| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:29 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 | ||||
| Package 56/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.4.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the AlpsNMR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: AlpsNMR |
| Version: 4.4.0 |
| 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_4.4.0.tar.gz |
| StartedAt: 2024-04-15 23:11:10 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 23:17:52 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 402.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_4.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.4.0’
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Peak_detection 20.502 4.401 18.633
nmr_pca_outliers_robust 15.056 1.091 16.473
SummarizedExperiment_to_nmr_data_1r 13.236 1.285 15.104
bp_VIP_analysis 4.829 3.201 4.582
format.nmr_dataset_peak_table 4.234 3.098 5.203
filter.nmr_dataset_family 4.078 3.010 4.853
nmr_meta_add 4.164 2.029 4.959
permutation_test_plot 4.115 1.582 5.503
permutation_test_model 4.075 1.505 5.521
nmr_pca_build_model 3.654 1.901 4.249
nmr_read_samples 3.321 2.079 3.869
nmr_interpolate_1D 3.348 1.832 4.184
* 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: OK
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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: future
Attaching package: 'AlpsNMR'
The following object is masked from 'package:stats':
filter
>
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]
>
> proc.time()
user system elapsed
28.916 10.244 31.668
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 3.063 | 0.772 | 3.549 | |
| HMDB_blood | 0.012 | 0.005 | 0.018 | |
| HMDB_cell | 0.005 | 0.002 | 0.007 | |
| HMDB_urine | 0.008 | 0.004 | 0.013 | |
| Parameters_blood | 0.004 | 0.004 | 0.008 | |
| Parameters_cell | 0.003 | 0.003 | 0.008 | |
| Parameters_urine | 0.003 | 0.003 | 0.008 | |
| Peak_detection | 20.502 | 4.401 | 18.633 | |
| Pipelines | 0.003 | 0.002 | 0.005 | |
| ROI_blood | 0.007 | 0.003 | 0.011 | |
| ROI_cell | 0.006 | 0.003 | 0.010 | |
| ROI_urine | 0.007 | 0.003 | 0.010 | |
| SummarizedExperiment_to_nmr_data_1r | 13.236 | 1.285 | 15.104 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 2.132 | 0.864 | 2.378 | |
| bp_VIP_analysis | 4.829 | 3.201 | 4.582 | |
| bp_kfold_VIP_analysis | 1.716 | 0.644 | 1.467 | |
| download_MTBLS242 | 0.000 | 0.001 | 0.001 | |
| file_lister | 0.164 | 0.033 | 0.206 | |
| files_to_rDolphin | 0.000 | 0.001 | 0.002 | |
| filter.nmr_dataset_family | 4.078 | 3.010 | 4.853 | |
| format.nmr_dataset | 1.578 | 0.859 | 2.026 | |
| format.nmr_dataset_1D | 1.644 | 0.873 | 2.086 | |
| format.nmr_dataset_peak_table | 4.234 | 3.098 | 5.203 | |
| get_integration_with_metadata | 0.048 | 0.001 | 0.054 | |
| hmdb | 0.100 | 0.007 | 0.118 | |
| is.nmr_dataset | 1.575 | 0.893 | 1.935 | |
| is.nmr_dataset_1D | 1.624 | 0.836 | 1.919 | |
| is.nmr_dataset_peak_table | 1.818 | 0.974 | 2.520 | |
| load_and_save_functions | 1.560 | 0.844 | 2.002 | |
| models_stability_plot_bootstrap | 0.003 | 0.003 | 0.007 | |
| models_stability_plot_plsda | 0.836 | 0.601 | 0.948 | |
| new_nmr_dataset | 0.002 | 0.002 | 0.004 | |
| new_nmr_dataset_1D | 0.003 | 0.001 | 0.003 | |
| new_nmr_dataset_peak_table | 1.843 | 0.965 | 2.304 | |
| nmr_baseline_estimation | 0.278 | 0.060 | 0.412 | |
| nmr_baseline_removal | 0.009 | 0.003 | 0.013 | |
| nmr_baseline_threshold | 0.002 | 0.001 | 0.006 | |
| nmr_baseline_threshold_plot | 0.883 | 0.136 | 1.141 | |
| nmr_batman | 0.005 | 0.001 | 0.006 | |
| nmr_batman_options | 0.000 | 0.000 | 0.001 | |
| nmr_build_peak_table | 0.064 | 0.003 | 0.074 | |
| nmr_data | 0.098 | 0.003 | 0.115 | |
| nmr_data_1r_to_SummarizedExperiment | 2.070 | 0.914 | 2.716 | |
| nmr_data_analysis | 0.845 | 0.523 | 0.931 | |
| nmr_dataset | 0.002 | 0.001 | 0.002 | |
| nmr_dataset_1D | 0.002 | 0.001 | 0.003 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 2.102 | 0.950 | 2.695 | |
| nmr_exclude_region | 0.011 | 0.003 | 0.016 | |
| nmr_export_data_1r | 1.744 | 0.918 | 2.480 | |
| nmr_get_peak_distances | 0.015 | 0.002 | 0.022 | |
| nmr_identify_regions_blood | 0.029 | 0.004 | 0.039 | |
| nmr_identify_regions_cell | 0.022 | 0.002 | 0.032 | |
| nmr_identify_regions_urine | 0.031 | 0.002 | 0.043 | |
| nmr_integrate_regions | 0.020 | 0.003 | 0.028 | |
| nmr_interpolate_1D | 3.348 | 1.832 | 4.184 | |
| nmr_meta_add | 4.164 | 2.029 | 4.959 | |
| nmr_meta_export | 1.529 | 0.871 | 1.775 | |
| nmr_meta_get | 1.630 | 0.937 | 1.826 | |
| nmr_meta_get_column | 1.596 | 0.831 | 1.864 | |
| nmr_meta_groups | 1.667 | 0.931 | 1.904 | |
| nmr_normalize | 0.683 | 0.099 | 0.812 | |
| nmr_pca_build_model | 3.654 | 1.901 | 4.249 | |
| nmr_pca_outliers | 1.956 | 0.981 | 2.189 | |
| nmr_pca_outliers_filter | 2.824 | 1.230 | 3.494 | |
| nmr_pca_outliers_plot | 0.000 | 0.001 | 0.001 | |
| nmr_pca_outliers_robust | 15.056 | 1.091 | 16.473 | |
| nmr_pca_plots | 1.005 | 0.028 | 1.073 | |
| nmr_peak_clustering | 0.135 | 0.003 | 0.146 | |
| nmr_ppm_resolution | 0.014 | 0.003 | 0.018 | |
| nmr_read_bruker_fid | 0.000 | 0.001 | 0.002 | |
| nmr_read_samples | 3.321 | 2.079 | 3.869 | |
| nmr_zip_bruker_samples | 0.324 | 0.068 | 0.416 | |
| peaklist_accept_peaks | 0.008 | 0.003 | 0.010 | |
| permutation_test_model | 4.075 | 1.505 | 5.521 | |
| permutation_test_plot | 4.115 | 1.582 | 5.503 | |
| plot.nmr_dataset_1D | 0.003 | 0.010 | 0.012 | |
| plot_bootstrap_multimodel | 0.004 | 0.011 | 0.015 | |
| plot_interactive | 1.840 | 1.137 | 2.278 | |
| plot_plsda_multimodel | 0.795 | 1.076 | 1.093 | |
| plot_plsda_samples | 0.402 | 0.512 | 0.876 | |
| plot_vip_scores | 0.003 | 0.003 | 0.006 | |
| plot_webgl | 0.003 | 0.003 | 0.005 | |
| plsda_auroc_vip_compare | 1.311 | 0.919 | 2.207 | |
| plsda_auroc_vip_method | 0.000 | 0.001 | 0.001 | |
| ppm_resolution | 0.005 | 0.002 | 0.007 | |
| print.nmr_dataset | 1.751 | 1.149 | 2.206 | |
| print.nmr_dataset_1D | 1.987 | 1.471 | 2.516 | |
| print.nmr_dataset_peak_table | 1.912 | 1.088 | 2.330 | |
| random_subsampling | 0.004 | 0.011 | 0.015 | |
| save_files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
| save_profiling_output | 0.000 | 0.000 | 0.001 | |
| sub-.nmr_dataset | 1.586 | 0.962 | 1.857 | |
| sub-.nmr_dataset_1D | 1.743 | 0.986 | 2.150 | |
| sub-.nmr_dataset_peak_table | 1.894 | 1.072 | 2.289 | |
| tidy.nmr_dataset_1D | 2.820 | 1.360 | 3.355 | |
| to_ChemoSpec | 1.847 | 0.879 | 2.141 | |
| validate_nmr_dataset | 3.198 | 1.756 | 3.821 | |
| validate_nmr_dataset_family | 2.498 | 1.167 | 3.093 | |
| validate_nmr_dataset_peak_table | 0.002 | 0.001 | 0.002 | |
| zzz | 0.00 | 0.00 | 2.02 | |