Mac ARM64 build report for BioC 3.18 - CHECK results for AlpsNMR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4388
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/AlpsNMR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.4.0’
* 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 for sufficient/correct file permissions ... 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 R 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 ... OK
* 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
Peak_detection                      7.915  2.184   7.488
nmr_pca_outliers_robust             7.633  2.123   8.156
SummarizedExperiment_to_nmr_data_1r 8.323  0.735   8.830
permutation_test_plot               6.115  2.084   2.518
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘AlpsNMR’ ...
** 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)

Tests output


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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)
Loading required package: future

Attaching package: 'AlpsNMR'

The following object is masked from 'package:stats':

    filter

> 
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]
> 
> proc.time()
   user  system elapsed 
 15.750   5.545  17.825

Example timings

name	user	system	elapsed
AlpsNMR-package	2.022	0.386	2.121
HMDB_blood	0.008	0.002	0.010
HMDB_cell	0.003	0.001	0.004
HMDB_urine	0.005	0.002	0.007
Parameters_blood	0.002	0.002	0.003
Parameters_cell	0.002	0.002	0.003
Parameters_urine	0.001	0.001	0.003
Peak_detection	7.915	2.184	7.488
Pipelines	0.002	0.001	0.003
ROI_blood	0.004	0.002	0.006
ROI_cell	0.003	0.002	0.004
ROI_urine	0.003	0.001	0.005
SummarizedExperiment_to_nmr_data_1r	8.323	0.735	8.830
SummarizedExperiment_to_nmr_dataset_peak_table	1.108	0.592	1.439
bp_VIP_analysis	1.486	1.222	1.780
bp_kfold_VIP_analysis	0.773	0.616	0.868
download_MTBLS242	0.000	0.001	0.000
file_lister	0.066	0.021	0.087
files_to_rDolphin	0.000	0.000	0.001
filter.nmr_dataset_family	0.811	0.485	1.029
format.nmr_dataset	0.744	0.568	0.951
format.nmr_dataset_1D	3.082	1.322	2.961
format.nmr_dataset_peak_table	0.833	0.466	1.058
get_integration_with_metadata	0.026	0.003	0.028
hmdb	0.059	0.009	0.069
is.nmr_dataset	0.337	0.244	0.927
is.nmr_dataset_1D	1.187	0.882	1.061
is.nmr_dataset_peak_table	0.841	0.484	1.013
load_and_save_functions	0.701	0.461	0.842
models_stability_plot_bootstrap	0.002	0.002	0.004
models_stability_plot_plsda	0.375	0.355	0.493
new_nmr_dataset	0.002	0.001	0.003
new_nmr_dataset_1D	0.001	0.001	0.002
new_nmr_dataset_peak_table	0.841	0.508	1.047
nmr_baseline_estimation	0.169	0.040	0.212
nmr_baseline_removal	0.006	0.001	0.007
nmr_baseline_threshold	0.001	0.000	0.002
nmr_baseline_threshold_plot	0.361	0.039	0.400
nmr_batman	0.004	0.001	0.005
nmr_batman_options	0.000	0.000	0.001
nmr_build_peak_table	0.047	0.004	0.052
nmr_data	0.054	0.006	0.060
nmr_data_1r_to_SummarizedExperiment	1.038	0.436	1.225
nmr_data_analysis	0.338	0.288	0.459
nmr_dataset	0.000	0.001	0.001
nmr_dataset_1D	0.001	0.001	0.002
nmr_dataset_peak_table_to_SummarizedExperiment	1.047	0.672	1.324
nmr_exclude_region	0.007	0.001	0.009
nmr_export_data_1r	0.744	0.484	0.953
nmr_get_peak_distances	0.009	0.002	0.010
nmr_identify_regions_blood	0.014	0.006	0.020
nmr_identify_regions_cell	0.010	0.002	0.012
nmr_identify_regions_urine	0.014	0.003	0.018
nmr_integrate_regions	0.012	0.002	0.014
nmr_interpolate_1D	1.618	1.043	2.012
nmr_meta_add	1.793	1.274	2.387
nmr_meta_export	0.716	0.618	0.951
nmr_meta_get	0.686	0.590	0.970
nmr_meta_get_column	0.722	0.655	1.035
nmr_meta_groups	0.755	0.678	1.042
nmr_normalize	0.294	0.122	0.429
nmr_pca_build_model	1.750	1.403	2.621
nmr_pca_outliers	0.790	0.634	1.232
nmr_pca_outliers_filter	0.962	0.726	1.388
nmr_pca_outliers_plot	0.001	0.001	0.000
nmr_pca_outliers_robust	7.633	2.123	8.156
nmr_pca_plots	0.454	0.011	0.473
nmr_peak_clustering	0.071	0.001	0.074
nmr_ppm_resolution	0.010	0.002	0.012
nmr_read_bruker_fid	0	0	0
nmr_read_samples	1.373	0.912	1.727
nmr_zip_bruker_samples	0.339	0.039	0.388
peaklist_accept_peaks	0.004	0.001	0.005
permutation_test_model	0.378	0.366	2.446
permutation_test_plot	6.115	2.084	2.518
plot.nmr_dataset_1D	0.002	0.002	0.004
plot_bootstrap_multimodel	0.002	0.002	0.005
plot_interactive	0.808	0.555	1.058
plot_plsda_multimodel	0.228	0.311	0.372
plot_plsda_samples	0.130	0.179	0.300
plot_vip_scores	0.002	0.002	0.004
plot_webgl	0.002	0.002	0.003
plsda_auroc_vip_compare	0.544	0.479	1.019
plsda_auroc_vip_method	0.001	0.000	0.001
ppm_resolution	0.004	0.002	0.005
print.nmr_dataset	0.745	0.687	0.963
print.nmr_dataset_1D	0.916	0.802	1.426
print.nmr_dataset_peak_table	0.902	0.773	1.279
random_subsampling	0.001	0.004	0.006
save_files_to_rDolphin	0	0	0
save_profiling_output	0.000	0.001	0.000
sub-.nmr_dataset	0.746	0.684	1.037
sub-.nmr_dataset_1D	0.852	0.839	1.246
sub-.nmr_dataset_peak_table	0.933	0.857	1.308
tidy.nmr_dataset_1D	0.945	0.829	1.323
to_ChemoSpec	0.919	0.781	1.338
validate_nmr_dataset	1.514	1.420	2.211
validate_nmr_dataset_family	0.859	0.756	1.261
validate_nmr_dataset_peak_table	0.001	0.001	0.002
zzz	0.000	0.001	2.151

CHECK results for AlpsNMR on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings