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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSPrep_1.21.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MSPrep.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSPrep/DESCRIPTION’ ... OK
* this is package ‘MSPrep’ version ‘1.21.1’
* 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 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      7.864  0.303   8.714
msImpute    6.254  0.280   6.713
msNormalize 5.187  0.266   5.632
msPrepare   5.214  0.152   5.561
msSummarize 5.028  0.206   5.456
msFilter    4.850  0.199   5.226
* 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:
    3. │ └─dplyr:::summarise.data.frame(.tbl, !!!funs)
    4. │   └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
    5. │     └─base::withCallingHandlers(...)
    6. ├─dplyr:::dplyr_internal_error(...)
    7. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
    8. │   └─rlang:::signal_abort(cnd, .file)
    9. │     └─base::signalCondition(cnd)
   10. └─dplyr (local) `<fn>`(`<dpl:::__>`)
   11.   └─dplyr (local) handler(cnd)
   12.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 11 | SKIP 0 | PASS 78 ]
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/MSPrep.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSPrep
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘MSPrep’ ...
** this is package ‘MSPrep’ version ‘1.21.1’
** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

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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_msNormalize-45.R
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch.
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  Found 7 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch.
Number of significant surrogate variables is:  4 
Iteration (out of 5 ):1  2  3  4  5  
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 78 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_msNormalize.R:44:1'): (code run outside of `test_that()`) ──────
Error in `summarise(.tbl, !!!funs)`: ℹ In argument: `1x_O1_01 = (function (x, ...) ...`.
Caused by error:
! `1x_O1_01` must be size 1, not 5.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─dplyr::summarise_all(quantNormalizedDF[3:20], quantile, probs = quantiles) at test_msNormalize.R:44:1
  2. │ ├─dplyr::summarise(.tbl, !!!funs)
  3. │ └─dplyr:::summarise.data.frame(.tbl, !!!funs)
  4. │   └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  5. │     └─base::withCallingHandlers(...)
  6. ├─dplyr:::dplyr_internal_error(...)
  7. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
  8. │   └─rlang:::signal_abort(cnd, .file)
  9. │     └─base::signalCondition(cnd)
 10. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 11.   └─dplyr (local) handler(cnd)
 12.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

[ FAIL 1 | WARN 11 | SKIP 0 | PASS 78 ]
Error:
! Test failures.
Execution halted