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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AlpsNMR_3.0.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘3.0.6’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* 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 ... WARNING
Undocumented arguments in documentation object 'MUVR_model_plot'
  ‘MVObj’ ‘model’ ‘factCols’ ‘sampLabels’ ‘ylim’

Undocumented arguments in documentation object 'confusion_matrix'
  ‘MVObj’ ‘model’

Undocumented arguments in documentation object 'model_VIP'
  ‘model’

Undocumented arguments in documentation object 'rdCV_PLS_RF'
  ‘X’ ‘Y’ ‘ID’ ‘scale’ ‘nRep’ ‘nOuter’ ‘nInner’ ‘varRatio’ ‘DA’
  ‘fitness’ ‘method’ ‘nCompMax’ ‘methParam’ ‘ML’ ‘modReturn’ ‘logg’
  ‘parallel’

Undocumented arguments in documentation object 'rdCV_PLS_RF_ML'
  ‘scale’ ‘nRep’ ‘nOuter’ ‘nInner’ ‘varRatio’ ‘DA’ ‘fitness’ ‘method’
  ‘ML’ ‘modReturn’ ‘logg’ ‘parallel’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: nmr_pca_plots
> ### Title: Plotting functions for PCA
> ### Aliases: nmr_pca_plots nmr_pca_plot_variance nmr_pca_scoreplot
> ###   nmr_pca_loadingplot
> 
> ### ** Examples
> 
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)

Attaching package: ‘purrr’

The following object is masked from ‘package:magrittr’:

    set_names

> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_plot_variance(model)
> 
> dir_to_demo_dataset <- system.file("dataset-demo", package = "AlpsNMR")
> dataset <- nmr_read_samples_dir(dir_to_demo_dataset)
> dataset_1D <- nmr_interpolate_1D(dataset, axis = c(min = -0.5, max = 10, by = 2.3E-4))
> model <- nmr_pca_build_model(dataset_1D)
> nmr_pca_scoreplot(dataset_1D, model)
Error: Join columns must be present in data.
✖ Problem with `NMRExperiment`.
Backtrace:
    █
 1. ├─AlpsNMR::nmr_pca_scoreplot(dataset_1D, model)
 2. │ └─`%>%`(...)
 3. ├─dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
 4. └─dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
 5.   └─dplyr:::join_mutate(...)
 6.     └─dplyr:::join_cols(...)
 7.       └─dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
 8.         └─dplyr:::check_join_vars(by$x, x_names)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ✖ Problem with `NMRExperiment`.
  Backtrace:
      █
   1. ├─AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
   2. │ └─`%>%`(...)
   3. ├─dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
   4. └─dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
   5.   └─dplyr:::join_mutate(...)
   6.     └─dplyr:::join_cols(...)
   7.       └─dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
   8.         └─dplyr:::check_join_vars(by$x, x_names)
  
  [ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
  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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL AlpsNMR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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
** 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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: future
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("AlpsNMR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-outliers.R:12:3): nmr_pca_outliers_robust works ─────────────────
Error: Join columns must be present in data.
✖ Problem with `NMRExperiment`.
Backtrace:
    █
 1. ├─AlpsNMR::nmr_pca_scoreplot(dataset, pca_built) test-outliers.R:12:2
 2. │ └─`%>%`(...)
 3. ├─dplyr::left_join(., nmr_metadata, by = "NMRExperiment")
 4. └─dplyr:::left_join.data.frame(., nmr_metadata, by = "NMRExperiment")
 5.   └─dplyr:::join_mutate(...)
 6.     └─dplyr:::join_cols(...)
 7.       └─dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
 8.         └─dplyr:::check_join_vars(by$x, x_names)

[ FAIL 1 | WARN 2 | SKIP 1 | PASS 73 ]
Error: Test failures
Execution halted