Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:04:50 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

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 46/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.4.0  (landing page)
Sergio Oller Moreno
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_14
git_last_commit: 8ef0246
git_last_commit_date: 2021-10-26 13:05:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AlpsNMR
Version: 3.4.0
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_3.4.0.tar.gz
StartedAt: 2022-01-20 06:16:16 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 06:21:01 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 284.2 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘3.4.0’
* 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 ... 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
nmr_pca_plots         25.770  0.376  26.146
Peak_detection        22.338  0.456  22.797
AlpsNMR-package        4.968  0.228   5.204
bp_kfold_VIP_analysis  0.984  0.167  20.703
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 13.847   0.776  14.616 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0000.001
AlpsNMR-package4.9680.2285.204
MUVR_model_plot000
Peak_detection22.338 0.45622.797
Pipelines0.0010.0000.001
SummarizedExperiment_to_nmr_data_1r0.740.020.76
SummarizedExperiment_to_nmr_dataset_peak_table0.7720.0080.781
bp_VIP_analysis2.1350.1832.316
bp_kfold_VIP_analysis 0.984 0.16720.703
confusion_matrix000
file_lister0.0500.0080.057
files_to_rDolphin0.0010.0000.000
filter.nmr_dataset_family0.5000.0720.572
format.nmr_dataset0.3810.0910.474
format.nmr_dataset_1D0.4740.0680.542
format.nmr_dataset_peak_table0.4840.0430.528
is.nmr_dataset0.3700.0280.398
is.nmr_dataset_1D0.4020.0080.410
is.nmr_dataset_peak_table0.4620.0440.506
load_and_save_functions0.3460.0840.430
model_VIP0.0010.0000.000
models_stability_plot_bootstrap0.0020.0000.002
models_stability_plot_plsda0.2760.0240.301
new_nmr_dataset0.0000.0010.001
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.4880.0410.528
nmr_baseline_removal0.9080.2911.200
nmr_baseline_threshold1.2500.0681.324
nmr_batman0.4270.0230.450
nmr_batman_options000
nmr_data0.4850.0080.493
nmr_data_1r_to_SummarizedExperiment0.6660.0440.710
nmr_data_analysis0.3400.0080.348
nmr_data_analysis_method0.0920.0060.105
nmr_dataset_peak_table_to_SummarizedExperiment0.6830.0120.696
nmr_exclude_region0.0040.0000.003
nmr_export_data_1r0.3820.0160.398
nmr_identify_regions_blood0.0160.0000.015
nmr_identify_regions_cell0.0090.0000.008
nmr_identify_regions_urine0.0320.0040.035
nmr_integrate_regions0.0060.0000.006
nmr_interpolate_1D0.7610.0280.790
nmr_meta_add1.2310.0761.307
nmr_meta_export0.3330.0080.341
nmr_meta_get0.4020.0280.430
nmr_meta_get_column0.4050.0400.444
nmr_normalize0.2720.0040.276
nmr_pca_build_model1.9250.3482.273
nmr_pca_outliers0.5380.0880.626
nmr_pca_outliers_filter0.6060.0120.618
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.3610.1124.474
nmr_pca_plots25.770 0.37626.146
nmr_ppm_resolution0.0090.0000.009
nmr_read_bruker_fid000
nmr_read_samples0.8710.0320.903
nmr_zip_bruker_samples0.2600.0120.271
p_value_perm0.0000.0000.001
permutation_test_model3.7570.0003.757
permutation_test_plot4.1710.0404.211
plot.nmr_dataset_1D0.0010.0000.001
plot_bootstrap_multimodel0.0020.0000.002
plot_interactive0.5260.0200.546
plot_plsda_multimodel0.2100.0000.211
plot_plsda_samples0.1400.0000.139
plot_vip_scores0.0020.0000.003
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.4660.0040.470
plsda_auroc_vip_method000
ppm_VIP_vector0.0000.0000.001
ppm_resolution0.0020.0000.003
print.nmr_dataset0.4700.0080.478
print.nmr_dataset_1D0.5150.0120.528
print.nmr_dataset_peak_table0.6140.0200.634
random_subsampling0.0010.0000.002
rdCV_PLS_RF0.0000.0000.001
rdCV_PLS_RF_ML0.0010.0000.000
save_files_to_rDolphin000
save_profiling_output0.0010.0000.000
sub-.nmr_dataset0.4050.0000.406
sub-.nmr_dataset_1D0.5280.0080.536
sub-.nmr_dataset_peak_table0.5650.0120.578
to_ChemoSpec0.7110.0480.759
validate_nmr_dataset0.9790.0241.003
validate_nmr_dataset_family0.5740.0120.587