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This page was generated on 2024-03-04 11:38:50 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 57/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 4.5.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: devel
git_last_commit: 4f8fc6e
git_last_commit_date: 2023-10-24 11:28:03 -0500 (Tue, 24 Oct 2023)
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
merida1macOS 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  

CHECK results for AlpsNMR on merida1


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: 4.5.0
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_4.5.0.tar.gz
StartedAt: 2024-03-01 23:58:42 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-02 00:05:52 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 429.4 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_4.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘4.5.0’
* 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 R 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                      22.483  5.536  23.039
nmr_pca_outliers_robust             15.628  1.153  18.684
permutation_test_plot               10.766  3.634   6.025
SummarizedExperiment_to_nmr_data_1r 12.920  1.426  16.055
print.nmr_dataset                    4.408  3.893   6.024
nmr_pca_outliers_filter              4.525  3.487   6.257
format.nmr_dataset                   3.998  3.405   5.841
nmr_meta_add                         4.115  1.899   5.413
nmr_pca_build_model                  3.769  1.994   5.037
permutation_test_model               4.109  1.559   5.860
nmr_read_samples                     3.341  2.039   4.297
validate_nmr_dataset                 3.344  1.983   4.298
nmr_interpolate_1D                   3.365  1.751   4.379
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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 
 29.299  10.077  34.593 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AlpsNMR-package3.1320.8383.909
HMDB_blood0.0130.0060.021
HMDB_cell0.0060.0030.011
HMDB_urine0.0080.0050.017
Parameters_blood0.0040.0030.007
Parameters_cell0.0030.0030.007
Parameters_urine0.0040.0030.009
Peak_detection22.483 5.53623.039
Pipelines0.0020.0020.004
ROI_blood0.0070.0030.013
ROI_cell0.0070.0030.011
ROI_urine0.0070.0030.012
SummarizedExperiment_to_nmr_data_1r12.920 1.42616.055
SummarizedExperiment_to_nmr_dataset_peak_table2.2090.9252.883
bp_VIP_analysis3.1111.2172.831
bp_kfold_VIP_analysis1.8100.7911.707
download_MTBLS242000
file_lister0.1670.0330.217
files_to_rDolphin0.0000.0010.002
filter.nmr_dataset_family1.8210.9242.394
format.nmr_dataset3.9983.4055.841
format.nmr_dataset_1D1.6780.8722.290
format.nmr_dataset_peak_table1.8500.8972.571
get_integration_with_metadata0.0600.0100.077
hmdb0.1160.0190.149
is.nmr_dataset1.6390.9162.291
is.nmr_dataset_1D1.6810.8952.344
is.nmr_dataset_peak_table1.8050.8712.379
load_and_save_functions1.5330.8132.028
models_stability_plot_bootstrap0.0040.0020.006
models_stability_plot_plsda0.8560.6260.991
new_nmr_dataset0.0030.0020.004
new_nmr_dataset_1D0.0020.0010.003
new_nmr_dataset_peak_table1.7570.7962.241
nmr_baseline_estimation0.2680.0530.378
nmr_baseline_removal0.0090.0020.014
nmr_baseline_threshold0.0020.0010.003
nmr_baseline_threshold_plot0.8730.0851.141
nmr_batman0.0050.0020.008
nmr_batman_options0.0000.0010.002
nmr_build_peak_table0.0780.0130.106
nmr_data0.1140.0170.152
nmr_data_1r_to_SummarizedExperiment2.0680.8322.806
nmr_data_analysis0.8600.5970.999
nmr_dataset0.0020.0000.002
nmr_dataset_1D0.0020.0010.003
nmr_dataset_peak_table_to_SummarizedExperiment3.0521.2974.098
nmr_exclude_region0.0110.0020.014
nmr_export_data_1r1.6400.8302.161
nmr_get_peak_distances0.0170.0030.022
nmr_identify_regions_blood0.0300.0070.042
nmr_identify_regions_cell0.0220.0040.029
nmr_identify_regions_urine0.0320.0060.045
nmr_integrate_regions0.0210.0040.029
nmr_interpolate_1D3.3651.7514.379
nmr_meta_add4.1151.8995.413
nmr_meta_export1.6330.9492.097
nmr_meta_get1.5790.8502.104
nmr_meta_get_column1.7191.0282.693
nmr_meta_groups1.6890.9942.235
nmr_normalize0.7050.1091.041
nmr_pca_build_model3.7691.9945.037
nmr_pca_outliers1.9240.9162.506
nmr_pca_outliers_filter4.5253.4876.257
nmr_pca_outliers_plot0.0000.0000.001
nmr_pca_outliers_robust15.628 1.15318.684
nmr_pca_plots1.0540.0321.312
nmr_peak_clustering0.1440.0030.156
nmr_ppm_resolution0.0150.0040.021
nmr_read_bruker_fid0.0000.0000.001
nmr_read_samples3.3412.0394.297
nmr_zip_bruker_samples0.3350.0720.440
peaklist_accept_peaks0.0080.0020.010
permutation_test_model4.1091.5595.860
permutation_test_plot10.766 3.634 6.025
plot.nmr_dataset_1D0.0020.0050.008
plot_bootstrap_multimodel0.0040.0050.009
plot_interactive1.7250.9512.228
plot_plsda_multimodel0.4580.5330.686
plot_plsda_samples0.2620.3060.568
plot_vip_scores0.0040.0050.008
plot_webgl0.0020.0020.005
plsda_auroc_vip_compare1.2290.7162.046
plsda_auroc_vip_method0.0000.0000.001
ppm_resolution0.0040.0020.008
print.nmr_dataset4.4083.8936.024
print.nmr_dataset_1D1.6290.8121.984
print.nmr_dataset_peak_table1.8581.0082.368
random_subsampling0.0040.0120.017
save_files_to_rDolphin0.0000.0000.001
save_profiling_output0.0000.0010.000
sub-.nmr_dataset1.6350.9882.134
sub-.nmr_dataset_1D1.6320.8131.989
sub-.nmr_dataset_peak_table1.8660.9462.482
tidy.nmr_dataset_1D1.8600.9342.446
to_ChemoSpec1.8940.9142.431
validate_nmr_dataset3.3441.9834.298
validate_nmr_dataset_family1.6470.8972.144
validate_nmr_dataset_peak_table0.0020.0020.004
zzz0.0010.0012.042