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 12:05 -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: 2024-12-19 23:37:17 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:43:41 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 383.7 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: x86_64-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 Monterey 12.7.6 * 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 21.875 4.634 20.512 nmr_pca_outliers_robust 16.553 1.468 18.153 permutation_test_plot 10.520 4.808 4.488 SummarizedExperiment_to_nmr_data_1r 13.576 1.479 14.145 format.nmr_dataset 5.374 5.288 5.036 nmr_pca_build_model 4.532 2.297 4.633 nmr_meta_add 4.456 2.346 4.133 validate_nmr_dataset 3.878 2.629 3.327 permutation_test_model 3.977 2.094 4.973 nmr_interpolate_1D 3.715 2.264 3.291 bp_VIP_analysis 3.758 1.909 2.302 nmr_read_samples 3.452 2.203 2.816 * 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-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 50.633 21.558 49.088
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 3.207 | 0.945 | 2.983 | |
HMDB_blood | 0.011 | 0.005 | 0.017 | |
HMDB_cell | 0.005 | 0.003 | 0.008 | |
HMDB_urine | 0.009 | 0.005 | 0.016 | |
Parameters_blood | 0.004 | 0.003 | 0.010 | |
Parameters_cell | 0.004 | 0.004 | 0.007 | |
Parameters_urine | 0.003 | 0.004 | 0.008 | |
Peak_detection | 21.875 | 4.634 | 20.512 | |
Pipelines | 0.003 | 0.002 | 0.005 | |
ROI_blood | 0.007 | 0.003 | 0.013 | |
ROI_cell | 0.007 | 0.003 | 0.009 | |
ROI_urine | 0.007 | 0.003 | 0.010 | |
SummarizedExperiment_to_nmr_data_1r | 13.576 | 1.479 | 14.145 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 2.245 | 0.917 | 2.039 | |
bp_VIP_analysis | 3.758 | 1.909 | 2.302 | |
bp_kfold_VIP_analysis | 2.118 | 0.923 | 1.330 | |
download_MTBLS242 | 0.000 | 0.000 | 0.001 | |
file_lister | 0.175 | 0.038 | 0.222 | |
files_to_rDolphin | 0.001 | 0.001 | 0.001 | |
filter.nmr_dataset_family | 1.587 | 1.019 | 1.879 | |
format.nmr_dataset | 5.374 | 5.288 | 5.036 | |
format.nmr_dataset_1D | 1.728 | 0.984 | 1.446 | |
format.nmr_dataset_peak_table | 1.956 | 1.078 | 1.766 | |
get_integration_with_metadata | 0.063 | 0.015 | 0.083 | |
hmdb | 0.103 | 0.020 | 0.131 | |
is.nmr_dataset | 1.706 | 1.030 | 1.432 | |
is.nmr_dataset_1D | 1.769 | 1.029 | 1.533 | |
is.nmr_dataset_peak_table | 1.829 | 0.878 | 1.634 | |
load_and_save_functions | 1.588 | 0.839 | 1.296 | |
models_stability_plot_bootstrap | 0.004 | 0.003 | 0.010 | |
models_stability_plot_plsda | 0.980 | 0.802 | 0.864 | |
new_nmr_dataset | 0.003 | 0.001 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
new_nmr_dataset_peak_table | 1.783 | 0.770 | 1.542 | |
nmr_autophase | 0.525 | 0.217 | 0.781 | |
nmr_baseline_estimation | 0.017 | 0.008 | 0.029 | |
nmr_baseline_removal | 0.010 | 0.003 | 0.014 | |
nmr_baseline_threshold | 0.002 | 0.001 | 0.003 | |
nmr_baseline_threshold_plot | 0.542 | 0.086 | 0.694 | |
nmr_batman | 0.005 | 0.002 | 0.008 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_build_peak_table | 0.076 | 0.012 | 0.094 | |
nmr_data | 0.116 | 0.017 | 0.146 | |
nmr_data_1r_to_SummarizedExperiment | 2.054 | 0.710 | 1.950 | |
nmr_data_analysis | 1.108 | 0.936 | 1.040 | |
nmr_dataset | 0.002 | 0.001 | 0.002 | |
nmr_dataset_1D | 0.002 | 0.002 | 0.005 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 2.283 | 1.049 | 2.167 | |
nmr_exclude_region | 0.010 | 0.002 | 0.016 | |
nmr_export_data_1r | 1.750 | 0.938 | 1.555 | |
nmr_get_peak_distances | 0.016 | 0.003 | 0.022 | |
nmr_identify_regions_blood | 0.032 | 0.007 | 0.043 | |
nmr_identify_regions_cell | 0.023 | 0.003 | 0.029 | |
nmr_identify_regions_urine | 0.033 | 0.004 | 0.041 | |
nmr_integrate_regions | 0.019 | 0.003 | 0.024 | |
nmr_interpolate_1D | 3.715 | 2.264 | 3.291 | |
nmr_meta_add | 4.456 | 2.346 | 4.133 | |
nmr_meta_export | 1.622 | 0.868 | 1.180 | |
nmr_meta_get | 1.886 | 1.219 | 2.098 | |
nmr_meta_get_column | 1.924 | 1.323 | 1.811 | |
nmr_meta_groups | 1.898 | 1.260 | 1.694 | |
nmr_normalize | 0.607 | 0.086 | 0.753 | |
nmr_pca_build_model | 4.532 | 2.297 | 4.633 | |
nmr_pca_outliers | 2.097 | 1.154 | 1.867 | |
nmr_pca_outliers_filter | 2.178 | 1.191 | 1.945 | |
nmr_pca_outliers_plot | 0.000 | 0.001 | 0.000 | |
nmr_pca_outliers_robust | 16.553 | 1.468 | 18.153 | |
nmr_pca_plots | 0.801 | 0.019 | 0.864 | |
nmr_peak_clustering | 0.142 | 0.003 | 0.149 | |
nmr_ppm_resolution | 0.014 | 0.003 | 0.019 | |
nmr_read_bruker_fid | 0.001 | 0.001 | 0.001 | |
nmr_read_samples | 3.452 | 2.203 | 2.816 | |
nmr_zip_bruker_samples | 0.322 | 0.072 | 0.415 | |
peaklist_accept_peaks | 0.008 | 0.003 | 0.010 | |
permutation_test_model | 3.977 | 2.094 | 4.973 | |
permutation_test_plot | 10.520 | 4.808 | 4.488 | |
plot.nmr_dataset_1D | 0.003 | 0.009 | 0.011 | |
plot_bootstrap_multimodel | 0.004 | 0.006 | 0.009 | |
plot_interactive | 1.828 | 1.088 | 1.603 | |
plot_plsda_multimodel | 0.555 | 0.647 | 0.653 | |
plot_plsda_samples | 0.274 | 0.287 | 0.544 | |
plot_vip_scores | 0.004 | 0.003 | 0.007 | |
plot_webgl | 0.002 | 0.003 | 0.005 | |
plsda_auroc_vip_compare | 1.092 | 0.671 | 1.782 | |
plsda_auroc_vip_method | 0.000 | 0.001 | 0.001 | |
ppm_resolution | 0.005 | 0.001 | 0.007 | |
print.nmr_dataset | 1.687 | 1.011 | 1.405 | |
print.nmr_dataset_1D | 1.962 | 1.325 | 1.718 | |
print.nmr_dataset_peak_table | 2.038 | 1.224 | 1.763 | |
random_subsampling | 0.004 | 0.011 | 0.016 | |
save_files_to_rDolphin | 0.001 | 0.001 | 0.001 | |
save_profiling_output | 0.000 | 0.000 | 0.001 | |
sub-.nmr_dataset | 1.824 | 1.195 | 1.488 | |
sub-.nmr_dataset_1D | 1.796 | 0.990 | 1.525 | |
sub-.nmr_dataset_peak_table | 2.044 | 1.240 | 1.860 | |
tidy.nmr_dataset_1D | 2.097 | 1.240 | 1.794 | |
to_ASICS | 2.163 | 0.264 | 2.476 | |
to_ChemoSpec | 2.067 | 1.026 | 1.814 | |
validate_nmr_dataset | 3.878 | 2.629 | 3.327 | |
validate_nmr_dataset_family | 1.916 | 1.272 | 1.625 | |
validate_nmr_dataset_peak_table | 0.002 | 0.001 | 0.002 | |
zzz | 0.000 | 0.000 | 2.043 | |