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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 4.5.1 (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 '4.10.0'
* 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            6.97   0.31   12.44
nmr_pca_outliers_robust                        6.30   0.11   11.28
Peak_detection                                 3.19   0.25   33.52
plsda_auroc_vip_compare                        3.29   0.07   19.64
permutation_test_plot                          2.42   0.03   17.45
nmr_meta_add                                   2.20   0.16   11.82
permutation_test_model                         2.27   0.05   16.95
bp_VIP_analysis                                2.19   0.10   15.83
nmr_pca_build_model                            2.18   0.09   12.00
validate_nmr_dataset                           2.08   0.07   11.61
nmr_interpolate_1D                             1.90   0.13   11.81
nmr_read_samples                               1.91   0.06   10.84
plot_plsda_multimodel                          1.66   0.07   10.22
models_stability_plot_plsda                    1.60   0.03   10.47
nmr_data_analysis                              1.51   0.06   10.43
plot_plsda_samples                             1.52   0.03   10.16
bp_kfold_VIP_analysis                          1.47   0.03   10.42
AlpsNMR-package                                1.36   0.05    6.60
nmr_data_1r_to_SummarizedExperiment            1.33   0.08    6.10
SummarizedExperiment_to_nmr_dataset_peak_table 1.30   0.06    5.90
to_ChemoSpec                                   1.31   0.05    7.12
nmr_dataset_peak_table_to_SummarizedExperiment 1.27   0.08    5.94
print.nmr_dataset_peak_table                   1.14   0.06    6.19
nmr_pca_outliers_filter                        1.08   0.09    5.97
nmr_pca_outliers                               1.06   0.10    5.75
nmr_export_data_1r                             1.08   0.03    6.04
sub-.nmr_dataset_peak_table                    1.05   0.06    5.86
validate_nmr_dataset_family                    1.06   0.05    5.78
plot_interactive                               1.09   0.01    6.86
tidy.nmr_dataset_1D                            1.04   0.05    5.86
filter.nmr_dataset_family                      1.05   0.03    5.86
print.nmr_dataset_1D                           0.97   0.08    5.80
sub-.nmr_dataset                               1.01   0.03    6.03
is.nmr_dataset_peak_table                      1.00   0.03    5.87
format.nmr_dataset_peak_table                  0.94   0.08    5.58
nmr_meta_get_column                            1.00   0.02    5.93
is.nmr_dataset_1D                              0.94   0.07    5.51
sub-.nmr_dataset_1D                            0.94   0.07    5.72
nmr_meta_get                                   0.99   0.01    6.21
nmr_meta_groups                                0.98   0.01    6.84
is.nmr_dataset                                 0.94   0.04    5.53
nmr_meta_export                                0.98   0.00    6.15
print.nmr_dataset                              0.91   0.05    5.40
load_and_save_functions                        0.94   0.02    5.74
new_nmr_dataset_peak_table                     0.96   0.00    5.65
format.nmr_dataset_1D                          0.89   0.06    5.59
format.nmr_dataset                             0.90   0.02    5.46
nmr_autophase                                  0.79   0.05    5.32
* 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 4.5.1 (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 
  24.78    1.46   86.92