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This page was generated on 2024-05-15 13:46:26 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 57/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.7.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: 1bcba03
git_last_commit_date: 2024-04-30 11:29:26 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for AlpsNMR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: AlpsNMR
Version: 4.6.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings AlpsNMR_4.6.0.tar.gz
StartedAt: 2024-05-09 04:42:07 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 04:45:36 -0000 (Thu, 09 May 2024)
EllapsedTime: 209.4 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings AlpsNMR_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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                      11.339  2.018   9.391
SummarizedExperiment_to_nmr_data_1r  9.054  1.055   9.284
nmr_pca_outliers_robust              7.813  1.002   8.335
permutation_test_plot                4.142  1.630   2.793
* 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: OK


Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘AlpsNMR’ ...
** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
Loading required package: future

Attaching package: 'AlpsNMR'

The following object is masked from 'package:stats':

    filter

> 
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]
> 
> proc.time()
   user  system elapsed 
 17.970   4.928  18.015 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.2390.3812.259
HMDB_blood0.0070.0000.007
HMDB_cell0.0030.0000.003
HMDB_urine0.0010.0040.004
Parameters_blood0.0020.0000.002
Parameters_cell0.0020.0000.001
Parameters_urine0.0020.0000.002
Peak_detection11.339 2.018 9.391
Pipelines0.0010.0000.002
ROI_blood0.0040.0000.004
ROI_cell0.0040.0000.003
ROI_urine0.0030.0000.004
SummarizedExperiment_to_nmr_data_1r9.0541.0559.284
SummarizedExperiment_to_nmr_dataset_peak_table1.9640.6582.201
bp_VIP_analysis0.3300.3061.346
bp_kfold_VIP_analysis2.5850.8860.885
download_MTBLS242000
file_lister0.0740.0280.103
files_to_rDolphin000
filter.nmr_dataset_family0.9240.3470.929
format.nmr_dataset0.8510.5380.935
format.nmr_dataset_1D0.9850.4381.006
format.nmr_dataset_peak_table1.0920.4941.150
get_integration_with_metadata0.0260.0080.034
hmdb0.0600.0080.068
is.nmr_dataset0.8920.4920.904
is.nmr_dataset_1D1.0570.5381.108
is.nmr_dataset_peak_table1.0530.5871.186
load_and_save_functions0.9320.4440.933
models_stability_plot_bootstrap0.0010.0020.002
models_stability_plot_plsda0.3740.2660.445
new_nmr_dataset0.0020.0000.002
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table1.1200.6401.164
nmr_baseline_estimation0.1700.0270.198
nmr_baseline_removal0.0060.0010.005
nmr_baseline_threshold0.0010.0000.001
nmr_baseline_threshold_plot0.2930.0180.312
nmr_batman0.0030.0000.003
nmr_batman_options000
nmr_build_peak_table0.0500.0010.050
nmr_data0.0690.0080.077
nmr_data_1r_to_SummarizedExperiment1.2240.4131.245
nmr_data_analysis0.4820.5400.586
nmr_dataset0.0000.0020.001
nmr_dataset_1D0.0010.0010.001
nmr_dataset_peak_table_to_SummarizedExperiment2.0580.8062.416
nmr_exclude_region0.0070.0000.006
nmr_export_data_1r0.9420.4630.985
nmr_get_peak_distances0.0110.0000.011
nmr_identify_regions_blood0.0210.0000.021
nmr_identify_regions_cell0.0090.0040.013
nmr_identify_regions_urine0.020.000.02
nmr_integrate_regions0.0100.0040.014
nmr_interpolate_1D1.9371.0522.059
nmr_meta_add2.2531.0232.387
nmr_meta_export0.8720.4760.899
nmr_meta_get0.8780.4720.908
nmr_meta_get_column0.8830.5310.962
nmr_meta_groups0.9360.4710.947
nmr_normalize0.3270.0360.364
nmr_pca_build_model2.2311.0172.336
nmr_pca_outliers1.1390.6131.313
nmr_pca_outliers_filter1.1650.5451.278
nmr_pca_outliers_plot000
nmr_pca_outliers_robust7.8131.0028.335
nmr_pca_plots0.4690.0240.493
nmr_peak_clustering0.090.000.09
nmr_ppm_resolution0.0090.0000.009
nmr_read_bruker_fid0.0000.0000.001
nmr_read_samples1.8021.0931.932
nmr_zip_bruker_samples0.2490.0080.260
peaklist_accept_peaks0.0020.0040.005
permutation_test_model2.2890.8773.084
permutation_test_plot4.1421.6302.793
plot.nmr_dataset_1D0.0020.0000.001
plot_bootstrap_multimodel0.0020.0000.002
plot_interactive2.8451.0551.132
plot_plsda_multimodel0.3390.4220.482
plot_plsda_samples0.2150.2760.399
plot_vip_scores0.0020.0010.003
plot_webgl0.0020.0000.002
plsda_auroc_vip_compare0.6390.6330.965
plsda_auroc_vip_method000
ppm_resolution0.0030.0000.003
print.nmr_dataset0.8650.5030.908
print.nmr_dataset_1D1.0200.5821.166
print.nmr_dataset_peak_table1.0670.5431.150
random_subsampling0.0020.0000.002
save_files_to_rDolphin0.0010.0000.000
save_profiling_output000
sub-.nmr_dataset1.0540.6481.098
sub-.nmr_dataset_1D0.9380.5651.050
sub-.nmr_dataset_peak_table1.1500.6941.267
tidy.nmr_dataset_1D1.1790.5611.216
to_ChemoSpec1.3110.5661.315
validate_nmr_dataset1.8321.2332.130
validate_nmr_dataset_family1.0850.6731.245
validate_nmr_dataset_peak_table0.0000.0020.001
zzz0.0000.0002.002