceColumns, maxIterRf, nTreeRf)
 4.       └─missForest::missForest(...)
 5.         └─ranger::ranger(...)
── Error ('test_sedf_equality.R:78:1'): (code run outside of `test_that()`) ────
Error in `ranger::ranger(x = obsX, y = obsY, num.trees = ntree, mtry = mtry, replace = replace, sample.fraction = sf, min.bucket = if (!is.null(nodesize)) nodesize[1] else 5, write.forest = TRUE, oob.error = TRUE, num.threads = if (!is.null(num.threads)) num.threads else if (parallelize == "forests") foreach::getDoParWorkers() else NULL, verbose = FALSE)`: Error: No covariates found.
Backtrace:
    ▆
 1. └─MSPrep::msImpute(...) at test_sedf_equality.R:78:1
 2.   └─MSPrep:::.dfImpute(...)
 3.     └─MSPrep:::.imputeRf(abundanceColumns, maxIterRf, nTreeRf)
 4.       └─missForest::missForest(...)
 5.         └─ranger::ranger(...)

[ FAIL 2 | WARN 6 | SKIP 0 | PASS 32 ]
Error:
! Test failures.
Execution halted