Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:16 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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: 2022-01-16 01:55:05 -0500 (Sun, 16 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: 2022-01-16 10:02:32 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 10:10:45 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 493.0 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_3.4.0.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           36.658 10.897  47.594
Peak_detection          44.689  1.121  45.851
nmr_pca_outliers_robust 11.951  0.161  12.153
AlpsNMR-package          5.700  0.316   6.036
permutation_test_model   5.687  0.034   5.725
permutation_test_plot    5.585  0.019   5.610
bp_kfold_VIP_analysis    0.755  0.023  54.049
* 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 
 21.142   1.438  22.708 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0000.001
AlpsNMR-package5.7000.3166.036
MUVR_model_plot0.0000.0000.001
Peak_detection44.689 1.12145.851
Pipelines0.0020.0020.003
SummarizedExperiment_to_nmr_data_1r1.1370.1291.269
SummarizedExperiment_to_nmr_dataset_peak_table1.1180.0821.203
bp_VIP_analysis3.6510.1023.765
bp_kfold_VIP_analysis 0.755 0.02354.049
confusion_matrix0.0010.0000.001
file_lister0.1080.0020.111
files_to_rDolphin0.0000.0010.001
filter.nmr_dataset_family0.7510.0860.838
format.nmr_dataset0.6420.0800.723
format.nmr_dataset_1D0.8070.1250.932
format.nmr_dataset_peak_table0.8460.0870.934
is.nmr_dataset0.6830.0930.777
is.nmr_dataset_1D0.7860.1260.917
is.nmr_dataset_peak_table0.9590.1091.135
load_and_save_functions0.7220.0850.810
model_VIP0.0010.0000.001
models_stability_plot_bootstrap0.0030.0010.005
models_stability_plot_plsda0.5310.0020.532
new_nmr_dataset0.0030.0010.004
new_nmr_dataset_1D0.0030.0010.003
new_nmr_dataset_peak_table0.8960.1211.060
nmr_baseline_removal1.3490.1831.538
nmr_baseline_threshold2.7930.1352.931
nmr_batman0.7250.0790.916
nmr_batman_options0.0010.0000.000
nmr_data0.7220.0890.812
nmr_data_1r_to_SummarizedExperiment1.1980.0871.287
nmr_data_analysis0.4890.0030.492
nmr_data_analysis_method0.1340.0380.189
nmr_dataset_peak_table_to_SummarizedExperiment1.2100.1091.323
nmr_exclude_region0.0080.0010.008
nmr_export_data_1r0.7250.0820.807
nmr_identify_regions_blood0.0200.0010.021
nmr_identify_regions_cell0.0200.0010.021
nmr_identify_regions_urine0.0300.0010.030
nmr_integrate_regions0.0110.0000.012
nmr_interpolate_1D1.5530.1991.756
nmr_meta_add1.9950.1772.217
nmr_meta_export0.5960.0830.681
nmr_meta_get0.6770.0830.764
nmr_meta_get_column0.7440.0820.825
nmr_normalize0.4950.0100.505
nmr_pca_build_model1.7770.1741.991
nmr_pca_outliers0.9110.0931.004
nmr_pca_outliers_filter1.1000.1851.301
nmr_pca_outliers_plot000
nmr_pca_outliers_robust11.951 0.16112.153
nmr_pca_plots36.65810.89747.594
nmr_ppm_resolution0.0110.0020.013
nmr_read_bruker_fid0.0000.0000.001
nmr_read_samples1.3150.2151.580
nmr_zip_bruker_samples0.2730.0470.321
p_value_perm0.0000.0010.001
permutation_test_model5.6870.0345.725
permutation_test_plot5.5850.0195.610
plot.nmr_dataset_1D0.0010.0000.002
plot_bootstrap_multimodel0.0030.0010.003
plot_interactive0.7150.0820.799
plot_plsda_multimodel0.2500.0030.252
plot_plsda_samples0.2000.0070.207
plot_vip_scores0.0030.0020.005
plot_webgl0.0010.0010.002
plsda_auroc_vip_compare0.5720.0050.577
plsda_auroc_vip_method0.0010.0010.000
ppm_VIP_vector0.0000.0000.001
ppm_resolution0.0030.0000.004
print.nmr_dataset0.6220.0750.699
print.nmr_dataset_1D0.7200.0870.808
print.nmr_dataset_peak_table0.9090.0881.040
random_subsampling0.0020.0050.008
rdCV_PLS_RF0.0010.0000.001
rdCV_PLS_RF_ML0.0010.0000.001
save_files_to_rDolphin0.0000.0000.001
save_profiling_output000
sub-.nmr_dataset0.6970.0740.773
sub-.nmr_dataset_1D0.8050.0940.900
sub-.nmr_dataset_peak_table0.8280.0770.906
to_ChemoSpec1.0040.1391.145
validate_nmr_dataset1.4350.1511.589
validate_nmr_dataset_family0.7400.0820.824