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This page was generated on 2021-10-23 14:06:51 -0400 (Sat, 23 Oct 2021).

CHECK results for AlpsNMR on merida1

To the developers/maintainers of the AlpsNMR package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 46/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.3.4  (landing page)
Sergio Oller Moreno
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: master
git_last_commit: 37a58ed
git_last_commit_date: 2021-09-16 08:25:44 -0400 (Thu, 16 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlpsNMR
Version: 3.3.4
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_3.3.4.tar.gz
StartedAt: 2021-10-23 00:34:51 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 00:42:19 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 447.9 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_3.3.4.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘3.3.4’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* 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          40.896  0.887  41.839
nmr_pca_plots           32.396  6.730  39.176
nmr_pca_outliers_robust 10.061  0.097  10.184
AlpsNMR-package          5.042  0.238   5.296
permutation_test_plot    5.084  0.015   5.105
bp_kfold_VIP_analysis    0.721  0.062  52.065
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.



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/4.1/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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: dplyr

Attaching package: 'dplyr'

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

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: future
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("AlpsNMR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
 18.779   1.194  19.959 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0000.001
AlpsNMR-package5.0420.2385.296
MUVR_model_plot0.0010.0000.001
Peak_detection40.896 0.88741.839
Pipelines0.0020.0000.002
SummarizedExperiment_to_nmr_data_1r1.0730.0441.119
SummarizedExperiment_to_nmr_dataset_peak_table1.0780.0791.159
bp_VIP_analysis3.3530.1933.569
bp_kfold_VIP_analysis 0.721 0.06252.065
confusion_matrix000
file_lister0.0930.0020.095
files_to_rDolphin0.0000.0000.001
filter.nmr_dataset_family0.6780.0440.723
format.nmr_dataset0.6130.0500.665
format.nmr_dataset_1D0.6950.0660.762
format.nmr_dataset_peak_table0.8570.0490.908
is.nmr_dataset0.6520.0500.704
is.nmr_dataset_1D0.6950.0890.786
is.nmr_dataset_peak_table0.7780.0530.833
load_and_save_functions0.6200.0710.693
model_VIP0.0010.0000.001
models_stability_plot_bootstrap0.0040.0000.004
models_stability_plot_plsda0.4500.0020.452
new_nmr_dataset0.0020.0000.002
new_nmr_dataset_1D0.0020.0000.002
new_nmr_dataset_peak_table0.8460.0510.900
nmr_baseline_removal1.2450.1751.465
nmr_baseline_threshold2.2260.0602.292
nmr_batman0.6350.0430.678
nmr_batman_options0.0010.0000.001
nmr_data0.6990.0590.757
nmr_data_1r_to_SummarizedExperiment1.0200.0431.065
nmr_data_analysis0.4670.0160.483
nmr_data_analysis_method0.1490.0530.216
nmr_dataset_peak_table_to_SummarizedExperiment1.1250.0561.186
nmr_exclude_region0.0050.0000.006
nmr_export_data_1r0.5500.0400.591
nmr_identify_regions_blood0.0210.0000.021
nmr_identify_regions_cell0.0130.0000.014
nmr_identify_regions_urine0.0220.0000.023
nmr_integrate_regions0.010.000.01
nmr_interpolate_1D1.1950.0891.287
nmr_meta_add1.9660.1232.098
nmr_meta_export0.5580.0460.610
nmr_meta_get0.6020.0400.642
nmr_meta_get_column0.6610.0490.711
nmr_normalize0.4120.0030.414
nmr_pca_build_model1.9740.1242.145
nmr_pca_outliers0.7460.0490.836
nmr_pca_outliers_filter0.7770.0740.851
nmr_pca_outliers_plot0.0000.0000.001
nmr_pca_outliers_robust10.061 0.09710.184
nmr_pca_plots32.396 6.73039.176
nmr_ppm_resolution0.0120.0010.013
nmr_read_bruker_fid0.0000.0010.000
nmr_read_samples1.0970.0901.190
nmr_zip_bruker_samples0.2770.0360.318
p_value_perm0.0000.0000.001
permutation_test_model4.9110.0374.952
permutation_test_plot5.0840.0155.105
plot.nmr_dataset_1D0.0010.0000.001
plot_bootstrap_multimodel0.0020.0010.002
plot_interactive0.7000.0480.749
plot_plsda_multimodel0.2700.0020.273
plot_plsda_samples0.1660.0020.168
plot_vip_scores0.0040.0010.003
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.5700.0020.578
plsda_auroc_vip_method000
ppm_VIP_vector0.0000.0000.001
ppm_resolution0.0040.0010.004
print.nmr_dataset0.6160.0490.667
print.nmr_dataset_1D0.6800.0530.735
print.nmr_dataset_peak_table0.8180.0640.884
random_subsampling0.0020.0010.003
rdCV_PLS_RF0.0000.0000.001
rdCV_PLS_RF_ML000
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.6360.0530.711
sub-.nmr_dataset_1D0.7000.0460.747
sub-.nmr_dataset_peak_table0.7130.0540.767
to_ChemoSpec0.9240.0630.988
validate_nmr_dataset1.2800.1191.401
validate_nmr_dataset_family0.6790.0640.743