Back to Multiple platform build/check report for BioC 3.21:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 59/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.10.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_21
git_last_commit: aa900cf
git_last_commit_date: 2025-04-15 12:14:56 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for AlpsNMR on kjohnson1

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: 4.10.0
Command: /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_4.10.0.tar.gz
StartedAt: 2025-08-01 11:45:10 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:48:41 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 211.3 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_4.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.10.0’
* 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 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 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                      11.130  3.068  10.457
SummarizedExperiment_to_nmr_data_1r  7.743  0.931   8.164
nmr_pca_outliers                     4.389  2.442   3.414
permutation_test_plot                4.335  2.464   2.065
format.nmr_dataset_peak_table        4.148  2.438   3.551
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘AlpsNMR’ ...
** this is package ‘AlpsNMR’ version ‘4.10.0’
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
 24.152   9.251  25.359 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.0870.5572.047
HMDB_blood0.0070.0030.010
HMDB_cell0.0030.0020.004
HMDB_urine0.0050.0030.007
Parameters_blood0.0020.0020.004
Parameters_cell0.0020.0020.003
Parameters_urine0.0020.0020.003
Peak_detection11.130 3.06810.457
Pipelines0.0020.0010.002
ROI_blood0.0030.0020.005
ROI_cell0.0020.0020.004
ROI_urine0.0030.0020.004
SummarizedExperiment_to_nmr_data_1r7.7430.9318.164
SummarizedExperiment_to_nmr_dataset_peak_table1.1950.7621.422
bp_VIP_analysis1.2341.0691.362
bp_kfold_VIP_analysis0.8690.8490.815
download_MTBLS242000
file_lister0.0600.0450.115
files_to_rDolphin0.0010.0000.001
filter.nmr_dataset_family1.4021.0901.091
format.nmr_dataset0.8210.7680.776
format.nmr_dataset_1D0.9200.8450.920
format.nmr_dataset_peak_table4.1482.4383.551
get_integration_with_metadata0.0300.0110.043
hmdb0.0570.0090.066
is.nmr_dataset0.8240.7280.787
is.nmr_dataset_1D0.7840.5340.832
is.nmr_dataset_peak_table0.9080.7590.971
load_and_save_functions0.7820.6430.721
models_stability_plot_bootstrap0.0020.0030.005
models_stability_plot_plsda0.4220.5260.475
new_nmr_dataset0.0010.0010.002
new_nmr_dataset_1D0.0010.0010.002
new_nmr_dataset_peak_table0.8940.6670.852
nmr_autophase0.2360.1320.368
nmr_baseline_estimation0.0100.0060.017
nmr_baseline_removal0.0060.0020.008
nmr_baseline_threshold0.0020.0010.002
nmr_baseline_threshold_plot0.2160.0460.262
nmr_batman0.0040.0020.005
nmr_batman_options000
nmr_build_peak_table0.0370.0090.047
nmr_data0.0460.0080.054
nmr_data_1r_to_SummarizedExperiment0.8780.5131.130
nmr_data_analysis0.6310.8900.693
nmr_dataset0.0010.0010.002
nmr_dataset_1D0.0010.0000.002
nmr_dataset_peak_table_to_SummarizedExperiment1.1991.1501.452
nmr_exclude_region0.0080.0020.010
nmr_export_data_1r0.8780.8210.917
nmr_get_peak_distances0.0100.0050.018
nmr_identify_regions_blood0.0150.0090.024
nmr_identify_regions_cell0.0100.0020.011
nmr_identify_regions_urine0.0150.0030.020
nmr_integrate_regions0.0080.0020.011
nmr_interpolate_1D1.6571.3531.771
nmr_meta_add1.9791.4261.994
nmr_meta_export0.7590.8010.759
nmr_meta_get0.5170.4980.514
nmr_meta_get_column0.5050.3860.479
nmr_meta_groups0.8410.7280.868
nmr_normalize0.2530.0580.358
nmr_pca_build_model1.8251.1721.789
nmr_pca_outliers4.3892.4423.414
nmr_pca_outliers_filter1.7230.6701.816
nmr_pca_outliers_plot0.0000.0000.001
nmr_pca_outliers_robust4.2930.5804.356
nmr_pca_plots0.3630.0210.385
nmr_peak_clustering0.0670.0020.070
nmr_ppm_resolution0.0090.0010.011
nmr_read_bruker_fid0.0000.0000.001
nmr_read_samples1.4491.1931.313
nmr_zip_bruker_samples0.3470.0440.404
peaklist_accept_peaks0.0040.0010.006
permutation_test_model2.5351.6892.027
permutation_test_plot4.3352.4642.065
plot.nmr_dataset_1D0.0020.0020.003
plot_bootstrap_multimodel0.0020.0040.006
plot_interactive0.8880.7830.865
plot_plsda_multimodel0.2530.4290.368
plot_plsda_samples0.1250.2150.331
plot_vip_scores0.0010.0010.004
plot_webgl0.0020.0010.003
plsda_auroc_vip_compare0.4710.4570.909
plsda_auroc_vip_method0.0000.0000.001
ppm_resolution0.0030.0010.005
print.nmr_dataset0.8350.8740.874
print.nmr_dataset_1D0.7860.7070.850
print.nmr_dataset_peak_table0.9610.8931.090
random_subsampling0.0020.0040.006
save_files_to_rDolphin000
save_profiling_output0.0000.0010.000
sub-.nmr_dataset0.8230.9060.901
sub-.nmr_dataset_1D0.8180.7590.884
sub-.nmr_dataset_peak_table1.2631.2721.425
tidy.nmr_dataset_1D0.9190.8561.017
to_ASICS1.0970.1951.328
to_ChemoSpec0.9780.7441.033
validate_nmr_dataset1.8451.8472.007
validate_nmr_dataset_family0.8570.8400.914
validate_nmr_dataset_peak_table0.0010.0000.002
zzz0.0010.0002.151