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This page was generated on 2021-10-19 12:04:22 -0400 (Tue, 19 Oct 2021).

CHECK results for AlpsNMR on nebbiolo2

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 46/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.3.4  (landing page)
Sergio Oller Moreno
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AlpsNMR_3.3.4.tar.gz
StartedAt: 2021-10-18 19:03:48 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 19:08:14 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 266.5 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AlpsNMR_3.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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        21.877  1.155  23.035
nmr_pca_plots         22.170  0.328  22.498
AlpsNMR-package        5.533  0.232   5.771
bp_kfold_VIP_analysis  0.695  0.053  17.309
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.



Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 13.385   0.586  13.964 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0000.000
AlpsNMR-package5.5330.2325.771
MUVR_model_plot0.0010.0000.000
Peak_detection21.877 1.15523.035
Pipelines0.0010.0010.001
SummarizedExperiment_to_nmr_data_1r0.6850.0310.717
SummarizedExperiment_to_nmr_dataset_peak_table0.6700.0170.687
bp_VIP_analysis1.8310.0901.919
bp_kfold_VIP_analysis 0.695 0.05317.309
confusion_matrix000
file_lister0.0390.0040.043
files_to_rDolphin0.0010.0000.000
filter.nmr_dataset_family0.3880.0160.404
format.nmr_dataset0.3140.0160.330
format.nmr_dataset_1D0.4100.0080.418
format.nmr_dataset_peak_table0.4550.0080.463
is.nmr_dataset0.3150.0240.339
is.nmr_dataset_1D0.3670.0080.375
is.nmr_dataset_peak_table0.4700.0240.494
load_and_save_functions0.3220.0400.362
model_VIP000
models_stability_plot_bootstrap0.0020.0000.001
models_stability_plot_plsda0.2520.0000.251
new_nmr_dataset0.0010.0000.001
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.4400.0040.444
nmr_baseline_removal0.7140.2360.951
nmr_baseline_threshold1.1320.0641.196
nmr_batman0.3990.0110.411
nmr_batman_options000
nmr_data0.4290.0040.432
nmr_data_1r_to_SummarizedExperiment0.6680.0080.676
nmr_data_analysis0.2820.0000.281
nmr_data_analysis_method0.0790.0080.096
nmr_dataset_peak_table_to_SummarizedExperiment0.6780.0320.710
nmr_exclude_region0.0040.0000.004
nmr_export_data_1r0.3870.0280.414
nmr_identify_regions_blood0.0140.0000.014
nmr_identify_regions_cell0.0080.0000.009
nmr_identify_regions_urine0.0120.0000.013
nmr_integrate_regions0.0060.0000.006
nmr_interpolate_1D0.7650.0360.801
nmr_meta_add1.0800.0281.108
nmr_meta_export0.3380.0200.358
nmr_meta_get0.3760.0160.392
nmr_meta_get_column0.3610.0160.378
nmr_normalize0.2580.0040.261
nmr_pca_build_model1.0010.0281.028
nmr_pca_outliers0.4470.0240.471
nmr_pca_outliers_filter0.5380.0160.555
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.3440.0204.365
nmr_pca_plots22.170 0.32822.498
nmr_ppm_resolution0.0070.0000.007
nmr_read_bruker_fid000
nmr_read_samples0.6750.0240.699
nmr_zip_bruker_samples0.2260.0100.236
p_value_perm0.0000.0000.001
permutation_test_model3.0660.0443.110
permutation_test_plot3.2240.0043.227
plot.nmr_dataset_1D0.0000.0000.001
plot_bootstrap_multimodel0.0020.0000.002
plot_interactive0.4270.0160.443
plot_plsda_multimodel0.150.000.15
plot_plsda_samples0.1080.0000.108
plot_vip_scores0.0020.0000.002
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.3840.0000.383
plsda_auroc_vip_method0.0000.0000.001
ppm_VIP_vector000
ppm_resolution0.0030.0000.002
print.nmr_dataset0.3590.0080.367
print.nmr_dataset_1D0.3910.0200.411
print.nmr_dataset_peak_table0.4760.0120.488
random_subsampling0.0020.0000.002
rdCV_PLS_RF0.0000.0000.001
rdCV_PLS_RF_ML000
save_files_to_rDolphin0.0000.0000.001
save_profiling_output000
sub-.nmr_dataset0.3220.0240.346
sub-.nmr_dataset_1D0.4030.0080.411
sub-.nmr_dataset_peak_table0.4740.0240.499
to_ChemoSpec0.5470.0160.563
validate_nmr_dataset0.8040.0240.827
validate_nmr_dataset_family0.3830.0240.408