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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pmp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pmp_1.23.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/pmp.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pmp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pmp’ version ‘1.23.1’
* 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 ‘pmp’ 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  [1] 73277 - 73277 ==  0.00918
  [2] 75291 - 75291 ==  0.02634
  [3] 77564 - 77564 ==  0.03099
  [4] 82382 - 82382 == -0.08216
  [5] 84708 - 84708 == -0.18951
  [6] 86864 - 86864 == -0.28131
  [7] 88757 - 88758 == -0.31244
  [8] 90292 - 90292 == -0.23486
  [9] 91922 - 91922 ==  0.39742
  ...
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 86 ]
  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/pmp.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pmp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘pmp’ ...
** this is package ‘pmp’ version ‘1.23.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (pmp)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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.

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(pmp)
> 
> test_check("pmp")
Saving _problems/test-glog_transformation-10.R
      NRMSE 
0.004229377 
Saving _problems/test-sbcWrapper-17.R
<simpleError in qcData[id, ]: incorrect number of dimensions>
Saving _problems/test-splineSmoother-11.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 86 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-glog_transformation.R:9:3'): Glog function returns expected output ──
Expected `lambda == as.integer(attributes(out)$processing_history$glog_transformation$lambda_opt)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

── Failure ('test-sbcWrapper.R:17:3'): sbcWrapper returns expected output ──────
Expected `out` to equal `testData$sbcWrapper`.
Differences:
149/172 mismatches (average diff: 0.00334)
[24] 12340 - 12340 == -0.003559
[25] 12430 - 12430 == -0.003102
[26] 12520 - 12520 == -0.002638
[27] 12611 - 12611 == -0.002167
[28] 12702 - 12702 == -0.001689
[29] 12794 - 12794 == -0.001204
[30] 12887 - 12887 == -0.000715
[31] 12981 - 12981 == -0.000235
[32] 13075 - 13075 ==  0.000217
...
── Failure ('test-splineSmoother.R:11:3'): splineSmoother returns expected output ──
Expected `out` to equal `testData$splineSmoother`.
Differences:
16/16 mismatches (average diff: 0.9)
[1] 73277 - 73277 ==  0.00918
[2] 75291 - 75291 ==  0.02634
[3] 77564 - 77564 ==  0.03099
[4] 82382 - 82382 == -0.08216
[5] 84708 - 84708 == -0.18951
[6] 86864 - 86864 == -0.28131
[7] 88757 - 88758 == -0.31244
[8] 90292 - 90292 == -0.23486
[9] 91922 - 91922 ==  0.39742
...

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 86 ]
Error:
! Test failures.
Execution halted