Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:03 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (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: 2022-04-12 06:21:03 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:25:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 268.4 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_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘3.4.0’
* 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
Peak_detection        22.596  0.572  23.169
nmr_pca_plots         21.971  0.356  22.327
AlpsNMR-package        5.203  0.536   5.746
bp_kfold_VIP_analysis  0.742  0.032  17.708
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
 13.302   0.748  14.039 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0000.000
AlpsNMR-package5.2030.5365.746
MUVR_model_plot000
Peak_detection22.596 0.57223.169
Pipelines0.0010.0000.001
SummarizedExperiment_to_nmr_data_1r0.7300.0120.741
SummarizedExperiment_to_nmr_dataset_peak_table0.6820.0080.691
bp_VIP_analysis1.8870.1101.993
bp_kfold_VIP_analysis 0.742 0.03217.708
confusion_matrix000
file_lister0.0400.0040.044
files_to_rDolphin000
filter.nmr_dataset_family0.4290.0120.441
format.nmr_dataset0.3480.0120.360
format.nmr_dataset_1D0.4110.0160.428
format.nmr_dataset_peak_table0.4770.0280.504
is.nmr_dataset0.3590.0000.359
is.nmr_dataset_1D0.4050.0120.417
is.nmr_dataset_peak_table0.4650.0200.485
load_and_save_functions0.3550.0200.376
model_VIP000
models_stability_plot_bootstrap0.0010.0000.002
models_stability_plot_plsda0.3160.0000.316
new_nmr_dataset0.0020.0000.001
new_nmr_dataset_1D0.0010.0000.001
new_nmr_dataset_peak_table0.4650.0040.470
nmr_baseline_removal0.8130.0800.894
nmr_baseline_threshold1.2850.0281.313
nmr_batman0.3850.0200.404
nmr_batman_options000
nmr_data0.4590.0120.471
nmr_data_1r_to_SummarizedExperiment0.7100.0120.721
nmr_data_analysis0.3230.0000.322
nmr_data_analysis_method0.0850.0100.123
nmr_dataset_peak_table_to_SummarizedExperiment0.6660.0450.709
nmr_exclude_region0.0040.0000.004
nmr_export_data_1r0.4290.0030.433
nmr_identify_regions_blood0.0160.0000.016
nmr_identify_regions_cell0.0090.0000.010
nmr_identify_regions_urine0.0130.0000.013
nmr_integrate_regions0.0080.0000.008
nmr_interpolate_1D0.8060.0230.829
nmr_meta_add1.2650.0331.298
nmr_meta_export0.3300.0110.341
nmr_meta_get0.3810.0090.389
nmr_meta_get_column0.4220.0070.430
nmr_normalize0.2330.0000.234
nmr_pca_build_model1.0130.0311.046
nmr_pca_outliers0.5210.0190.540
nmr_pca_outliers_filter0.6290.0080.637
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.5340.0514.586
nmr_pca_plots21.971 0.35622.327
nmr_ppm_resolution0.0070.0000.007
nmr_read_bruker_fid0.0010.0000.000
nmr_read_samples0.7410.0320.772
nmr_zip_bruker_samples0.2200.0220.243
p_value_perm0.0000.0000.001
permutation_test_model3.5200.0163.536
permutation_test_plot3.6850.0243.710
plot.nmr_dataset_1D0.0010.0000.000
plot_bootstrap_multimodel0.0020.0000.002
plot_interactive0.4320.0200.451
plot_plsda_multimodel0.1860.0000.186
plot_plsda_samples0.1360.0040.140
plot_vip_scores0.0020.0000.002
plot_webgl000
plsda_auroc_vip_compare1.1430.0161.159
plsda_auroc_vip_method000
ppm_VIP_vector000
ppm_resolution0.0020.0000.003
print.nmr_dataset0.3420.0120.355
print.nmr_dataset_1D0.3890.0200.408
print.nmr_dataset_peak_table0.5170.0040.521
random_subsampling0.0020.0000.002
rdCV_PLS_RF0.0010.0000.000
rdCV_PLS_RF_ML0.0000.0000.001
save_files_to_rDolphin000
save_profiling_output000
sub-.nmr_dataset0.3570.0160.373
sub-.nmr_dataset_1D0.4210.0240.445
sub-.nmr_dataset_peak_table0.4960.0120.507
to_ChemoSpec0.5660.0200.585
validate_nmr_dataset0.7520.0320.784
validate_nmr_dataset_family0.4220.0040.427