Back to Multiple platform build/check report for BioC 3.14
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-21 13:07:21 -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 machv2


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: /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_3.4.0.tar.gz
StartedAt: 2022-01-20 09:56:22 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 10:04:44 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 502.0 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘3.4.0’
* 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           36.773 10.800  47.656
Peak_detection          45.993  1.066  47.095
nmr_pca_outliers_robust 11.728  0.152  11.890
permutation_test_plot    5.523  0.018   5.544
AlpsNMR-package          5.228  0.279   5.517
permutation_test_model   5.427  0.011   5.442
bp_kfold_VIP_analysis    0.684  0.022  57.185
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 21.336   1.476  22.925 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0010.001
AlpsNMR-package5.2280.2795.517
MUVR_model_plot0.0000.0000.001
Peak_detection45.993 1.06647.095
Pipelines0.0020.0060.063
SummarizedExperiment_to_nmr_data_1r1.3140.1171.470
SummarizedExperiment_to_nmr_dataset_peak_table1.1160.0921.211
bp_VIP_analysis3.7290.0893.830
bp_kfold_VIP_analysis 0.684 0.02257.185
confusion_matrix0.0010.0000.001
file_lister0.1010.0020.104
files_to_rDolphin0.0000.0000.001
filter.nmr_dataset_family0.8540.0790.936
format.nmr_dataset0.6500.0880.740
format.nmr_dataset_1D0.7450.1030.853
format.nmr_dataset_peak_table0.8230.0860.910
is.nmr_dataset0.6680.0850.754
is.nmr_dataset_1D0.7300.1100.841
is.nmr_dataset_peak_table0.8380.0880.925
load_and_save_functions0.6640.0770.745
model_VIP0.0000.0000.001
models_stability_plot_bootstrap0.0040.0010.005
models_stability_plot_plsda0.5250.0030.528
new_nmr_dataset0.0030.0010.004
new_nmr_dataset_1D0.0020.0010.003
new_nmr_dataset_peak_table0.8360.1050.941
nmr_baseline_removal1.2730.1951.472
nmr_baseline_threshold2.8260.1322.961
nmr_batman0.7170.0840.800
nmr_batman_options0.0010.0000.000
nmr_data0.8680.0940.962
nmr_data_1r_to_SummarizedExperiment1.1640.0871.254
nmr_data_analysis0.5600.0030.563
nmr_data_analysis_method0.1470.0440.206
nmr_dataset_peak_table_to_SummarizedExperiment1.1240.0961.223
nmr_exclude_region0.0080.0010.008
nmr_export_data_1r0.7570.0750.833
nmr_identify_regions_blood0.0330.0020.034
nmr_identify_regions_cell0.0230.0010.024
nmr_identify_regions_urine0.0280.0010.030
nmr_integrate_regions0.0120.0010.013
nmr_interpolate_1D1.5120.1671.682
nmr_meta_add2.2610.1982.543
nmr_meta_export0.5960.0740.670
nmr_meta_get0.7380.0820.820
nmr_meta_get_column0.7630.0760.859
nmr_normalize0.5090.0080.517
nmr_pca_build_model1.7680.1711.957
nmr_pca_outliers0.9260.0951.023
nmr_pca_outliers_filter1.1340.1521.287
nmr_pca_outliers_plot0.0000.0010.000
nmr_pca_outliers_robust11.728 0.15211.890
nmr_pca_plots36.77310.80047.656
nmr_ppm_resolution0.0100.0010.012
nmr_read_bruker_fid0.0000.0000.001
nmr_read_samples1.4340.1751.636
nmr_zip_bruker_samples0.3100.0500.364
p_value_perm0.0000.0000.001
permutation_test_model5.4270.0115.442
permutation_test_plot5.5230.0185.544
plot.nmr_dataset_1D0.0010.0000.001
plot_bootstrap_multimodel0.0030.0010.004
plot_interactive0.7330.0780.812
plot_plsda_multimodel0.2900.0020.293
plot_plsda_samples0.1790.0030.182
plot_vip_scores0.0020.0010.004
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.6380.0210.661
plsda_auroc_vip_method000
ppm_VIP_vector0.0010.0010.000
ppm_resolution0.0020.0000.003
print.nmr_dataset0.7120.0800.793
print.nmr_dataset_1D0.8260.0951.002
print.nmr_dataset_peak_table0.8440.0920.938
random_subsampling0.0020.0070.009
rdCV_PLS_RF0.0000.0000.001
rdCV_PLS_RF_ML000
save_files_to_rDolphin0.0000.0010.001
save_profiling_output0.0000.0000.001
sub-.nmr_dataset0.5860.0750.662
sub-.nmr_dataset_1D0.7640.1040.869
sub-.nmr_dataset_peak_table0.9010.0820.985
to_ChemoSpec0.9550.1161.072
validate_nmr_dataset1.3370.1601.501
validate_nmr_dataset_family0.7590.0870.847