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This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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: 2024-05-06 14:00:02 -0400 (Mon, 06 May 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)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for AlpsNMR on kjohnson3


To the developers/maintainers of the AlpsNMR package:
- 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: 2024-05-06 19:34:58 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 19:36:05 -0400 (Mon, 06 May 2024)
EllapsedTime: 66.8 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_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/AlpsNMR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* 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
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
  5.044   1.920   5.369 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package0.6070.1100.627
HMDB_blood0.0020.0010.003
HMDB_cell0.0010.0000.001
HMDB_urine0.0010.0010.002
Parameters_blood0.0010.0010.001
Parameters_cell0.0010.0000.001
Parameters_urine0.0000.0010.001
Peak_detection2.6170.6792.330
Pipelines000
ROI_blood0.0010.0000.002
ROI_cell0.0010.0010.001
ROI_urine0.0010.0000.002
SummarizedExperiment_to_nmr_data_1r2.2490.2112.350
SummarizedExperiment_to_nmr_dataset_peak_table0.3140.1510.367
bp_VIP_analysis0.3980.2640.396
bp_kfold_VIP_analysis0.2130.1560.224
download_MTBLS242000
file_lister0.0220.0070.028
files_to_rDolphin000
filter.nmr_dataset_family0.7740.3541.001
format.nmr_dataset0.1960.1370.242
format.nmr_dataset_1D0.2300.1530.279
format.nmr_dataset_peak_table0.2530.1550.322
get_integration_with_metadata0.0070.0010.008
hmdb0.0170.0020.019
is.nmr_dataset0.2120.1790.266
is.nmr_dataset_1D0.2390.1710.309
is.nmr_dataset_peak_table0.2490.1690.326
load_and_save_functions0.2100.1430.250
models_stability_plot_bootstrap0.0010.0000.000
models_stability_plot_plsda0.1120.1370.162
new_nmr_dataset0.0010.0000.001
new_nmr_dataset_1D0.0000.0000.001
new_nmr_dataset_peak_table0.7560.3220.976
nmr_baseline_estimation0.0420.0040.046
nmr_baseline_removal0.0020.0000.001
nmr_baseline_threshold000
nmr_baseline_threshold_plot0.0610.0010.061
nmr_batman0.0010.0000.001
nmr_batman_options000
nmr_build_peak_table0.010.000.01
nmr_data0.0130.0010.015
nmr_data_1r_to_SummarizedExperiment0.3230.1600.377
nmr_data_analysis0.1110.1170.151
nmr_dataset0.0000.0000.001
nmr_dataset_1D0.0010.0000.000
nmr_dataset_peak_table_to_SummarizedExperiment0.2890.1690.361
nmr_exclude_region0.0020.0000.002
nmr_export_data_1r0.2360.1500.296
nmr_get_peak_distances0.0020.0010.003
nmr_identify_regions_blood0.0040.0010.006
nmr_identify_regions_cell0.0030.0000.003
nmr_identify_regions_urine0.0030.0010.005
nmr_integrate_regions0.0020.0010.003
nmr_interpolate_1D0.4550.2940.564
nmr_meta_add0.7700.3930.952
nmr_meta_export0.2090.1510.251
nmr_meta_get0.2010.1370.258
nmr_meta_get_column0.2010.1540.262
nmr_meta_groups0.2060.1550.261
nmr_normalize0.0650.0160.080
nmr_pca_build_model0.5050.3240.644
nmr_pca_outliers0.2840.1680.359
nmr_pca_outliers_filter0.2660.1420.321
nmr_pca_outliers_plot000
nmr_pca_outliers_robust1.6850.2181.801
nmr_pca_plots0.0990.0030.103
nmr_peak_clustering0.0180.0010.018
nmr_ppm_resolution0.0030.0000.004
nmr_read_bruker_fid0.0000.0010.000
nmr_read_samples0.4360.3570.571
nmr_zip_bruker_samples0.1070.0130.123
peaklist_accept_peaks0.0020.0000.002
permutation_test_model0.7660.3701.070
permutation_test_plot2.130.871.10
plot.nmr_dataset_1D0.0010.0010.001
plot_bootstrap_multimodel0.0010.0000.001
plot_interactive0.7880.4071.079
plot_plsda_multimodel0.0630.1010.111
plot_plsda_samples0.0370.0610.095
plot_vip_scores0.0000.0000.001
plot_webgl0.0010.0010.001
plsda_auroc_vip_compare0.1320.1300.258
plsda_auroc_vip_method0.0000.0010.001
ppm_resolution0.0010.0000.001
print.nmr_dataset0.2030.1640.270
print.nmr_dataset_1D0.2420.1830.301
print.nmr_dataset_peak_table0.2650.1750.328
random_subsampling0.0010.0010.002
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.2060.1280.248
sub-.nmr_dataset_1D0.2480.2020.319
sub-.nmr_dataset_peak_table0.2570.1740.320
tidy.nmr_dataset_1D0.1470.1030.316
to_ChemoSpec0.2730.1650.330
validate_nmr_dataset0.4380.3230.538
validate_nmr_dataset_family0.3300.2350.281
validate_nmr_dataset_peak_table000
zzz0.0000.0012.010