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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AlpsNMR_4.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.1.4’
* 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 ‘AlpsNMR’ 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 ... ERROR
Running examples in ‘AlpsNMR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bp_kfold_VIP_analysis
> ### Title: K-fold bootstrap and permutation over PLS-VIP
> ### Aliases: bp_kfold_VIP_analysis
> 
> ### ** Examples
> 
> # Data analysis for a table of integrated peaks
> set.seed(42)
> ## Generate an artificial nmr_dataset_peak_table:
> ### Generate artificial metadata:
> num_samples <- 64 # use an even number in this example
> num_peaks <- 10
> metadata <- data.frame(
+     NMRExperiment = as.character(1:num_samples),
+     Condition = sample(rep(c("A", "B"), times = num_samples / 2), num_samples)
+ )
> 
> ### The matrix with peaks
> peak_means <- runif(n = num_peaks, min = 300, max = 600)
> peak_sd <- runif(n = num_peaks, min = 30, max = 60)
> peak_matrix <- mapply(function(mu, sd) rnorm(num_samples, mu, sd),
+     mu = peak_means, sd = peak_sd
+ )
> colnames(peak_matrix) <- paste0("Peak", 1:num_peaks)
> rownames(peak_matrix) <- paste0("Sample", 1:num_samples)
> 
> ## Artificial differences depending on the condition:
> peak_matrix[metadata$Condition == "A", "Peak2"] <-
+     peak_matrix[metadata$Condition == "A", "Peak2"] + 70
> 
> peak_matrix[metadata$Condition == "A", "Peak6"] <-
+     peak_matrix[metadata$Condition == "A", "Peak6"] - 60
> 
> ### The nmr_dataset_peak_table
> peak_table <- new_nmr_dataset_peak_table(
+     peak_table = peak_matrix,
+     metadata = list(external = metadata)
+ )
> 
> ## We will use bootstrap and permutation method for VIPs selection
> ## in a a k-fold cross validation
> bp_results <- bp_kfold_VIP_analysis(peak_table, # Data to be analized
+     y_column = "Condition", # Label
+     k = 2,
+     nbootstrap = 5
+ )
Warning in perf.mixo_plsda(model, newdata = x_test) :
  Values in '$choice.ncomp' will reflect component count with the minimum error rate rather than the best based on a one-way t.test
Warning in MCVfold.spls(X, Y, multilevel = multilevel, validation = validation,  :
  At least one class is not represented in one fold, which may unbalance the error rate.
  Consider a number of folds lower than the minimum in table(Y): 8
Warning in MCVfold.spls(X, Y, multilevel = multilevel, validation = validation,  :
  At least one class is not represented in one fold, which may unbalance the error rate.
  Consider a number of folds lower than the minimum in table(Y): 8
Warning in MCVfold.spls(X, Y, multilevel = multilevel, validation = validation,  :
  At least one class is not represented in one fold, which may unbalance the error rate.
  Consider a number of folds lower than the minimum in table(Y): 8
Warning in perf.mixo_plsda(model, newdata = x_test) :
  Values in '$choice.ncomp' will reflect component count with the minimum error rate rather than the best based on a one-way t.test

Warning in perf.mixo_plsda(model, newdata = x_test) :
  Values in '$choice.ncomp' will reflect component count with the minimum error rate rather than the best based on a one-way t.test
Warning in perf.mixo_plsda(model, newdata = x_test) :
  Values in '$choice.ncomp' will reflect component count with the minimum error rate rather than the best based on a one-way t.test

Error: BiocParallel errors
  1 remote errors, element index: 2
  1 unevaluated and other errors
  first remote error:
Error in ncomp_opt[measure, ijk] <- which(t(rowMeans(mat.error.rate[[measure_i]][[ijk]])) == : number of items to replace is not a multiple of replacement length
Execution halted
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-nmr-data-analysis.R:65'): nmr_data_analysis works ──────────────
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(., auc_diff = .data$auc - dplyr::lag(.data$auc, 
      default = 0), auc_diff_above_thres = .data$auc_diff > !!auc_threshold, 
      still_improving = dplyr::cumall(.data$auc_diff_above_thres), 
      good_ncomp = (.data$still_improving == TRUE & dplyr::lead(.data$still_improving, 
          default = FALSE) == FALSE))`: ℹ In argument: `good_ncomp = (...)`.
  ℹ In group 2: `cv_outer_iteration = 1`, `cv_inner_iteration = 2`.
  Caused by error in `vec_c()`:
  ! Can't convert `..2` <logical> to <vctrs_unspecified>.
  
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 90 ]
  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 ...
  ‘Vig01-introduction-to-alpsnmr.Rmd’ using ‘UTF-8’... OK
  ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using ‘UTF-8’... OK
  ‘Vig02-handling-metadata-and-annotations.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL AlpsNMR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘AlpsNMR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (AlpsNMR)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.

> library(testthat)
> library(AlpsNMR)
Loading required package: future

Attaching package: 'AlpsNMR'

The following object is masked from 'package:stats':

    filter

> 
> test_check("AlpsNMR")
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 90 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-nmr-data-analysis.R:65'): nmr_data_analysis works ──────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(., auc_diff = .data$auc - dplyr::lag(.data$auc, 
    default = 0), auc_diff_above_thres = .data$auc_diff > !!auc_threshold, 
    still_improving = dplyr::cumall(.data$auc_diff_above_thres), 
    good_ncomp = (.data$still_improving == TRUE & dplyr::lead(.data$still_improving, 
        default = FALSE) == FALSE))`: ℹ In argument: `good_ncomp = (...)`.
ℹ In group 2: `cv_outer_iteration = 1`, `cv_inner_iteration = 2`.
Caused by error in `vec_c()`:
! Can't convert `..2` <logical> to <vctrs_unspecified>.

[ FAIL 1 | WARN 2 | SKIP 1 | PASS 90 ]
Error: Test failures
Execution halted