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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) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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            6.76   0.29   11.28
nmr_pca_outliers_robust                        6.22   0.12   10.64
Peak_detection                                 2.98   0.27   29.67
plsda_auroc_vip_compare                        2.92   0.03   18.77
nmr_meta_add                                   2.25   0.08   11.40
permutation_test_model                         2.23   0.03   15.81
permutation_test_plot                          2.19   0.03   16.38
bp_VIP_analysis                                2.10   0.05   14.00
nmr_interpolate_1D                             1.91   0.14   11.01
nmr_pca_build_model                            1.94   0.11   14.00
validate_nmr_dataset                           1.96   0.06   10.70
nmr_read_samples                               1.81   0.08   10.39
nmr_data_analysis                              1.54   0.05   10.11
AlpsNMR-package                                1.38   0.14    6.66
models_stability_plot_plsda                    1.44   0.05   10.14
plot_plsda_multimodel                          1.42   0.04    9.27
nmr_data_1r_to_SummarizedExperiment            1.36   0.09    6.20
bp_kfold_VIP_analysis                          1.33   0.08    9.67
plot_plsda_samples                             1.31   0.02    8.45
SummarizedExperiment_to_nmr_dataset_peak_table 1.18   0.15    5.83
to_ChemoSpec                                   1.20   0.10    5.85
nmr_dataset_peak_table_to_SummarizedExperiment 1.27   0.02    5.96
nmr_pca_outliers_filter                        1.16   0.06    5.50
tidy.nmr_dataset_1D                            1.08   0.05    5.73
nmr_pca_outliers                               1.09   0.02    5.92
print.nmr_dataset_peak_table                   1.03   0.05    5.42
sub-.nmr_dataset_1D                            1.04   0.03    5.46
filter.nmr_dataset_family                      1.04   0.01    5.67
print.nmr_dataset_1D                           0.97   0.08    5.14
sub-.nmr_dataset_peak_table                    1.02   0.03    5.56
is.nmr_dataset_peak_table                      1.02   0.02    5.58
validate_nmr_dataset_family                    0.98   0.03    5.25
format.nmr_dataset_1D                          0.97   0.03    5.25
new_nmr_dataset_peak_table                     0.97   0.03    5.79
sub-.nmr_dataset                               0.96   0.03    5.47
format.nmr_dataset_peak_table                  0.87   0.11    5.36
nmr_meta_get                                   0.97   0.01    5.45
plot_interactive                               0.94   0.04    5.28
nmr_autophase                                  0.88   0.09    5.44
is.nmr_dataset                                 0.94   0.01    5.43
nmr_meta_get_column                            0.91   0.02    5.22
nmr_meta_export                                0.89   0.03    5.51
nmr_export_data_1r                             0.89   0.02    5.44
format.nmr_dataset                             0.88   0.02    5.17
is.nmr_dataset_1D                              0.87   0.03    5.78
print.nmr_dataset                              0.86   0.03    5.23
load_and_save_functions                        0.87   0.00    5.28
nmr_meta_groups                                0.81   0.03    6.41
* 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' ...
** this is package 'AlpsNMR' version '4.9.0'
** 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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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 
  24.18    1.35   82.10