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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_4.10.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '4.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
  '[magrittr:pipe]{%>%}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

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            6.73   0.27   12.23
nmr_pca_outliers_robust                        6.38   0.29   11.35
plsda_auroc_vip_compare                        3.13   0.09   19.45
Peak_detection                                 3.00   0.17   31.27
nmr_meta_add                                   2.35   0.06   12.26
permutation_test_model                         2.20   0.05   16.33
permutation_test_plot                          2.19   0.06   16.30
bp_VIP_analysis                                2.13   0.01   15.03
nmr_pca_build_model                            1.99   0.14   11.44
nmr_interpolate_1D                             2.01   0.07   12.02
validate_nmr_dataset                           1.98   0.07   11.19
nmr_read_samples                               1.75   0.01   11.11
nmr_data_analysis                              1.54   0.03   10.22
plot_plsda_multimodel                          1.50   0.03   10.00
plot_plsda_samples                             1.47   0.02    9.36
bp_kfold_VIP_analysis                          1.42   0.05   10.44
models_stability_plot_plsda                    1.42   0.02    9.79
AlpsNMR-package                                1.36   0.06    7.73
to_ChemoSpec                                   1.28   0.06    5.88
SummarizedExperiment_to_nmr_dataset_peak_table 1.26   0.06    6.23
nmr_data_1r_to_SummarizedExperiment            1.25   0.03    6.01
nmr_dataset_peak_table_to_SummarizedExperiment 1.19   0.05    6.22
nmr_pca_outliers_filter                        1.14   0.05    5.61
nmr_pca_outliers                               1.08   0.05    6.08
filter.nmr_dataset_family                      1.05   0.06    6.06
validate_nmr_dataset_family                    1.10   0.01    5.80
nmr_export_data_1r                             0.97   0.11    5.72
sub-.nmr_dataset_1D                            1.02   0.06    5.87
new_nmr_dataset_peak_table                     1.00   0.03    5.67
sub-.nmr_dataset_peak_table                    0.98   0.05    5.81
format.nmr_dataset_peak_table                  0.96   0.06    5.69
plot_interactive                               1.01   0.00    5.72
sub-.nmr_dataset                               0.98   0.02    5.84
is.nmr_dataset_peak_table                      0.92   0.06    5.83
nmr_autophase                                  0.92   0.06    5.13
print.nmr_dataset_1D                           0.92   0.05    5.53
tidy.nmr_dataset_1D                            0.94   0.03    5.65
is.nmr_dataset_1D                              0.91   0.05    5.68
format.nmr_dataset_1D                          0.91   0.03    5.64
print.nmr_dataset_peak_table                   0.90   0.04    5.62
nmr_meta_get                                   0.91   0.02    5.75
print.nmr_dataset                              0.93   0.00    5.77
nmr_meta_groups                                0.88   0.03    5.42
nmr_meta_export                                0.87   0.03    6.16
load_and_save_functions                        0.86   0.03    5.61
nmr_meta_get_column                            0.89   0.00    5.96
is.nmr_dataset                                 0.84   0.04    5.55
format.nmr_dataset                             0.81   0.02    5.59
* 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 '4.10.0'
** 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 version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
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 
  23.18    1.35   85.68