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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            7.17   0.37   13.03
nmr_pca_outliers_robust                        6.86   0.21   11.67
Peak_detection                                 3.02   0.18   29.56
plsda_auroc_vip_compare                        3.14   0.06   18.37
nmr_meta_add                                   2.25   0.06   11.36
bp_VIP_analysis                                2.06   0.08   14.61
permutation_test_model                         2.11   0.03   15.98
validate_nmr_dataset                           2.04   0.08   11.08
permutation_test_plot                          2.06   0.04   16.04
nmr_pca_build_model                            1.93   0.06   10.22
nmr_interpolate_1D                             1.86   0.06   10.45
nmr_read_samples                               1.78   0.03   11.26
plot_plsda_multimodel                          1.53   0.03    9.92
nmr_data_analysis                              1.45   0.03    9.50
bp_kfold_VIP_analysis                          1.36   0.05    9.75
plot_plsda_samples                             1.36   0.04    9.68
SummarizedExperiment_to_nmr_dataset_peak_table 1.35   0.03    5.98
AlpsNMR-package                                1.25   0.13    5.58
nmr_dataset_peak_table_to_SummarizedExperiment 1.28   0.08    5.92
to_ChemoSpec                                   1.25   0.10    6.17
nmr_data_1r_to_SummarizedExperiment            1.27   0.05    5.70
models_stability_plot_plsda                    1.25   0.01   10.82
nmr_pca_outliers_filter                        1.13   0.04    5.31
tidy.nmr_dataset_1D                            1.04   0.08    6.35
nmr_pca_outliers                               1.07   0.02    5.13
print.nmr_dataset_peak_table                   1.05   0.01    5.50
sub-.nmr_dataset_peak_table                    1.00   0.03    5.32
validate_nmr_dataset_family                    1.00   0.02    5.39
nmr_export_data_1r                             0.97   0.03    5.45
sub-.nmr_dataset_1D                            0.95   0.05    5.52
filter.nmr_dataset_family                      0.97   0.02    5.25
plot_interactive                               0.94   0.04    5.51
format.nmr_dataset_1D                          0.91   0.03    5.31
is.nmr_dataset_peak_table                      0.90   0.03    5.22
format.nmr_dataset_peak_table                  0.87   0.05    5.16
nmr_autophase                                  0.86   0.05    6.71
load_and_save_functions                        0.86   0.04    7.00
print.nmr_dataset_1D                           0.90   0.00    5.25
is.nmr_dataset                                 0.86   0.03    5.14
is.nmr_dataset_1D                              0.86   0.03    5.34
nmr_meta_export                                0.86   0.03    5.25
sub-.nmr_dataset                               0.86   0.03    5.44
new_nmr_dataset_peak_table                     0.84   0.03    6.03
format.nmr_dataset                             0.77   0.04    5.33
* 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 
  23.28    1.42   83.54