| Back to Multiple platform build/check report for BioC 3.21: simplified long | 
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This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 | 
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 | 
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 | 
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 | 
| 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 | ||||
| Package 59/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.10.1  (landing page) Sergio Oller Moreno 
 | nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| To the developers/maintainers of the AlpsNMR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlpsNMR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. | 
| Package: AlpsNMR | 
| Version: 4.10.1 | 
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings AlpsNMR_4.10.1.tar.gz | 
| StartedAt: 2025-10-15 20:44:28 -0400 (Wed, 15 Oct 2025) | 
| EndedAt: 2025-10-15 20:49:15 -0400 (Wed, 15 Oct 2025) | 
| EllapsedTime: 287.4 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: AlpsNMR.Rcheck | 
| Warnings: 0 | 
##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings AlpsNMR_4.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.10.1’
* 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 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 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
Peak_detection                      8.075  1.851   7.135
SummarizedExperiment_to_nmr_data_1r 6.566  0.860   6.803
permutation_test_plot               4.091  2.008   1.557
nmr_pca_outliers_robust             4.983  1.037   5.234
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘AlpsNMR’ ... ** this is package ‘AlpsNMR’ version ‘4.10.1’ ** 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)
AlpsNMR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 
 20.987   6.680  20.424 
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 1.801 | 0.319 | 1.611 | |
| HMDB_blood | 0.004 | 0.002 | 0.007 | |
| HMDB_cell | 0.000 | 0.002 | 0.003 | |
| HMDB_urine | 0.004 | 0.001 | 0.005 | |
| Parameters_blood | 0.001 | 0.001 | 0.002 | |
| Parameters_cell | 0.002 | 0.000 | 0.002 | |
| Parameters_urine | 0.000 | 0.002 | 0.002 | |
| Peak_detection | 8.075 | 1.851 | 7.135 | |
| Pipelines | 0.000 | 0.002 | 0.002 | |
| ROI_blood | 0.002 | 0.001 | 0.003 | |
| ROI_cell | 0.003 | 0.000 | 0.003 | |
| ROI_urine | 0.002 | 0.001 | 0.003 | |
| SummarizedExperiment_to_nmr_data_1r | 6.566 | 0.860 | 6.803 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.036 | 0.526 | 0.897 | |
| bp_VIP_analysis | 2.618 | 1.578 | 2.628 | |
| bp_kfold_VIP_analysis | 0.861 | 0.644 | 0.642 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.059 | 0.012 | 0.070 | |
| files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
| filter.nmr_dataset_family | 0.688 | 0.376 | 0.539 | |
| format.nmr_dataset | 0.709 | 0.522 | 0.537 | |
| format.nmr_dataset_1D | 0.752 | 0.522 | 0.590 | |
| format.nmr_dataset_peak_table | 0.858 | 0.678 | 0.779 | |
| get_integration_with_metadata | 0.029 | 0.009 | 0.038 | |
| hmdb | 0.044 | 0.012 | 0.056 | |
| is.nmr_dataset | 0.731 | 0.583 | 0.580 | |
| is.nmr_dataset_1D | 0.775 | 0.642 | 0.661 | |
| is.nmr_dataset_peak_table | 0.932 | 0.687 | 0.757 | |
| load_and_save_functions | 0.647 | 0.577 | 0.521 | |
| models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
| models_stability_plot_plsda | 0.339 | 0.412 | 0.381 | |
| new_nmr_dataset | 0.001 | 0.001 | 0.002 | |
| new_nmr_dataset_1D | 0.024 | 0.038 | 0.002 | |
| new_nmr_dataset_peak_table | 0.841 | 0.608 | 0.709 | |
| nmr_autophase | 0.235 | 0.112 | 0.320 | |
| nmr_baseline_estimation | 0.010 | 0.001 | 0.011 | |
| nmr_baseline_removal | 0.004 | 0.001 | 0.005 | |
| nmr_baseline_threshold | 0.000 | 0.001 | 0.001 | |
| nmr_baseline_threshold_plot | 0.310 | 0.057 | 0.367 | |
| nmr_batman | 0.004 | 0.002 | 0.005 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.037 | 0.017 | 0.054 | |
| nmr_data | 0.051 | 0.004 | 0.054 | |
| nmr_data_1r_to_SummarizedExperiment | 1.004 | 0.639 | 0.930 | |
| nmr_data_analysis | 0.434 | 0.588 | 0.485 | |
| nmr_dataset | 0.000 | 0.001 | 0.002 | |
| nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.021 | 0.674 | 0.942 | |
| nmr_exclude_region | 0.006 | 0.001 | 0.007 | |
| nmr_export_data_1r | 0.768 | 0.624 | 0.641 | |
| nmr_get_peak_distances | 0.010 | 0.000 | 0.011 | |
| nmr_identify_regions_blood | 0.010 | 0.004 | 0.015 | |
| nmr_identify_regions_cell | 0.009 | 0.000 | 0.009 | |
| nmr_identify_regions_urine | 0.011 | 0.003 | 0.014 | |
| nmr_integrate_regions | 0.006 | 0.002 | 0.008 | |
| nmr_interpolate_1D | 1.566 | 1.415 | 1.446 | |
| nmr_meta_add | 1.869 | 1.411 | 1.692 | |
| nmr_meta_export | 0.775 | 0.671 | 0.615 | |
| nmr_meta_get | 0.736 | 0.625 | 0.598 | |
| nmr_meta_get_column | 0.699 | 0.505 | 0.550 | |
| nmr_meta_groups | 0.777 | 0.621 | 0.622 | |
| nmr_normalize | 0.315 | 0.041 | 0.356 | |
| nmr_pca_build_model | 2.583 | 1.685 | 2.676 | |
| nmr_pca_outliers | 0.800 | 0.488 | 0.652 | |
| nmr_pca_outliers_filter | 0.902 | 0.462 | 0.719 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 4.983 | 1.037 | 5.234 | |
| nmr_pca_plots | 0.500 | 0.059 | 0.559 | |
| nmr_peak_clustering | 0.071 | 0.001 | 0.072 | |
| nmr_ppm_resolution | 0.008 | 0.001 | 0.008 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 1.329 | 1.109 | 1.057 | |
| nmr_zip_bruker_samples | 0.251 | 0.013 | 0.265 | |
| peaklist_accept_peaks | 0.003 | 0.000 | 0.003 | |
| permutation_test_model | 0.715 | 0.716 | 1.572 | |
| permutation_test_plot | 4.091 | 2.008 | 1.557 | |
| plot.nmr_dataset_1D | 0.003 | 0.001 | 0.003 | |
| plot_bootstrap_multimodel | 0.005 | 0.000 | 0.004 | |
| plot_interactive | 1.661 | 0.930 | 0.720 | |
| plot_plsda_multimodel | 0.201 | 0.425 | 0.329 | |
| plot_plsda_samples | 0.118 | 0.157 | 0.206 | |
| plot_vip_scores | 0.001 | 0.001 | 0.003 | |
| plot_webgl | 0.002 | 0.000 | 0.002 | |
| plsda_auroc_vip_compare | 0.537 | 0.431 | 0.782 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0.003 | 0.000 | 0.003 | |
| print.nmr_dataset | 0.676 | 0.552 | 0.529 | |
| print.nmr_dataset_1D | 0.838 | 0.657 | 0.689 | |
| print.nmr_dataset_peak_table | 0.872 | 0.592 | 0.707 | |
| random_subsampling | 0.002 | 0.002 | 0.004 | |
| save_files_to_rDolphin | 0.000 | 0.001 | 0.000 | |
| save_profiling_output | 0.000 | 0.000 | 0.001 | |
| sub-.nmr_dataset | 0.792 | 0.540 | 0.567 | |
| sub-.nmr_dataset_1D | 0.717 | 0.538 | 0.604 | |
| sub-.nmr_dataset_peak_table | 0.899 | 0.652 | 0.849 | |
| tidy.nmr_dataset_1D | 0.869 | 0.743 | 0.793 | |
| to_ASICS | 0.871 | 0.132 | 1.003 | |
| to_ChemoSpec | 0.865 | 0.582 | 0.808 | |
| validate_nmr_dataset | 1.555 | 1.282 | 1.248 | |
| validate_nmr_dataset_family | 0.872 | 0.717 | 0.736 | |
| validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.001 | |
| zzz | 0.000 | 0.000 | 2.002 | |