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### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings AlpsNMR_4.11.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.5.1 (2025-06-13 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 '4.11.0'
* 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            7.56   0.36   12.55
nmr_pca_outliers_robust                        6.23   0.20   11.02
Peak_detection                                 3.25   0.36   31.08
plsda_auroc_vip_compare                        3.24   0.01   19.60
nmr_meta_add                                   2.47   0.10   11.72
permutation_test_plot                          2.17   0.09   16.80
permutation_test_model                         2.18   0.05   16.84
bp_VIP_analysis                                2.17   0.03   15.58
validate_nmr_dataset                           2.10   0.06   11.97
nmr_pca_build_model                            2.00   0.09   11.25
nmr_interpolate_1D                             1.94   0.11   11.33
nmr_read_samples                               1.80   0.06   10.95
nmr_data_analysis                              1.65   0.01   11.04
plot_plsda_multimodel                          1.58   0.02    9.63
models_stability_plot_plsda                    1.53   0.05   10.32
bp_kfold_VIP_analysis                          1.52   0.02   10.58
plot_plsda_samples                             1.50   0.02    9.53
nmr_data_1r_to_SummarizedExperiment            1.43   0.00    6.27
SummarizedExperiment_to_nmr_dataset_peak_table 1.27   0.12    5.92
nmr_dataset_peak_table_to_SummarizedExperiment 1.32   0.03    6.00
to_ChemoSpec                                   1.23   0.09    5.89
AlpsNMR-package                                1.19   0.13    5.81
nmr_pca_outliers_filter                        1.16   0.10    5.82
validate_nmr_dataset_family                    1.12   0.05    6.19
format.nmr_dataset_peak_table                  1.07   0.06    5.64
print.nmr_dataset_peak_table                   1.08   0.04    5.81
nmr_pca_outliers                               1.06   0.05    5.81
filter.nmr_dataset_family                      1.03   0.06    5.88
is.nmr_dataset_peak_table                      1.01   0.07    5.63
tidy.nmr_dataset_1D                            1.01   0.05    5.71
print.nmr_dataset_1D                           0.95   0.10    5.44
new_nmr_dataset_peak_table                     0.95   0.08    5.67
plot_interactive                               1.00   0.03    5.90
sub-.nmr_dataset_1D                            0.99   0.03    5.58
is.nmr_dataset_1D                              0.97   0.03    5.68
nmr_export_data_1r                             0.98   0.02    5.89
nmr_meta_groups                                0.93   0.05    5.55
sub-.nmr_dataset                               0.92   0.05    5.29
format.nmr_dataset_1D                          0.97   0.00    5.72
nmr_autophase                                  0.91   0.06    5.22
nmr_meta_get                                   0.96   0.01    5.81
sub-.nmr_dataset_peak_table                    0.97   0.00    5.70
nmr_meta_export                                0.90   0.04    5.69
is.nmr_dataset                                 0.89   0.03    5.75
load_and_save_functions                        0.88   0.04    5.59
nmr_meta_get_column                            0.86   0.06    5.45
format.nmr_dataset                             0.86   0.05    5.43
print.nmr_dataset                              0.86   0.03    5.42
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL AlpsNMR
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'AlpsNMR' ...
** this is package 'AlpsNMR' version '4.11.0'
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
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 
  25.59    1.32   89.85