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This page was generated on 2024-05-04 11:38:49 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 4.6.0
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: 2024-05-03 20:04:44 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:08:26 -0400 (Fri, 03 May 2024)
EllapsedTime: 222.0 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 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* 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                      10.593  2.824   9.362
SummarizedExperiment_to_nmr_data_1r  7.593  0.834   8.068
nmr_pca_outliers_robust              6.653  0.920   7.165
permutation_test_plot                3.892  1.520   2.908
* 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-x86_64/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 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 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)
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 
 17.509   6.812  19.070 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package2.0160.4822.143
HMDB_blood0.0070.0030.010
HMDB_cell0.0020.0010.004
HMDB_urine0.0030.0020.005
Parameters_blood0.0020.0020.003
Parameters_cell0.0020.0010.003
Parameters_urine0.0030.0020.004
Peak_detection10.593 2.824 9.362
Pipelines0.0010.0010.002
ROI_blood0.0030.0020.005
ROI_cell0.0040.0010.005
ROI_urine0.0040.0020.006
SummarizedExperiment_to_nmr_data_1r7.5930.8348.068
SummarizedExperiment_to_nmr_dataset_peak_table1.1610.5511.319
bp_VIP_analysis1.6640.8371.475
bp_kfold_VIP_analysis0.8830.3890.776
download_MTBLS242000
file_lister0.0670.0130.083
files_to_rDolphin0.0000.0010.001
filter.nmr_dataset_family1.7030.7272.019
format.nmr_dataset0.8250.4870.957
format.nmr_dataset_1D0.9280.5571.099
format.nmr_dataset_peak_table1.0150.5421.187
get_integration_with_metadata0.0300.0030.033
hmdb0.0630.0080.071
is.nmr_dataset0.8860.5330.968
is.nmr_dataset_1D0.9620.6121.164
is.nmr_dataset_peak_table0.9990.5441.188
load_and_save_functions0.4790.3231.067
models_stability_plot_bootstrap0.0020.0010.004
models_stability_plot_plsda0.5080.4000.575
new_nmr_dataset0.0020.0010.002
new_nmr_dataset_1D0.0010.0010.002
new_nmr_dataset_peak_table2.9651.7493.511
nmr_baseline_estimation0.1420.0150.161
nmr_baseline_removal0.0060.0010.007
nmr_baseline_threshold0.0020.0010.001
nmr_baseline_threshold_plot0.2160.0060.224
nmr_batman0.0030.0000.004
nmr_batman_options000
nmr_build_peak_table0.0410.0020.043
nmr_data0.0560.0070.063
nmr_data_1r_to_SummarizedExperiment0.5450.2091.483
nmr_data_analysis1.3401.0960.777
nmr_dataset0.0010.0010.002
nmr_dataset_1D0.0010.0000.002
nmr_dataset_peak_table_to_SummarizedExperiment1.2560.6461.394
nmr_exclude_region0.0070.0020.008
nmr_export_data_1r1.0040.5791.203
nmr_get_peak_distances0.0100.0010.011
nmr_identify_regions_blood0.0180.0040.021
nmr_identify_regions_cell0.0120.0030.014
nmr_identify_regions_urine0.0160.0030.019
nmr_integrate_regions0.0140.0020.016
nmr_interpolate_1D1.8611.0822.188
nmr_meta_add2.2361.1392.494
nmr_meta_export0.8990.5661.015
nmr_meta_get0.8720.5261.017
nmr_meta_get_column0.9710.6401.172
nmr_meta_groups0.9870.6461.140
nmr_normalize0.3060.0430.353
nmr_pca_build_model2.1951.4502.869
nmr_pca_outliers1.8620.7592.234
nmr_pca_outliers_filter1.0580.5501.247
nmr_pca_outliers_plot0.0000.0000.001
nmr_pca_outliers_robust6.6530.9207.165
nmr_pca_plots0.3460.0080.359
nmr_peak_clustering0.0780.0010.079
nmr_ppm_resolution0.0080.0020.011
nmr_read_bruker_fid000
nmr_read_samples1.8081.2462.263
nmr_zip_bruker_samples0.2360.0450.299
peaklist_accept_peaks0.0320.0270.060
permutation_test_model0.4920.3482.744
permutation_test_plot3.8921.5202.908
plot.nmr_dataset_1D3.5801.0370.034
plot_bootstrap_multimodel0.0020.0180.021
plot_interactive0.9360.5561.094
plot_plsda_multimodel0.2870.3520.425
plot_plsda_samples0.1670.2140.369
plot_vip_scores0.0020.0020.004
plot_webgl0.0020.0010.003
plsda_auroc_vip_compare0.5680.4691.009
plsda_auroc_vip_method000
ppm_resolution0.0020.0010.003
print.nmr_dataset0.9360.6821.113
print.nmr_dataset_1D0.9250.5471.079
print.nmr_dataset_peak_table1.0570.6431.327
random_subsampling0.0020.0040.006
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.8090.5170.949
sub-.nmr_dataset_1D1.0260.6311.274
sub-.nmr_dataset_peak_table1.0470.5991.265
tidy.nmr_dataset_1D1.1540.6811.356
to_ChemoSpec1.0880.6491.300
validate_nmr_dataset1.9831.3802.449
validate_nmr_dataset_family1.0930.7681.301
validate_nmr_dataset_peak_table0.0020.0000.002
zzz0.0010.0002.131