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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSPrep.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSPrep/DESCRIPTION’ ... OK
* this is package ‘MSPrep’ version ‘1.10.0’
* 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 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 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      19.394  0.404  30.645
msImpute    18.801  0.299  29.188
msPrepare   14.855  0.198  23.284
msFilter    14.367  0.179  22.523
msNormalize 13.864  0.200  21.943
msSummarize 13.186  0.170  20.721
* 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:
  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 12 | SKIP 0 | PASS 83 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_sedf_equality.R:294:5'): Check msNormalize(crmn) ─────────────
  all(assay(crmnNormalizedSE) == as.matrix(crmnNormalizedDF[, 3:20])) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 12 | SKIP 0 | PASS 83 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘MSPrep’ ...
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(MSPrep)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> test_check("MSPrep")
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:  5 
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 12 | SKIP 0 | PASS 83 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_sedf_equality.R:294:5'): Check msNormalize(crmn) ─────────────
all(assay(crmnNormalizedSE) == as.matrix(crmnNormalizedDF[, 3:20])) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 12 | SKIP 0 | PASS 83 ]
Error: Test failures
Execution halted