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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AlpsNMR_3.6.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.6.1'
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                user system elapsed
nmr_pca_plots                                  26.93   3.15   33.77
permutation_test_plot                          16.79   0.23  126.15
permutation_test_model                         16.42   0.22  125.02
nmr_pca_outliers_robust                         4.90   0.14    8.85
SummarizedExperiment_to_nmr_data_1r             4.61   0.24    8.67
Peak_detection                                  3.47   0.53   39.55
AlpsNMR-package                                 3.78   0.20    7.68
plsda_auroc_vip_compare                         3.16   0.06   17.44
bp_VIP_analysis                                 3.00   0.11   12.18
nmr_meta_add                                    2.26   0.05    9.37
nmr_pca_build_model                             2.24   0.03    9.73
validate_nmr_dataset                            1.95   0.03    9.78
nmr_read_samples                                1.72   0.07    9.51
nmr_interpolate_1D                              1.64   0.01    8.80
nmr_baseline_removal                            1.45   0.16    5.83
nmr_dataset_peak_table_to_SummarizedExperiment  1.47   0.06    5.40
models_stability_plot_plsda                     1.50   0.02   10.67
plot_plsda_multimodel                           1.48   0.02   11.23
plot_plsda_samples                              1.44   0.00    8.64
SummarizedExperiment_to_nmr_dataset_peak_table  1.31   0.03    5.61
nmr_data_analysis                               1.30   0.03   11.48
to_ChemoSpec                                    1.24   0.03    5.22
nmr_pca_outliers_filter                         1.15   0.03    5.13
new_nmr_dataset_peak_table                      1.02   0.04    5.55
print.nmr_dataset_peak_table                    0.96   0.07    5.22
sub-.nmr_dataset_1D                             1.02   0.01    5.10
nmr_pca_outliers                                0.92   0.05    5.36
sub-.nmr_dataset                                0.91   0.05    5.05
is.nmr_dataset_1D                               0.91   0.00    5.03
bp_kfold_VIP_analysis                           0.61   0.02   17.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: OK

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
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* installing to library 'F:/biocbuild/bbs-3.15-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 version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 87 ]

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

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
  12.84    0.84   69.54