Back to Multiple platform build/check report for BioC 3.19:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-07-16 17:42 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 57/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.6.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_19
git_last_commit: 75a7fce
git_last_commit_date: 2024-04-30 11:29:26 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 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


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: 4.6.0
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_4.6.0.tar.gz
StartedAt: 2024-07-15 10:46:09 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 10:49:26 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 197.2 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_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.6.0’
* 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 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 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                      7.947  2.075   7.035
SummarizedExperiment_to_nmr_data_1r 7.654  0.624   7.966
permutation_test_plot               4.567  1.657   2.329
validate_nmr_dataset                3.848  2.201   3.885
nmr_pca_outliers_robust             5.110  0.612   5.381
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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)
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 
 15.624   5.103  16.511 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.0120.3682.096
HMDB_blood0.0070.0030.010
HMDB_cell0.0030.0020.004
HMDB_urine0.0040.0030.007
Parameters_blood0.0020.0020.003
Parameters_cell0.0020.0020.003
Parameters_urine0.0010.0020.003
Peak_detection7.9472.0757.035
Pipelines0.0020.0010.002
ROI_blood0.0030.0010.006
ROI_cell0.0030.0020.005
ROI_urine0.0030.0020.006
SummarizedExperiment_to_nmr_data_1r7.6540.6247.966
SummarizedExperiment_to_nmr_dataset_peak_table1.0450.4611.189
bp_VIP_analysis2.1371.0172.324
bp_kfold_VIP_analysis0.7230.4000.675
download_MTBLS2420.0010.0000.000
file_lister0.0670.0150.082
files_to_rDolphin0.0000.0000.001
filter.nmr_dataset_family1.5800.6521.861
format.nmr_dataset0.6340.4050.761
format.nmr_dataset_1D0.7570.5090.928
format.nmr_dataset_peak_table0.7880.4360.945
get_integration_with_metadata0.0300.0040.033
hmdb0.0560.0090.064
is.nmr_dataset0.6700.4620.765
is.nmr_dataset_1D0.5910.3930.965
is.nmr_dataset_peak_table0.9680.6691.050
load_and_save_functions0.6710.4190.747
models_stability_plot_bootstrap0.0020.0010.003
models_stability_plot_plsda0.3600.3620.460
new_nmr_dataset0.0020.0010.003
new_nmr_dataset_1D0.0010.0010.001
new_nmr_dataset_peak_table1.5720.6251.926
nmr_baseline_estimation0.0930.0090.104
nmr_baseline_removal0.0050.0010.005
nmr_baseline_threshold0.0000.0000.001
nmr_baseline_threshold_plot0.1200.0030.127
nmr_batman0.0030.0010.005
nmr_batman_options000
nmr_build_peak_table0.0380.0020.040
nmr_data0.0490.0060.055
nmr_data_1r_to_SummarizedExperiment0.5140.2780.865
nmr_data_analysis0.3700.3690.479
nmr_dataset0.0010.0010.001
nmr_dataset_1D0.0010.0010.002
nmr_dataset_peak_table_to_SummarizedExperiment1.1500.6401.223
nmr_exclude_region0.0070.0010.008
nmr_export_data_1r0.7790.4310.956
nmr_get_peak_distances0.0080.0010.010
nmr_identify_regions_blood0.0140.0040.017
nmr_identify_regions_cell0.0080.0010.009
nmr_identify_regions_urine0.0130.0020.015
nmr_integrate_regions0.0100.0020.011
nmr_interpolate_1D1.5230.9301.810
nmr_meta_add1.7351.0652.083
nmr_meta_export0.6740.4880.832
nmr_meta_get0.7120.4850.826
nmr_meta_get_column0.6740.4650.847
nmr_meta_groups0.7450.6130.944
nmr_normalize0.2340.0520.287
nmr_pca_build_model1.7761.0202.085
nmr_pca_outliers0.8830.4651.044
nmr_pca_outliers_filter2.4031.0493.147
nmr_pca_outliers_plot0.0000.0010.000
nmr_pca_outliers_robust5.1100.6125.381
nmr_pca_plots0.3430.0130.356
nmr_peak_clustering0.0590.0020.062
nmr_ppm_resolution0.0090.0010.010
nmr_read_bruker_fid0.0010.0000.001
nmr_read_samples1.3010.9521.628
nmr_zip_bruker_samples0.3460.0350.384
peaklist_accept_peaks0.0040.0030.006
permutation_test_model1.7640.8372.385
permutation_test_plot4.5671.6572.329
plot.nmr_dataset_1D0.0010.0030.005
plot_bootstrap_multimodel0.0010.0020.004
plot_interactive0.8300.6011.026
plot_plsda_multimodel0.2120.3010.339
plot_plsda_samples0.1180.1660.269
plot_vip_scores0.0020.0020.004
plot_webgl0.0020.0000.002
plsda_auroc_vip_compare0.4500.4300.852
plsda_auroc_vip_method000
ppm_resolution0.0030.0020.005
print.nmr_dataset0.7440.5740.971
print.nmr_dataset_1D0.9850.7441.202
print.nmr_dataset_peak_table0.8510.6061.108
random_subsampling0.0010.0040.005
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.7210.5840.877
sub-.nmr_dataset_1D0.6320.4311.006
sub-.nmr_dataset_peak_table1.0690.8581.147
tidy.nmr_dataset_1D0.9070.5771.072
to_ChemoSpec0.8810.5621.113
validate_nmr_dataset3.8482.2013.885
validate_nmr_dataset_family0.7520.5070.865
validate_nmr_dataset_peak_table0.0010.0010.001
zzz0.0000.0012.151