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This page was generated on 2021-09-22 15:04:45 -0400 (Wed, 22 Sep 2021).

CHECK results for AlpsNMR on nebbiolo1

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 48/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlpsNMR 3.2.3  (landing page)
Luis Fernandez
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/AlpsNMR
git_branch: RELEASE_3_13
git_last_commit: 92db448
git_last_commit_date: 2021-09-16 08:28:27 -0400 (Thu, 16 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 3.2.3
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz
StartedAt: 2021-09-21 08:49:28 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 08:54:09 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 281.2 seconds
RetCode: 0
Status:   OK  
CheckDir: AlpsNMR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘3.2.3’
* 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        22.116  0.520  22.638
nmr_pca_plots         21.619  0.556  22.175
AlpsNMR-package        5.949  0.289   6.254
bp_kfold_VIP_analysis  0.771  0.066  20.233
* 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-3.13-bioc/meat/AlpsNMR.Rcheck/00check.log’
for details.



Installation output

AlpsNMR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL AlpsNMR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 84 ]
> 
> proc.time()
   user  system elapsed 
 13.722   0.838  14.660 

Example timings

AlpsNMR.Rcheck/AlpsNMR-Ex.timings

nameusersystemelapsed
AUC_model0.0010.0010.001
AlpsNMR-package5.9490.2896.254
MUVR_model_plot0.0010.0000.000
Peak_detection22.116 0.52022.638
Pipelines0.0020.0000.001
SummarizedExperiment_to_nmr_data_1r0.9150.0160.932
SummarizedExperiment_to_nmr_dataset_peak_table0.7750.0280.803
bp_VIP_analysis2.1200.0642.167
bp_kfold_VIP_analysis 0.771 0.06620.233
confusion_matrix000
file_lister0.0680.0000.069
files_to_rDolphin0.0010.0000.001
filter.nmr_dataset_family0.5950.0240.619
format.nmr_dataset0.4240.0360.460
format.nmr_dataset_1D0.4660.0120.478
format.nmr_dataset_peak_table0.5900.0120.601
is.nmr_dataset0.4340.0080.442
is.nmr_dataset_1D0.4890.0240.514
is.nmr_dataset_peak_table0.5670.0230.590
load_and_save_functions0.4190.0040.423
model_VIP000
models_stability_plot_bootstrap0.0020.0000.002
models_stability_plot_plsda0.2680.0040.273
new_nmr_dataset0.0010.0000.002
new_nmr_dataset_1D0.0000.0010.001
new_nmr_dataset_peak_table0.5690.0140.582
nmr_baseline_removal0.8880.1080.995
nmr_baseline_threshold1.2670.0121.279
nmr_batman0.4950.0360.531
nmr_batman_options0.0000.0000.001
nmr_data0.5280.0120.539
nmr_data_1r_to_SummarizedExperiment0.8100.0160.826
nmr_data_analysis0.2910.0120.303
nmr_data_analysis_method0.0940.0130.123
nmr_dataset_peak_table_to_SummarizedExperiment0.8740.0280.902
nmr_exclude_region0.0040.0000.005
nmr_export_data_1r0.5490.0000.550
nmr_identify_regions_blood0.0160.0000.016
nmr_identify_regions_cell0.0090.0000.009
nmr_identify_regions_urine0.0100.0040.014
nmr_integrate_regions0.0070.0000.007
nmr_interpolate_1D0.9750.0761.051
nmr_meta_add1.4190.0511.471
nmr_meta_export0.4300.0150.444
nmr_meta_get0.4650.0160.480
nmr_meta_get_column0.4500.0160.466
nmr_normalize0.2900.0120.301
nmr_pca_build_model1.1890.0521.240
nmr_pca_outliers0.6460.0280.674
nmr_pca_outliers_filter0.6910.0160.707
nmr_pca_outliers_plot000
nmr_pca_outliers_robust4.7510.0604.812
nmr_pca_plots21.619 0.55622.175
nmr_ppm_resolution0.0080.0000.007
nmr_read_bruker_fid0.0010.0000.000
nmr_read_samples0.9140.0160.929
nmr_zip_bruker_samples0.2100.0460.256
p_value_perm0.0010.0000.001
permutation_test_model3.4910.0083.500
permutation_test_plot3.6110.0603.671
plot.nmr_dataset_1D0.0010.0000.001
plot_bootstrap_multimodel0.0030.0000.003
plot_interactive0.5510.0320.582
plot_plsda_multimodel0.1920.0040.195
plot_plsda_samples0.1280.0000.127
plot_vip_scores0.0030.0000.002
plot_webgl0.0010.0000.001
plsda_auroc_vip_compare0.4400.0000.441
plsda_auroc_vip_method0.0000.0010.001
ppm_VIP_vector0.0000.0010.001
ppm_resolution0.0030.0010.003
print.nmr_dataset0.4890.0200.509
print.nmr_dataset_1D0.5360.0120.548
print.nmr_dataset_peak_table0.5790.0200.599
random_subsampling0.0000.0040.005
rdCV_PLS_RF0.0000.0000.001
rdCV_PLS_RF_ML0.0000.0000.001
save_files_to_rDolphin0.0000.0000.001
save_profiling_output000
sub-.nmr_dataset0.4760.0280.504
sub-.nmr_dataset_1D0.5490.0310.580
sub-.nmr_dataset_peak_table0.6220.0160.639
to_ChemoSpec0.5630.0040.567
validate_nmr_dataset0.9560.0320.989
validate_nmr_dataset_family0.5740.0200.594