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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 59/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.11.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 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    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 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: 2025-08-31 20:14:10 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 20:18:46 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 276.3 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_4.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘4.11.0’
* 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                      8.640  1.972   7.477
SummarizedExperiment_to_nmr_data_1r 6.474  0.756   6.593
nmr_pca_outliers_robust             5.576  0.983   5.885
permutation_test_plot               3.881  2.270   1.636
format.nmr_dataset_peak_table       3.435  2.073   2.507
* 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

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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


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 
 23.882   8.707  22.033 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package1.7470.3921.567
HMDB_blood0.0040.0010.005
HMDB_cell0.0010.0010.003
HMDB_urine0.0030.0010.004
Parameters_blood0.0020.0000.002
Parameters_cell0.0020.0000.001
Parameters_urine0.0010.0000.001
Peak_detection8.6401.9727.477
Pipelines0.0010.0000.001
ROI_blood0.0010.0010.003
ROI_cell0.0020.0000.003
ROI_urine0.0030.0000.003
SummarizedExperiment_to_nmr_data_1r6.4740.7566.593
SummarizedExperiment_to_nmr_dataset_peak_table0.9930.4570.809
bp_VIP_analysis1.4910.8860.873
bp_kfold_VIP_analysis0.8120.6470.599
download_MTBLS242000
file_lister0.0610.0110.072
files_to_rDolphin000
filter.nmr_dataset_family0.9270.5760.721
format.nmr_dataset0.7790.5560.586
format.nmr_dataset_1D0.8220.5930.660
format.nmr_dataset_peak_table3.4352.0732.507
get_integration_with_metadata0.0250.0010.026
hmdb0.0440.0010.046
is.nmr_dataset0.7500.5030.572
is.nmr_dataset_1D0.7050.5030.570
is.nmr_dataset_peak_table0.8020.5090.630
load_and_save_functions0.7190.4570.528
models_stability_plot_bootstrap0.0010.0000.002
models_stability_plot_plsda0.3380.3870.355
new_nmr_dataset0.0010.0000.002
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.8020.5260.671
nmr_autophase0.2270.1170.350
nmr_baseline_estimation0.0060.0050.011
nmr_baseline_removal0.0030.0020.005
nmr_baseline_threshold0.0000.0010.001
nmr_baseline_threshold_plot0.2230.0280.251
nmr_batman0.0020.0010.003
nmr_batman_options000
nmr_build_peak_table0.0350.0070.041
nmr_data0.0510.0030.053
nmr_data_1r_to_SummarizedExperiment0.9500.4790.807
nmr_data_analysis0.3970.4810.415
nmr_dataset000
nmr_dataset_1D0.0010.0000.001
nmr_dataset_peak_table_to_SummarizedExperiment1.0750.7340.955
nmr_exclude_region0.0060.0000.006
nmr_export_data_1r0.7970.6010.628
nmr_get_peak_distances0.0090.0020.010
nmr_identify_regions_blood0.0110.0090.020
nmr_identify_regions_cell0.0080.0030.011
nmr_identify_regions_urine0.0140.0030.017
nmr_integrate_regions0.0070.0010.008
nmr_interpolate_1D1.5031.1521.232
nmr_meta_add1.9171.1901.698
nmr_meta_export0.7780.6570.623
nmr_meta_get0.7210.6310.612
nmr_meta_get_column0.6500.4720.514
nmr_meta_groups0.7230.5180.540
nmr_normalize0.2410.0210.262
nmr_pca_build_model1.6630.9981.412
nmr_pca_outliers1.4290.9881.703
nmr_pca_outliers_filter0.8580.5520.758
nmr_pca_outliers_plot000
nmr_pca_outliers_robust5.5760.9835.885
nmr_pca_plots0.3540.0220.377
nmr_peak_clustering0.0680.0000.068
nmr_ppm_resolution0.0080.0000.008
nmr_read_bruker_fid000
nmr_read_samples1.4811.1521.152
nmr_zip_bruker_samples0.2540.0110.267
peaklist_accept_peaks0.0030.0010.004
permutation_test_model1.5811.2581.789
permutation_test_plot3.8812.2701.636
plot.nmr_dataset_1D0.0020.0000.002
plot_bootstrap_multimodel0.0010.0010.002
plot_interactive1.6080.8070.557
plot_plsda_multimodel0.1850.3910.320
plot_plsda_samples0.1180.1570.215
plot_vip_scores0.0010.0000.002
plot_webgl0.0010.0010.002
plsda_auroc_vip_compare0.4820.3450.712
plsda_auroc_vip_method0.0010.0000.000
ppm_resolution0.0030.0000.003
print.nmr_dataset0.6660.4810.497
print.nmr_dataset_1D0.7230.5230.606
print.nmr_dataset_peak_table0.8240.5430.690
random_subsampling0.0010.0010.002
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.6650.5960.544
sub-.nmr_dataset_1D0.8460.7280.724
sub-.nmr_dataset_peak_table0.7830.6180.662
tidy.nmr_dataset_1D0.7540.5220.647
to_ASICS0.8840.2381.123
to_ChemoSpec0.8800.5960.799
validate_nmr_dataset1.6621.4781.396
validate_nmr_dataset_family0.8660.7830.876
validate_nmr_dataset_peak_table0.0010.0000.002
zzz0.0000.0002.002