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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 59/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.11.1  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: 205bd1b
git_last_commit_date: 2025-09-24 17:19:41 -0400 (Wed, 24 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for AlpsNMR on lconway

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: 4.11.1
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_4.11.1.tar.gz
StartedAt: 2025-10-10 19:55:53 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 19:59:37 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 224.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_4.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.11.1’
* 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 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                      10.207  3.053   9.500
SummarizedExperiment_to_nmr_data_1r  7.650  0.961   7.755
nmr_pca_outliers_robust              7.078  1.515   7.022
permutation_test_plot                4.392  2.416   2.322
* 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-3.22-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-x86_64/Resources/library’
* installing *source* package ‘AlpsNMR’ ...
** this is package ‘AlpsNMR’ version ‘4.11.1’
** 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)

Tests output

AlpsNMR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
 27.087  10.719  27.100 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.1850.5272.009
HMDB_blood0.0060.0020.009
HMDB_cell0.0030.0010.003
HMDB_urine0.0060.0030.008
Parameters_blood0.0010.0020.003
Parameters_cell0.0020.0010.003
Parameters_urine0.0020.0020.004
Peak_detection10.207 3.053 9.500
Pipelines0.0010.0010.003
ROI_blood0.0040.0010.005
ROI_cell0.0040.0010.005
ROI_urine0.0040.0010.005
SummarizedExperiment_to_nmr_data_1r7.6500.9617.755
SummarizedExperiment_to_nmr_dataset_peak_table2.1970.9632.151
bp_VIP_analysis1.4310.8511.149
bp_kfold_VIP_analysis1.1110.5690.755
download_MTBLS242000
file_lister0.0810.0260.109
files_to_rDolphin000
filter.nmr_dataset_family1.4370.7760.880
format.nmr_dataset1.0010.7360.813
format.nmr_dataset_1D1.1460.8210.965
format.nmr_dataset_peak_table1.2020.7781.030
get_integration_with_metadata0.0330.0060.040
hmdb0.0610.0050.067
is.nmr_dataset0.9730.6780.743
is.nmr_dataset_1D1.0830.7850.886
is.nmr_dataset_peak_table1.1900.8681.026
load_and_save_functions0.9570.6990.759
models_stability_plot_bootstrap0.0010.0010.002
models_stability_plot_plsda0.5300.5330.523
new_nmr_dataset0.0020.0020.004
new_nmr_dataset_1D0.0010.0010.002
new_nmr_dataset_peak_table1.1900.8481.016
nmr_autophase0.2650.1470.403
nmr_baseline_estimation0.0130.0050.017
nmr_baseline_removal0.0060.0020.008
nmr_baseline_threshold0.0010.0000.002
nmr_baseline_threshold_plot0.3590.0360.398
nmr_batman0.0030.0010.004
nmr_batman_options000
nmr_build_peak_table0.0410.0050.046
nmr_data0.8160.1520.973
nmr_data_1r_to_SummarizedExperiment1.1560.5911.002
nmr_data_analysis0.5090.4840.497
nmr_dataset0.0010.0010.002
nmr_dataset_1D0.0010.0000.001
nmr_dataset_peak_table_to_SummarizedExperiment1.3170.7901.125
nmr_exclude_region0.0060.0020.009
nmr_export_data_1r1.0480.7460.851
nmr_get_peak_distances0.0090.0030.013
nmr_identify_regions_blood0.0150.0050.020
nmr_identify_regions_cell0.0100.0030.012
nmr_identify_regions_urine0.0160.0030.020
nmr_integrate_regions0.0090.0010.010
nmr_interpolate_1D2.1261.5311.726
nmr_meta_add2.2031.3072.230
nmr_meta_export1.4061.2200.991
nmr_meta_get0.9460.6050.749
nmr_meta_get_column1.0080.7220.821
nmr_meta_groups0.9140.5000.707
nmr_normalize0.4180.0610.482
nmr_pca_build_model2.2411.3071.886
nmr_pca_outliers1.2780.9381.165
nmr_pca_outliers_filter1.2060.8921.439
nmr_pca_outliers_plot000
nmr_pca_outliers_robust7.0781.5157.022
nmr_pca_plots0.5980.0180.622
nmr_peak_clustering0.0880.0010.089
nmr_ppm_resolution0.0080.0020.011
nmr_read_bruker_fid000
nmr_read_samples1.7981.2331.445
nmr_zip_bruker_samples0.2380.0480.305
peaklist_accept_peaks0.0040.0010.005
permutation_test_model0.9210.7452.150
permutation_test_plot4.3922.4162.322
plot.nmr_dataset_1D1.1890.5550.034
plot_bootstrap_multimodel0.0020.0120.015
plot_interactive1.0100.6880.866
plot_plsda_multimodel0.3080.3170.359
plot_plsda_samples0.1760.1620.323
plot_vip_scores0.0020.0020.005
plot_webgl0.0010.0020.003
plsda_auroc_vip_compare0.6830.5241.079
plsda_auroc_vip_method0.0000.0010.000
ppm_resolution0.0030.0010.003
print.nmr_dataset0.8510.5920.666
print.nmr_dataset_1D0.9680.6250.822
print.nmr_dataset_peak_table1.0440.6110.875
random_subsampling0.0020.0050.007
save_files_to_rDolphin0.0000.0000.001
save_profiling_output0.0000.0010.000
sub-.nmr_dataset0.8960.5800.691
sub-.nmr_dataset_1D0.9870.6280.817
sub-.nmr_dataset_peak_table1.6901.7251.645
tidy.nmr_dataset_1D1.1250.7771.043
to_ASICS1.1040.2101.332
to_ChemoSpec1.1380.7231.038
validate_nmr_dataset2.2081.6721.864
validate_nmr_dataset_family1.0000.6920.855
validate_nmr_dataset_peak_table0.0010.0000.002
zzz0.0000.0002.148