##############################################################################
##############################################################################
###
### 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/pmp.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pmp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pmp’ version ‘1.17.0’
* 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 ‘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:
  16/16 mismatches (average diff: 0.894)
  [1] 73277 - 73277 ==  0.00918
  [2] 75291 - 75291 ==  0.02623
  [3] 77564 - 77564 ==  0.03082
  [4] 82382 - 82382 == -0.08162
  [5] 84708 - 84708 == -0.18823
  [6] 86864 - 86864 == -0.27938
  [7] 88757 - 88758 == -0.31029
  [8] 90292 - 90292 == -0.23323
  [9] 91922 - 91922 ==  0.39465
  ...
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ]
  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-3.20-bioc-mac-arm64/meat/pmp.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pmp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘pmp’ ...
** 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 version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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")
      NRMSE 
0.003724107 
<simpleError in qcData[id, ]: incorrect number of dimensions>
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-glog_transformation.R:9:3'): Glog function returns expected output ──
lambda == as.integer(attributes(out)$processing_history$glog_transformation$lambda_opt) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-sbcWrapper.R:17:3'): sbcWrapper returns expected output ──────
`out` not equal to testData$sbcWrapper.
149/172 mismatches (average diff: 0.00325)
[24] 12340 - 12340 == -0.004236
[25] 12430 - 12430 == -0.003694
[26] 12520 - 12520 == -0.003143
[27] 12611 - 12611 == -0.002584
[28] 12702 - 12702 == -0.002017
[29] 12794 - 12794 == -0.001441
[30] 12887 - 12887 == -0.000860
[31] 12981 - 12981 == -0.000291
[32] 13075 - 13075 ==  0.000245
...
── Failure ('test-splineSmoother.R:11:3'): splineSmoother returns expected output ──
`out` not equal to testData$splineSmoother.
16/16 mismatches (average diff: 0.894)
[1] 73277 - 73277 ==  0.00918
[2] 75291 - 75291 ==  0.02623
[3] 77564 - 77564 ==  0.03082
[4] 82382 - 82382 == -0.08162
[5] 84708 - 84708 == -0.18823
[6] 86864 - 86864 == -0.27938
[7] 88757 - 88758 == -0.31029
[8] 90292 - 90292 == -0.23323
[9] 91922 - 91922 ==  0.39465
...

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 87 ]
Error: Test failures
Execution halted