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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 59/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.11.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: 487e98f
git_last_commit_date: 2025-04-15 12:14:56 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


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: 4.11.0
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_4.11.0.tar.gz
StartedAt: 2025-09-21 20:53:41 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 20:58:28 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 287.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: AlpsNMR.Rcheck
Warnings: NA

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_4.11.0.tar.gz
###
##############################################################################
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* 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 ‘4.11.0’
* 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                      7.461  1.871   6.843
SummarizedExperiment_to_nmr_data_1r 6.629  0.826   6.819
nmr_interpolate_1D                  4.179  3.080   3.440
nmr_pca_outliers_robust             4.946  1.155   5.247
permutation_test_plot               3.262  1.895   1.766
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: TRUE 
  ── Failure ('test-outliers.R:29:5'): nmr_pca_outliers_robust works ─────────────
  is.list(outliers_plot) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-outliers.R:30:5'): nmr_pca_outliers_robust works ─────────────
  is.list(plot) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 5 | WARN 0 | SKIP 1 | PASS 88 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.


Installation output

AlpsNMR.Rcheck/00install.out

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###
### 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 ‘4.11.0’
** 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.fail


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 5 | WARN 0 | SKIP 1 | PASS 88 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-outliers.R:26:5'): nmr_pca_outliers_robust works ─────────────
is.list(plot_variance) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-outliers.R:27:5'): nmr_pca_outliers_robust works ─────────────
is.list(score) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-outliers.R:28:5'): nmr_pca_outliers_robust works ─────────────
is.list(loadings) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-outliers.R:29:5'): nmr_pca_outliers_robust works ─────────────
is.list(outliers_plot) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-outliers.R:30:5'): nmr_pca_outliers_robust works ─────────────
is.list(plot) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 5 | WARN 0 | SKIP 1 | PASS 88 ]
Error: Test failures
Execution halted

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.1980.3712.038
HMDB_blood0.0060.0010.007
HMDB_cell0.0030.0000.003
HMDB_urine0.0040.0000.004
Parameters_blood0.0010.0010.002
Parameters_cell0.0020.0000.002
Parameters_urine0.0020.0000.002
Peak_detection7.4611.8716.843
Pipelines0.0010.0010.002
ROI_blood0.0020.0010.003
ROI_cell0.0020.0010.003
ROI_urine0.0030.0000.003
SummarizedExperiment_to_nmr_data_1r6.6290.8266.819
SummarizedExperiment_to_nmr_dataset_peak_table0.9900.5920.891
bp_VIP_analysis1.3910.8770.844
bp_kfold_VIP_analysis0.7480.5050.532
download_MTBLS242000
file_lister0.0560.0170.073
files_to_rDolphin0.0010.0010.001
filter.nmr_dataset_family1.6320.7401.568
format.nmr_dataset0.6490.4210.482
format.nmr_dataset_1D0.7210.5000.578
format.nmr_dataset_peak_table0.8060.4900.660
get_integration_with_metadata0.0310.0020.033
hmdb0.0530.0230.076
is.nmr_dataset0.6540.4920.508
is.nmr_dataset_1D0.8080.6110.656
is.nmr_dataset_peak_table0.8470.4780.644
load_and_save_functions0.6920.5380.541
models_stability_plot_bootstrap0.0020.0010.002
models_stability_plot_plsda0.3620.3990.379
new_nmr_dataset0.0020.0000.001
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.7900.5940.672
nmr_autophase0.2170.1370.311
nmr_baseline_estimation0.0080.0020.010
nmr_baseline_removal0.0030.0010.005
nmr_baseline_threshold0.0010.0000.001
nmr_baseline_threshold_plot0.2990.0470.347
nmr_batman0.0010.0020.003
nmr_batman_options000
nmr_build_peak_table0.0340.0070.042
nmr_data0.0680.0280.096
nmr_data_1r_to_SummarizedExperiment0.9910.5050.862
nmr_data_analysis0.3960.5100.430
nmr_dataset000
nmr_dataset_1D0.0010.0010.001
nmr_dataset_peak_table_to_SummarizedExperiment0.9500.5470.821
nmr_exclude_region0.0060.0000.006
nmr_export_data_1r0.7260.5970.669
nmr_get_peak_distances0.010.000.01
nmr_identify_regions_blood0.0150.0000.015
nmr_identify_regions_cell0.0090.0000.010
nmr_identify_regions_urine0.0130.0010.014
nmr_integrate_regions0.0070.0000.007
nmr_interpolate_1D4.1793.0803.440
nmr_meta_add1.6830.9321.398
nmr_meta_export0.7060.4800.508
nmr_meta_get0.6530.4770.506
nmr_meta_get_column0.6940.6580.616
nmr_meta_groups0.7050.5850.558
nmr_normalize0.3070.0660.373
nmr_pca_build_model1.6611.2461.414
nmr_pca_outliers0.8920.6680.799
nmr_pca_outliers_filter1.0230.7990.908
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.9461.1555.247
nmr_pca_plots0.4940.0230.516
nmr_peak_clustering0.0690.0050.074
nmr_ppm_resolution0.0060.0010.008
nmr_read_bruker_fid000
nmr_read_samples1.3901.2481.138
nmr_zip_bruker_samples0.2530.0120.265
peaklist_accept_peaks0.0040.0000.004
permutation_test_model2.3931.4961.724
permutation_test_plot3.2621.8951.766
plot.nmr_dataset_1D0.0030.0010.004
plot_bootstrap_multimodel0.0030.0010.004
plot_interactive1.7351.0480.698
plot_plsda_multimodel0.1980.4190.320
plot_plsda_samples0.1070.1570.210
plot_vip_scores0.0010.0000.001
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.5500.4420.792
plsda_auroc_vip_method000
ppm_resolution0.0030.0000.003
print.nmr_dataset0.8190.8870.793
print.nmr_dataset_1D0.7230.6620.645
print.nmr_dataset_peak_table0.8380.7030.838
random_subsampling0.0010.0000.001
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.7360.6540.613
sub-.nmr_dataset_1D0.7320.7050.680
sub-.nmr_dataset_peak_table0.8440.8090.837
tidy.nmr_dataset_1D0.9350.7510.797
to_ASICS0.8920.1811.074
to_ChemoSpec1.1381.1621.113
validate_nmr_dataset1.8891.9681.708
validate_nmr_dataset_family0.7570.6080.650
validate_nmr_dataset_peak_table0.0010.0000.001
zzz0.0010.0002.003