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This page was generated on 2025-11-03 12:02 -0500 (Mon, 03 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4902
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4692
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4638
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 59/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.12.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-11-02 13:45 -0500 (Sun, 02 Nov 2025)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_22
git_last_commit: a1d41e5
git_last_commit_date: 2025-10-29 11:04:39 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for AlpsNMR on nebbiolo2

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.

raw results


Summary

Package: AlpsNMR
Version: 4.12.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AlpsNMR_4.12.0.tar.gz
StartedAt: 2025-11-02 21:15:23 -0500 (Sun, 02 Nov 2025)
EndedAt: 2025-11-02 21:20:09 -0500 (Sun, 02 Nov 2025)
EllapsedTime: 286.2 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AlpsNMR_4.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘4.12.0’
* 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 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                      7.882  1.619   6.966
SummarizedExperiment_to_nmr_data_1r 6.794  0.859   6.967
permutation_test_plot               3.983  2.310   1.807
nmr_pca_outliers_robust             4.791  1.124   5.019
* 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-3.22-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘AlpsNMR’ ...
** this is package ‘AlpsNMR’ version ‘4.12.0’
** 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)

Tests output

AlpsNMR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "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 
 21.038   7.206  20.378 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package1.8040.3221.617
HMDB_blood0.0040.0010.005
HMDB_cell0.0030.0000.003
HMDB_urine0.0040.0000.004
Parameters_blood0.0020.0000.002
Parameters_cell0.0020.0000.001
Parameters_urine0.0010.0000.001
Peak_detection7.8821.6196.966
Pipelines0.0010.0000.002
ROI_blood0.0020.0010.003
ROI_cell0.0020.0010.003
ROI_urine0.0030.0000.002
SummarizedExperiment_to_nmr_data_1r6.7940.8596.967
SummarizedExperiment_to_nmr_dataset_peak_table1.0220.5460.888
bp_VIP_analysis2.5441.5672.659
bp_kfold_VIP_analysis0.8300.5670.624
download_MTBLS242000
file_lister0.0580.0200.078
files_to_rDolphin000
filter.nmr_dataset_family0.6910.3770.538
format.nmr_dataset0.7260.5660.553
format.nmr_dataset_1D0.7100.4730.549
format.nmr_dataset_peak_table0.8540.6160.685
get_integration_with_metadata0.0310.0070.038
hmdb0.0450.0090.054
is.nmr_dataset0.7080.6780.583
is.nmr_dataset_1D0.7630.5610.634
is.nmr_dataset_peak_table0.9360.6300.818
load_and_save_functions0.6970.6400.579
models_stability_plot_bootstrap0.0020.0000.001
models_stability_plot_plsda0.3880.4470.392
new_nmr_dataset0.0020.0010.002
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.7910.6040.724
nmr_autophase0.2430.1470.383
nmr_baseline_estimation0.0090.0020.011
nmr_baseline_removal0.0050.0000.005
nmr_baseline_threshold0.0010.0010.001
nmr_baseline_threshold_plot0.3630.0780.441
nmr_batman0.0020.0010.003
nmr_batman_options0.0000.0010.000
nmr_build_peak_table0.0370.0050.042
nmr_data0.0490.0100.059
nmr_data_1r_to_SummarizedExperiment0.9100.5180.812
nmr_data_analysis0.5800.7160.581
nmr_dataset0.0010.0010.001
nmr_dataset_1D0.0000.0010.001
nmr_dataset_peak_table_to_SummarizedExperiment1.0400.6920.923
nmr_exclude_region0.0060.0000.006
nmr_export_data_1r0.7890.6130.629
nmr_get_peak_distances0.0080.0020.010
nmr_identify_regions_blood0.0130.0010.017
nmr_identify_regions_cell0.0070.0030.010
nmr_identify_regions_urine0.0130.0010.013
nmr_integrate_regions0.0070.0000.007
nmr_interpolate_1D1.6321.2701.407
nmr_meta_add1.9021.5001.765
nmr_meta_export0.7150.5890.561
nmr_meta_get0.6630.5440.544
nmr_meta_get_column0.7010.4920.541
nmr_meta_groups0.7790.7090.634
nmr_normalize0.3130.0750.388
nmr_pca_build_model2.5071.4892.432
nmr_pca_outliers0.9040.6390.763
nmr_pca_outliers_filter0.9480.6370.799
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.7911.1245.019
nmr_pca_plots0.5060.0240.530
nmr_peak_clustering0.0710.0010.073
nmr_ppm_resolution0.0060.0020.008
nmr_read_bruker_fid000
nmr_read_samples1.3271.3261.075
nmr_zip_bruker_samples0.2500.0120.264
peaklist_accept_peaks0.0030.0010.004
permutation_test_model0.6310.7021.546
permutation_test_plot3.9832.3101.807
plot.nmr_dataset_1D0.0020.0000.003
plot_bootstrap_multimodel0.0030.0000.003
plot_interactive2.6541.9130.827
plot_plsda_multimodel0.2250.4340.360
plot_plsda_samples0.1090.1810.223
plot_vip_scores0.0020.0000.002
plot_webgl0.0020.0000.002
plsda_auroc_vip_compare0.5520.4520.798
plsda_auroc_vip_method0.0010.0000.000
ppm_resolution0.0030.0000.003
print.nmr_dataset0.8080.5610.561
print.nmr_dataset_1D0.7020.5350.562
print.nmr_dataset_peak_table1.1771.0631.025
random_subsampling0.0010.0010.002
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.6960.5330.551
sub-.nmr_dataset_1D0.8120.7250.700
sub-.nmr_dataset_peak_table0.9040.7160.795
tidy.nmr_dataset_1D0.8880.7270.822
to_ASICS0.9390.1801.120
to_ChemoSpec1.1730.9751.159
validate_nmr_dataset1.4341.3661.259
validate_nmr_dataset_family0.8100.6830.691
validate_nmr_dataset_peak_table0.0010.0000.001
zzz0.0010.0002.002