Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
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. |
Package 48/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 3.2.3 (landing page) Luis Fernandez
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: AlpsNMR |
Version: 3.2.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz |
StartedAt: 2021-10-14 16:10:38 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:17:45 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 426.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AlpsNMR_3.2.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘3.2.3’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 31.959 9.354 41.339 Peak_detection 39.566 1.075 40.659 nmr_pca_outliers_robust 9.463 0.153 9.629 AlpsNMR-package 5.009 0.228 5.247 bp_kfold_VIP_analysis 0.745 0.047 45.081 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/AlpsNMR.Rcheck/00check.log’ for details.
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/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)
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-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 84 ] > > proc.time() user system elapsed 17.856 1.150 19.065
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AUC_model | 0.000 | 0.000 | 0.001 | |
AlpsNMR-package | 5.009 | 0.228 | 5.247 | |
MUVR_model_plot | 0.001 | 0.000 | 0.001 | |
Peak_detection | 39.566 | 1.075 | 40.659 | |
Pipelines | 0.001 | 0.001 | 0.002 | |
SummarizedExperiment_to_nmr_data_1r | 1.093 | 0.163 | 1.256 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.166 | 0.090 | 1.258 | |
bp_VIP_analysis | 3.438 | 0.081 | 3.528 | |
bp_kfold_VIP_analysis | 0.745 | 0.047 | 45.081 | |
confusion_matrix | 0.001 | 0.001 | 0.001 | |
file_lister | 0.111 | 0.003 | 0.113 | |
files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
filter.nmr_dataset_family | 0.667 | 0.075 | 0.744 | |
format.nmr_dataset | 0.581 | 0.077 | 0.659 | |
format.nmr_dataset_1D | 0.719 | 0.108 | 0.829 | |
format.nmr_dataset_peak_table | 0.918 | 0.091 | 1.010 | |
is.nmr_dataset | 0.600 | 0.077 | 0.678 | |
is.nmr_dataset_1D | 0.716 | 0.131 | 0.847 | |
is.nmr_dataset_peak_table | 0.845 | 0.089 | 0.936 | |
load_and_save_functions | 0.605 | 0.078 | 0.687 | |
model_VIP | 0.001 | 0.000 | 0.000 | |
models_stability_plot_bootstrap | 0.003 | 0.002 | 0.004 | |
models_stability_plot_plsda | 0.523 | 0.054 | 0.577 | |
new_nmr_dataset | 0.002 | 0.000 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_peak_table | 0.788 | 0.085 | 0.877 | |
nmr_baseline_removal | 1.191 | 0.149 | 1.345 | |
nmr_baseline_threshold | 2.483 | 0.154 | 2.640 | |
nmr_batman | 0.671 | 0.074 | 0.745 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_data | 0.654 | 0.074 | 0.728 | |
nmr_data_1r_to_SummarizedExperiment | 1.077 | 0.107 | 1.226 | |
nmr_data_analysis | 0.483 | 0.003 | 0.486 | |
nmr_data_analysis_method | 0.125 | 0.038 | 0.176 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.979 | 0.083 | 1.063 | |
nmr_exclude_region | 0.005 | 0.000 | 0.005 | |
nmr_export_data_1r | 0.672 | 0.073 | 0.746 | |
nmr_identify_regions_blood | 0.026 | 0.002 | 0.028 | |
nmr_identify_regions_cell | 0.012 | 0.001 | 0.013 | |
nmr_identify_regions_urine | 0.029 | 0.001 | 0.031 | |
nmr_integrate_regions | 0.012 | 0.000 | 0.013 | |
nmr_interpolate_1D | 1.160 | 0.135 | 1.296 | |
nmr_meta_add | 1.862 | 0.165 | 2.029 | |
nmr_meta_export | 0.552 | 0.060 | 0.613 | |
nmr_meta_get | 0.589 | 0.062 | 0.655 | |
nmr_meta_get_column | 0.546 | 0.071 | 0.619 | |
nmr_normalize | 0.305 | 0.008 | 0.312 | |
nmr_pca_build_model | 1.430 | 0.147 | 1.639 | |
nmr_pca_outliers | 0.855 | 0.073 | 0.930 | |
nmr_pca_outliers_filter | 1.126 | 0.113 | 1.245 | |
nmr_pca_outliers_plot | 0.000 | 0.001 | 0.000 | |
nmr_pca_outliers_robust | 9.463 | 0.153 | 9.629 | |
nmr_pca_plots | 31.959 | 9.354 | 41.339 | |
nmr_ppm_resolution | 0.011 | 0.002 | 0.014 | |
nmr_read_bruker_fid | 0.001 | 0.000 | 0.000 | |
nmr_read_samples | 1.123 | 0.169 | 1.334 | |
nmr_zip_bruker_samples | 0.261 | 0.045 | 0.308 | |
p_value_perm | 0.001 | 0.000 | 0.000 | |
permutation_test_model | 4.730 | 0.016 | 4.751 | |
permutation_test_plot | 4.219 | 0.020 | 4.241 | |
plot.nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
plot_bootstrap_multimodel | 0.003 | 0.001 | 0.003 | |
plot_interactive | 0.742 | 0.070 | 0.856 | |
plot_plsda_multimodel | 0.256 | 0.003 | 0.259 | |
plot_plsda_samples | 0.153 | 0.002 | 0.156 | |
plot_vip_scores | 0.002 | 0.001 | 0.003 | |
plot_webgl | 0.001 | 0.001 | 0.002 | |
plsda_auroc_vip_compare | 0.537 | 0.005 | 0.543 | |
plsda_auroc_vip_method | 0.000 | 0.001 | 0.001 | |
ppm_VIP_vector | 0 | 0 | 0 | |
ppm_resolution | 0.002 | 0.000 | 0.003 | |
print.nmr_dataset | 0.609 | 0.077 | 0.687 | |
print.nmr_dataset_1D | 0.713 | 0.075 | 0.788 | |
print.nmr_dataset_peak_table | 0.723 | 0.063 | 0.786 | |
random_subsampling | 0.002 | 0.004 | 0.006 | |
rdCV_PLS_RF | 0.001 | 0.000 | 0.000 | |
rdCV_PLS_RF_ML | 0.000 | 0.001 | 0.000 | |
save_files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
save_profiling_output | 0.001 | 0.001 | 0.001 | |
sub-.nmr_dataset | 0.501 | 0.081 | 0.582 | |
sub-.nmr_dataset_1D | 0.707 | 0.067 | 0.776 | |
sub-.nmr_dataset_peak_table | 0.789 | 0.073 | 0.863 | |
to_ChemoSpec | 0.837 | 0.102 | 0.940 | |
validate_nmr_dataset | 1.278 | 0.163 | 1.442 | |
validate_nmr_dataset_family | 0.659 | 0.073 | 0.732 | |