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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings AlpsNMR_4.9.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AlpsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlpsNMR' version '4.9.0'
* 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 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter.nmr_dataset_family.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                               user system elapsed
SummarizedExperiment_to_nmr_data_1r            7.03   0.17   11.76
nmr_pca_outliers_robust                        5.47   0.19    9.70
Peak_detection                                 2.81   0.39   29.25
plsda_auroc_vip_compare                        2.97   0.05   17.50
bp_VIP_analysis                                2.19   0.03   14.17
permutation_test_model                         2.11   0.06   14.89
nmr_pca_build_model                            2.00   0.14   10.86
validate_nmr_dataset                           2.06   0.05   10.96
permutation_test_plot                          2.01   0.08   15.39
nmr_meta_add                                   2.03   0.05   10.14
nmr_interpolate_1D                             1.71   0.08    9.75
nmr_read_samples                               1.68   0.07    9.89
bp_kfold_VIP_analysis                          1.44   0.07    9.15
plot_plsda_samples                             1.44   0.01    9.20
nmr_data_analysis                              1.36   0.05   10.17
AlpsNMR-package                                1.35   0.03    5.71
models_stability_plot_plsda                    1.38   0.00    9.45
SummarizedExperiment_to_nmr_dataset_peak_table 1.31   0.01    5.88
nmr_dataset_peak_table_to_SummarizedExperiment 1.23   0.08    6.08
plot_plsda_multimodel                          1.28   0.02    9.01
to_ChemoSpec                                   1.22   0.05    5.76
validate_nmr_dataset_family                    1.12   0.06    5.70
nmr_pca_outliers_filter                        1.08   0.08    5.41
nmr_data_1r_to_SummarizedExperiment            1.12   0.03    5.72
tidy.nmr_dataset_1D                            1.09   0.05    5.35
nmr_autophase                                  1.05   0.05    5.13
nmr_pca_outliers                               1.02   0.06    5.54
sub-.nmr_dataset_peak_table                    1.02   0.06    5.23
format.nmr_dataset_peak_table                  0.97   0.05    5.26
is.nmr_dataset_peak_table                      0.97   0.05    5.25
new_nmr_dataset_peak_table                     0.92   0.09    5.34
print.nmr_dataset_peak_table                   0.95   0.05    5.17
is.nmr_dataset_1D                              0.94   0.05    5.28
nmr_export_data_1r                             0.95   0.04    5.13
plot_interactive                               0.92   0.03    6.96
filter.nmr_dataset_family                      0.94   0.00    5.20
sub-.nmr_dataset_1D                            0.90   0.03    5.13
print.nmr_dataset                              0.89   0.03   10.59
nmr_meta_get_column                            0.89   0.02    5.35
nmr_meta_get                                   0.84   0.04    5.13
nmr_meta_groups                                0.83   0.00    5.05
format.nmr_dataset                             0.81   0.01    5.25
is.nmr_dataset                                 0.81   0.01    5.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
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* installing to library 'E:/biocbuild/bbs-3.21-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) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)

Attaching package: 'AlpsNMR'

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

    filter

> 
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
  21.29    1.25   79.68