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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSPrep_1.21.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSPrep.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-12 05:35:45 UTC
* 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 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      18.707  0.397  19.105
msImpute    18.143  0.348  18.497
msPrepare   13.374  0.159  13.535
msNormalize 13.248  0.029  13.279
msSummarize 12.644  0.092  12.738
msFilter    12.490  0.132  12.624
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/MSPrep.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSPrep
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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_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