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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            7.00   0.35   12.14
nmr_pca_outliers_robust                        5.93   0.37   11.25
plsda_auroc_vip_compare                        3.32   0.10   20.41
Peak_detection                                 3.00   0.25   31.67
nmr_meta_add                                   2.43   0.03   11.86
permutation_test_model                         2.25   0.01   16.82
bp_VIP_analysis                                2.23   0.00   22.75
permutation_test_plot                          2.20   0.03   16.74
nmr_pca_build_model                            2.09   0.11   12.63
nmr_interpolate_1D                             2.04   0.11   11.41
validate_nmr_dataset                           1.97   0.08   11.73
nmr_read_samples                               1.83   0.02   10.87
nmr_data_analysis                              1.63   0.05   10.43
bp_kfold_VIP_analysis                          1.56   0.07   10.32
plot_plsda_multimodel                          1.58   0.03   10.07
SummarizedExperiment_to_nmr_dataset_peak_table 1.46   0.12    6.19
plot_plsda_samples                             1.56   0.01    9.86
models_stability_plot_plsda                    1.50   0.06   10.39
nmr_dataset_peak_table_to_SummarizedExperiment 1.44   0.04    6.10
nmr_data_1r_to_SummarizedExperiment            1.43   0.03    6.09
AlpsNMR-package                                1.19   0.19    5.98
to_ChemoSpec                                   1.28   0.09    6.52
nmr_pca_outliers_filter                        1.23   0.08    5.99
nmr_pca_outliers                               1.17   0.06    6.09
tidy.nmr_dataset_1D                            1.09   0.09    6.00
sub-.nmr_dataset_peak_table                    1.11   0.06    6.05
print.nmr_dataset_peak_table                   1.08   0.05    5.71
sub-.nmr_dataset_1D                            1.05   0.07    5.59
filter.nmr_dataset_family                      1.00   0.11    6.11
format.nmr_dataset_peak_table                  1.04   0.07    6.00
validate_nmr_dataset_family                    1.03   0.06    5.69
nmr_autophase                                  1.04   0.04    6.79
print.nmr_dataset_1D                           1.08   0.00    5.85
new_nmr_dataset_peak_table                     1.00   0.05    5.71
plot_interactive                               0.92   0.10    6.08
is.nmr_dataset_peak_table                      0.95   0.06    5.30
is.nmr_dataset_1D                              0.97   0.03    5.84
nmr_export_data_1r                             0.98   0.02    5.72
is.nmr_dataset                                 0.92   0.05    5.83
load_and_save_functions                        0.92   0.05    5.94
nmr_meta_groups                                0.94   0.03    5.82
format.nmr_dataset_1D                          0.89   0.07    5.64
print.nmr_dataset                              0.92   0.03    5.53
nmr_meta_export                                0.91   0.02    5.57
nmr_meta_get_column                            0.92   0.01    5.69
sub-.nmr_dataset                               0.90   0.03    5.55
nmr_meta_get                                   0.89   0.03    5.60
format.nmr_dataset                             0.83   0.06    5.49
* 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 
  25.12    1.60   88.04