Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 58/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.8.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 4.8.0 |
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_4.8.0.tar.gz |
StartedAt: 2024-12-20 11:02:01 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:05:15 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 193.8 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_4.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.8.0’ * 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 code 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 9.452 2.607 8.727 permutation_test_plot 6.051 3.090 1.858 SummarizedExperiment_to_nmr_data_1r 8.171 0.848 8.346 format.nmr_dataset 3.955 2.183 2.933 nmr_pca_outliers_robust 5.187 0.887 5.293 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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/4.4-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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) Attaching package: 'AlpsNMR' The following object is masked from 'package:stats': filter > > test_check("AlpsNMR") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_rDolphin.R:2:5' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ] > > proc.time() user system elapsed 28.147 10.849 26.759
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.064 | 0.520 | 1.956 | |
HMDB_blood | 0.007 | 0.003 | 0.010 | |
HMDB_cell | 0.003 | 0.002 | 0.004 | |
HMDB_urine | 0.005 | 0.002 | 0.007 | |
Parameters_blood | 0.002 | 0.002 | 0.003 | |
Parameters_cell | 0.002 | 0.001 | 0.004 | |
Parameters_urine | 0.002 | 0.002 | 0.004 | |
Peak_detection | 9.452 | 2.607 | 8.727 | |
Pipelines | 0.001 | 0.001 | 0.002 | |
ROI_blood | 0.003 | 0.002 | 0.005 | |
ROI_cell | 0.003 | 0.002 | 0.004 | |
ROI_urine | 0.003 | 0.002 | 0.004 | |
SummarizedExperiment_to_nmr_data_1r | 8.171 | 0.848 | 8.346 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.097 | 0.529 | 1.022 | |
bp_VIP_analysis | 1.619 | 1.205 | 1.231 | |
bp_kfold_VIP_analysis | 0.835 | 0.494 | 0.597 | |
download_MTBLS242 | 0.000 | 0.000 | 0.001 | |
file_lister | 0.066 | 0.017 | 0.084 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.929 | 0.811 | 0.887 | |
format.nmr_dataset | 3.955 | 2.183 | 2.933 | |
format.nmr_dataset_1D | 0.762 | 0.589 | 0.717 | |
format.nmr_dataset_peak_table | 0.873 | 0.628 | 0.784 | |
get_integration_with_metadata | 0.029 | 0.009 | 0.038 | |
hmdb | 0.055 | 0.010 | 0.065 | |
is.nmr_dataset | 0.752 | 0.609 | 0.681 | |
is.nmr_dataset_1D | 0.779 | 0.594 | 0.697 | |
is.nmr_dataset_peak_table | 0.814 | 0.438 | 0.689 | |
load_and_save_functions | 0.654 | 0.415 | 0.506 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.003 | |
models_stability_plot_plsda | 0.421 | 0.589 | 0.493 | |
new_nmr_dataset | 0.001 | 0.002 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.002 | 0.003 | |
new_nmr_dataset_peak_table | 0.822 | 0.449 | 0.697 | |
nmr_autophase | 0.232 | 0.164 | 0.382 | |
nmr_baseline_estimation | 0.009 | 0.008 | 0.017 | |
nmr_baseline_removal | 0.006 | 0.002 | 0.007 | |
nmr_baseline_threshold | 0.001 | 0.001 | 0.002 | |
nmr_baseline_threshold_plot | 0.211 | 0.070 | 0.280 | |
nmr_batman | 0.004 | 0.002 | 0.006 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.038 | 0.006 | 0.044 | |
nmr_data | 0.048 | 0.006 | 0.055 | |
nmr_data_1r_to_SummarizedExperiment | 1.020 | 0.411 | 0.896 | |
nmr_data_analysis | 0.505 | 0.624 | 0.554 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.043 | 0.579 | 0.998 | |
nmr_exclude_region | 0.007 | 0.001 | 0.008 | |
nmr_export_data_1r | 0.775 | 0.478 | 0.638 | |
nmr_get_peak_distances | 0.008 | 0.003 | 0.012 | |
nmr_identify_regions_blood | 0.013 | 0.004 | 0.017 | |
nmr_identify_regions_cell | 0.010 | 0.003 | 0.012 | |
nmr_identify_regions_urine | 0.015 | 0.004 | 0.018 | |
nmr_integrate_regions | 0.010 | 0.002 | 0.011 | |
nmr_interpolate_1D | 1.675 | 1.212 | 1.478 | |
nmr_meta_add | 1.832 | 1.205 | 1.710 | |
nmr_meta_export | 0.673 | 0.458 | 0.543 | |
nmr_meta_get | 0.774 | 0.654 | 0.674 | |
nmr_meta_get_column | 0.782 | 0.711 | 0.721 | |
nmr_meta_groups | 0.621 | 0.614 | 0.582 | |
nmr_normalize | 0.137 | 0.038 | 0.178 | |
nmr_pca_build_model | 2.227 | 1.101 | 2.311 | |
nmr_pca_outliers | 0.946 | 0.713 | 0.864 | |
nmr_pca_outliers_filter | 1.003 | 0.668 | 0.918 | |
nmr_pca_outliers_plot | 0.001 | 0.000 | 0.000 | |
nmr_pca_outliers_robust | 5.187 | 0.887 | 5.293 | |
nmr_pca_plots | 0.330 | 0.017 | 0.348 | |
nmr_peak_clustering | 0.068 | 0.001 | 0.070 | |
nmr_ppm_resolution | 0.009 | 0.002 | 0.011 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.496 | 1.285 | 1.278 | |
nmr_zip_bruker_samples | 0.343 | 0.040 | 0.389 | |
peaklist_accept_peaks | 0.003 | 0.002 | 0.005 | |
permutation_test_model | 0.760 | 0.777 | 1.873 | |
permutation_test_plot | 6.051 | 3.090 | 1.858 | |
plot.nmr_dataset_1D | 0.001 | 0.002 | 0.003 | |
plot_bootstrap_multimodel | 0.002 | 0.002 | 0.004 | |
plot_interactive | 0.790 | 0.609 | 0.727 | |
plot_plsda_multimodel | 0.249 | 0.446 | 0.360 | |
plot_plsda_samples | 0.130 | 0.203 | 0.322 | |
plot_vip_scores | 0.002 | 0.001 | 0.004 | |
plot_webgl | 0.001 | 0.001 | 0.003 | |
plsda_auroc_vip_compare | 0.443 | 0.420 | 0.838 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.001 | 0.004 | |
print.nmr_dataset | 0.681 | 0.576 | 0.590 | |
print.nmr_dataset_1D | 0.895 | 0.742 | 0.790 | |
print.nmr_dataset_peak_table | 1.760 | 1.190 | 2.172 | |
random_subsampling | 0.002 | 0.004 | 0.005 | |
save_files_to_rDolphin | 0.000 | 0.001 | 0.000 | |
save_profiling_output | 0.001 | 0.000 | 0.000 | |
sub-.nmr_dataset | 0.681 | 0.558 | 0.580 | |
sub-.nmr_dataset_1D | 0.765 | 0.465 | 0.635 | |
sub-.nmr_dataset_peak_table | 0.794 | 0.462 | 0.677 | |
tidy.nmr_dataset_1D | 0.684 | 0.502 | 0.824 | |
to_ASICS | 1.258 | 0.554 | 1.463 | |
to_ChemoSpec | 0.910 | 0.622 | 0.878 | |
validate_nmr_dataset | 1.667 | 1.379 | 1.528 | |
validate_nmr_dataset_family | 0.766 | 0.571 | 0.705 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.002 | |
zzz | 0.00 | 0.00 | 2.15 | |