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This page was generated on 2024-05-20 11:32:07 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 57/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.7.0 (landing page) Sergio Oller Moreno
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the AlpsNMR package: - 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: 4.7.0 |
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_4.7.0.tar.gz |
StartedAt: 2024-05-19 04:58:06 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 05:01:20 -0400 (Sun, 19 May 2024) |
EllapsedTime: 193.7 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_4.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/AlpsNMR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.7.0’ * 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 8.418 2.183 7.262 SummarizedExperiment_to_nmr_data_1r 7.526 0.632 7.833 permutation_test_plot 5.705 2.030 2.335 nmr_pca_outliers_robust 5.799 0.825 6.259 * 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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) 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 15.462 5.187 16.577
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.858 | 0.323 | 2.167 | |
HMDB_blood | 0.008 | 0.003 | 0.011 | |
HMDB_cell | 0.003 | 0.002 | 0.004 | |
HMDB_urine | 0.005 | 0.002 | 0.007 | |
Parameters_blood | 0.002 | 0.001 | 0.003 | |
Parameters_cell | 0.002 | 0.001 | 0.003 | |
Parameters_urine | 0.001 | 0.001 | 0.003 | |
Peak_detection | 8.418 | 2.183 | 7.262 | |
Pipelines | 0.002 | 0.000 | 0.003 | |
ROI_blood | 0.004 | 0.002 | 0.005 | |
ROI_cell | 0.003 | 0.002 | 0.004 | |
ROI_urine | 0.003 | 0.002 | 0.005 | |
SummarizedExperiment_to_nmr_data_1r | 7.526 | 0.632 | 7.833 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.057 | 0.554 | 1.278 | |
bp_VIP_analysis | 1.406 | 0.790 | 1.340 | |
bp_kfold_VIP_analysis | 0.711 | 0.383 | 0.673 | |
download_MTBLS242 | 0.000 | 0.000 | 0.001 | |
file_lister | 0.066 | 0.017 | 0.084 | |
files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
filter.nmr_dataset_family | 1.591 | 0.763 | 1.963 | |
format.nmr_dataset | 0.625 | 0.419 | 0.781 | |
format.nmr_dataset_1D | 0.762 | 0.482 | 0.929 | |
format.nmr_dataset_peak_table | 0.793 | 0.469 | 0.974 | |
get_integration_with_metadata | 0.022 | 0.006 | 0.029 | |
hmdb | 0.056 | 0.008 | 0.065 | |
is.nmr_dataset | 0.672 | 0.438 | 0.764 | |
is.nmr_dataset_1D | 0.773 | 0.516 | 0.958 | |
is.nmr_dataset_peak_table | 0.790 | 0.483 | 0.983 | |
load_and_save_functions | 0.684 | 0.431 | 0.780 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.003 | |
models_stability_plot_plsda | 0.365 | 0.407 | 0.496 | |
new_nmr_dataset | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_peak_table | 2.294 | 0.990 | 2.963 | |
nmr_baseline_estimation | 0.138 | 0.012 | 0.149 | |
nmr_baseline_removal | 0.006 | 0.001 | 0.006 | |
nmr_baseline_threshold | 0.001 | 0.001 | 0.002 | |
nmr_baseline_threshold_plot | 0.194 | 0.004 | 0.198 | |
nmr_batman | 0.003 | 0.001 | 0.005 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.035 | 0.001 | 0.036 | |
nmr_data | 0.048 | 0.005 | 0.053 | |
nmr_data_1r_to_SummarizedExperiment | 1.042 | 0.521 | 1.214 | |
nmr_data_analysis | 0.421 | 0.415 | 0.527 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.011 | 0.542 | 1.127 | |
nmr_exclude_region | 0.007 | 0.001 | 0.008 | |
nmr_export_data_1r | 0.770 | 0.447 | 0.924 | |
nmr_get_peak_distances | 0.009 | 0.002 | 0.010 | |
nmr_identify_regions_blood | 0.015 | 0.004 | 0.019 | |
nmr_identify_regions_cell | 0.009 | 0.002 | 0.011 | |
nmr_identify_regions_urine | 0.013 | 0.003 | 0.015 | |
nmr_integrate_regions | 0.009 | 0.002 | 0.012 | |
nmr_interpolate_1D | 1.463 | 0.896 | 1.782 | |
nmr_meta_add | 1.707 | 0.942 | 1.967 | |
nmr_meta_export | 0.346 | 0.287 | 0.824 | |
nmr_meta_get | 0.644 | 0.425 | 0.785 | |
nmr_meta_get_column | 1.035 | 0.858 | 0.954 | |
nmr_meta_groups | 0.709 | 0.561 | 0.920 | |
nmr_normalize | 0.236 | 0.080 | 0.317 | |
nmr_pca_build_model | 1.752 | 1.034 | 2.204 | |
nmr_pca_outliers | 1.698 | 0.652 | 2.045 | |
nmr_pca_outliers_filter | 0.845 | 0.483 | 1.030 | |
nmr_pca_outliers_plot | 0.001 | 0.000 | 0.000 | |
nmr_pca_outliers_robust | 5.799 | 0.825 | 6.259 | |
nmr_pca_plots | 0.326 | 0.006 | 0.332 | |
nmr_peak_clustering | 0.063 | 0.000 | 0.064 | |
nmr_ppm_resolution | 0.008 | 0.002 | 0.011 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 1.155 | 0.843 | 1.688 | |
nmr_zip_bruker_samples | 0.344 | 0.041 | 0.390 | |
peaklist_accept_peaks | 0.004 | 0.002 | 0.007 | |
permutation_test_model | 0.553 | 0.654 | 2.292 | |
permutation_test_plot | 5.705 | 2.030 | 2.335 | |
plot.nmr_dataset_1D | 0.001 | 0.003 | 0.004 | |
plot_bootstrap_multimodel | 0.002 | 0.001 | 0.004 | |
plot_interactive | 0.704 | 0.399 | 0.811 | |
plot_plsda_multimodel | 0.21 | 0.31 | 0.34 | |
plot_plsda_samples | 0.126 | 0.162 | 0.277 | |
plot_vip_scores | 0.001 | 0.001 | 0.003 | |
plot_webgl | 0.001 | 0.001 | 0.003 | |
plsda_auroc_vip_compare | 0.442 | 0.437 | 0.851 | |
plsda_auroc_vip_method | 0.000 | 0.000 | 0.001 | |
ppm_resolution | 0.003 | 0.001 | 0.005 | |
print.nmr_dataset | 0.707 | 0.574 | 0.869 | |
print.nmr_dataset_1D | 0.707 | 0.399 | 0.825 | |
print.nmr_dataset_peak_table | 0.817 | 0.528 | 1.035 | |
random_subsampling | 0.002 | 0.004 | 0.006 | |
save_files_to_rDolphin | 0.000 | 0.001 | 0.000 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.625 | 0.423 | 0.742 | |
sub-.nmr_dataset_1D | 0.759 | 0.506 | 0.953 | |
sub-.nmr_dataset_peak_table | 0.800 | 0.446 | 0.954 | |
tidy.nmr_dataset_1D | 0.898 | 0.543 | 1.063 | |
to_ChemoSpec | 0.847 | 0.615 | 1.120 | |
validate_nmr_dataset | 1.444 | 1.074 | 1.805 | |
validate_nmr_dataset_family | 0.811 | 0.645 | 1.028 | |
validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.003 | |
zzz | 0.000 | 0.000 | 2.151 | |