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This page was generated on 2025-08-11 12:09 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 59/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.11.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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: 4.11.0
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_4.11.0.tar.gz
StartedAt: 2025-08-10 19:20:36 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 19:24:25 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 228.9 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_4.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘4.11.0’
* 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                      12.219  4.065  11.264
SummarizedExperiment_to_nmr_data_1r  7.754  0.964   7.824
nmr_pca_outliers                     4.562  3.452   3.643
format.nmr_dataset_peak_table        4.129  3.423   3.619
permutation_test_plot                4.430  2.489   2.300
nmr_pca_outliers_robust              6.058  0.735   6.006
* 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 ‘4.11.0’
** 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-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 
 31.811  13.861  29.954 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package1.9110.5002.031
HMDB_blood0.0070.0040.010
HMDB_cell0.0030.0020.004
HMDB_urine0.0050.0020.007
Parameters_blood0.0020.0010.003
Parameters_cell0.0020.0010.002
Parameters_urine0.0030.0010.004
Peak_detection12.219 4.06511.264
Pipelines0.0020.0010.003
ROI_blood0.0040.0020.004
ROI_cell0.0030.0010.004
ROI_urine0.0030.0010.005
SummarizedExperiment_to_nmr_data_1r7.7540.9647.824
SummarizedExperiment_to_nmr_dataset_peak_table1.4680.8231.259
bp_VIP_analysis2.0201.2961.385
bp_kfold_VIP_analysis1.1980.8460.881
download_MTBLS2420.0000.0010.000
file_lister0.0890.0160.106
files_to_rDolphin0.0000.0000.001
filter.nmr_dataset_family1.2810.8931.034
format.nmr_dataset1.1180.8660.865
format.nmr_dataset_1D1.2141.0101.056
format.nmr_dataset_peak_table4.1293.4233.619
get_integration_with_metadata0.0380.0060.044
hmdb0.0600.0070.067
is.nmr_dataset1.0190.7030.793
is.nmr_dataset_1D1.0060.6210.805
is.nmr_dataset_peak_table1.1330.7560.941
load_and_save_functions0.7510.5400.813
models_stability_plot_bootstrap0.0020.0020.003
models_stability_plot_plsda0.5690.5280.522
new_nmr_dataset0.0020.0010.003
new_nmr_dataset_1D0.0010.0010.002
new_nmr_dataset_peak_table1.3921.0741.039
nmr_autophase0.2670.1400.397
nmr_baseline_estimation0.0110.0060.017
nmr_baseline_removal0.0070.0020.009
nmr_baseline_threshold0.0010.0000.002
nmr_baseline_threshold_plot0.2620.0340.299
nmr_batman0.0030.0010.005
nmr_batman_options000
nmr_build_peak_table0.0450.0050.049
nmr_data0.0590.0070.066
nmr_data_1r_to_SummarizedExperiment1.1760.5461.066
nmr_data_analysis0.5650.5820.582
nmr_dataset0.0010.0000.001
nmr_dataset_1D0.0010.0000.002
nmr_dataset_peak_table_to_SummarizedExperiment1.4490.9181.232
nmr_exclude_region0.0070.0020.010
nmr_export_data_1r1.0880.8290.914
nmr_get_peak_distances0.0090.0010.010
nmr_identify_regions_blood0.0120.0030.015
nmr_identify_regions_cell0.0090.0010.011
nmr_identify_regions_urine0.0140.0020.016
nmr_integrate_regions0.0060.0010.007
nmr_interpolate_1D2.0091.3671.699
nmr_meta_add2.5711.5472.203
nmr_meta_export1.0930.8210.876
nmr_meta_get1.0540.8260.867
nmr_meta_get_column0.7190.4430.772
nmr_meta_groups1.3370.9950.954
nmr_normalize0.3300.0490.380
nmr_pca_build_model2.2671.3271.967
nmr_pca_outliers4.5623.4523.643
nmr_pca_outliers_filter1.8880.7611.870
nmr_pca_outliers_plot000
nmr_pca_outliers_robust6.0580.7356.006
nmr_pca_plots0.4500.0170.471
nmr_peak_clustering0.0820.0010.084
nmr_ppm_resolution0.0070.0020.010
nmr_read_bruker_fid000
nmr_read_samples1.9181.3821.521
nmr_zip_bruker_samples0.2370.0460.301
peaklist_accept_peaks0.0050.0010.007
permutation_test_model1.0561.0022.271
permutation_test_plot4.4302.4892.300
plot.nmr_dataset_1D1.1210.5100.016
plot_bootstrap_multimodel2.2721.0420.030
plot_interactive1.0090.6750.869
plot_plsda_multimodel0.3380.5370.482
plot_plsda_samples0.1710.2300.387
plot_vip_scores0.0020.0020.004
plot_webgl0.0020.0020.005
plsda_auroc_vip_compare0.6280.5221.131
plsda_auroc_vip_method000
ppm_resolution0.0040.0010.004
print.nmr_dataset1.1100.8770.882
print.nmr_dataset_1D0.9820.6540.815
print.nmr_dataset_peak_table1.1000.6460.922
random_subsampling0.0020.0040.006
save_files_to_rDolphin0.0010.0010.001
save_profiling_output0.0000.0010.000
sub-.nmr_dataset1.2641.1041.076
sub-.nmr_dataset_1D0.8280.6350.964
sub-.nmr_dataset_peak_table1.4011.0601.090
tidy.nmr_dataset_1D1.2290.8331.064
to_ASICS1.1640.1991.375
to_ChemoSpec1.3360.7711.237
validate_nmr_dataset2.1011.5951.742
validate_nmr_dataset_family1.0070.8801.203
validate_nmr_dataset_peak_table0.0010.0010.002
zzz0.3330.3162.147