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This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 57/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.6.0 (landing page) Sergio Oller Moreno
| kjohnson3 | macOS 13.6.5 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: 4.6.0 |
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_4.6.0.tar.gz |
StartedAt: 2024-05-06 19:34:58 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 19:36:05 -0400 (Mon, 06 May 2024) |
EllapsedTime: 66.8 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_4.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/AlpsNMR.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.6.0’ * 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 * 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 (2024-04-24) -- "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 5.044 1.920 5.369
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 0.607 | 0.110 | 0.627 | |
HMDB_blood | 0.002 | 0.001 | 0.003 | |
HMDB_cell | 0.001 | 0.000 | 0.001 | |
HMDB_urine | 0.001 | 0.001 | 0.002 | |
Parameters_blood | 0.001 | 0.001 | 0.001 | |
Parameters_cell | 0.001 | 0.000 | 0.001 | |
Parameters_urine | 0.000 | 0.001 | 0.001 | |
Peak_detection | 2.617 | 0.679 | 2.330 | |
Pipelines | 0 | 0 | 0 | |
ROI_blood | 0.001 | 0.000 | 0.002 | |
ROI_cell | 0.001 | 0.001 | 0.001 | |
ROI_urine | 0.001 | 0.000 | 0.002 | |
SummarizedExperiment_to_nmr_data_1r | 2.249 | 0.211 | 2.350 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.314 | 0.151 | 0.367 | |
bp_VIP_analysis | 0.398 | 0.264 | 0.396 | |
bp_kfold_VIP_analysis | 0.213 | 0.156 | 0.224 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.022 | 0.007 | 0.028 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.774 | 0.354 | 1.001 | |
format.nmr_dataset | 0.196 | 0.137 | 0.242 | |
format.nmr_dataset_1D | 0.230 | 0.153 | 0.279 | |
format.nmr_dataset_peak_table | 0.253 | 0.155 | 0.322 | |
get_integration_with_metadata | 0.007 | 0.001 | 0.008 | |
hmdb | 0.017 | 0.002 | 0.019 | |
is.nmr_dataset | 0.212 | 0.179 | 0.266 | |
is.nmr_dataset_1D | 0.239 | 0.171 | 0.309 | |
is.nmr_dataset_peak_table | 0.249 | 0.169 | 0.326 | |
load_and_save_functions | 0.210 | 0.143 | 0.250 | |
models_stability_plot_bootstrap | 0.001 | 0.000 | 0.000 | |
models_stability_plot_plsda | 0.112 | 0.137 | 0.162 | |
new_nmr_dataset | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_1D | 0.000 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.756 | 0.322 | 0.976 | |
nmr_baseline_estimation | 0.042 | 0.004 | 0.046 | |
nmr_baseline_removal | 0.002 | 0.000 | 0.001 | |
nmr_baseline_threshold | 0 | 0 | 0 | |
nmr_baseline_threshold_plot | 0.061 | 0.001 | 0.061 | |
nmr_batman | 0.001 | 0.000 | 0.001 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.01 | 0.00 | 0.01 | |
nmr_data | 0.013 | 0.001 | 0.015 | |
nmr_data_1r_to_SummarizedExperiment | 0.323 | 0.160 | 0.377 | |
nmr_data_analysis | 0.111 | 0.117 | 0.151 | |
nmr_dataset | 0.000 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.000 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.289 | 0.169 | 0.361 | |
nmr_exclude_region | 0.002 | 0.000 | 0.002 | |
nmr_export_data_1r | 0.236 | 0.150 | 0.296 | |
nmr_get_peak_distances | 0.002 | 0.001 | 0.003 | |
nmr_identify_regions_blood | 0.004 | 0.001 | 0.006 | |
nmr_identify_regions_cell | 0.003 | 0.000 | 0.003 | |
nmr_identify_regions_urine | 0.003 | 0.001 | 0.005 | |
nmr_integrate_regions | 0.002 | 0.001 | 0.003 | |
nmr_interpolate_1D | 0.455 | 0.294 | 0.564 | |
nmr_meta_add | 0.770 | 0.393 | 0.952 | |
nmr_meta_export | 0.209 | 0.151 | 0.251 | |
nmr_meta_get | 0.201 | 0.137 | 0.258 | |
nmr_meta_get_column | 0.201 | 0.154 | 0.262 | |
nmr_meta_groups | 0.206 | 0.155 | 0.261 | |
nmr_normalize | 0.065 | 0.016 | 0.080 | |
nmr_pca_build_model | 0.505 | 0.324 | 0.644 | |
nmr_pca_outliers | 0.284 | 0.168 | 0.359 | |
nmr_pca_outliers_filter | 0.266 | 0.142 | 0.321 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 1.685 | 0.218 | 1.801 | |
nmr_pca_plots | 0.099 | 0.003 | 0.103 | |
nmr_peak_clustering | 0.018 | 0.001 | 0.018 | |
nmr_ppm_resolution | 0.003 | 0.000 | 0.004 | |
nmr_read_bruker_fid | 0.000 | 0.001 | 0.000 | |
nmr_read_samples | 0.436 | 0.357 | 0.571 | |
nmr_zip_bruker_samples | 0.107 | 0.013 | 0.123 | |
peaklist_accept_peaks | 0.002 | 0.000 | 0.002 | |
permutation_test_model | 0.766 | 0.370 | 1.070 | |
permutation_test_plot | 2.13 | 0.87 | 1.10 | |
plot.nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
plot_bootstrap_multimodel | 0.001 | 0.000 | 0.001 | |
plot_interactive | 0.788 | 0.407 | 1.079 | |
plot_plsda_multimodel | 0.063 | 0.101 | 0.111 | |
plot_plsda_samples | 0.037 | 0.061 | 0.095 | |
plot_vip_scores | 0.000 | 0.000 | 0.001 | |
plot_webgl | 0.001 | 0.001 | 0.001 | |
plsda_auroc_vip_compare | 0.132 | 0.130 | 0.258 | |
plsda_auroc_vip_method | 0.000 | 0.001 | 0.001 | |
ppm_resolution | 0.001 | 0.000 | 0.001 | |
print.nmr_dataset | 0.203 | 0.164 | 0.270 | |
print.nmr_dataset_1D | 0.242 | 0.183 | 0.301 | |
print.nmr_dataset_peak_table | 0.265 | 0.175 | 0.328 | |
random_subsampling | 0.001 | 0.001 | 0.002 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.206 | 0.128 | 0.248 | |
sub-.nmr_dataset_1D | 0.248 | 0.202 | 0.319 | |
sub-.nmr_dataset_peak_table | 0.257 | 0.174 | 0.320 | |
tidy.nmr_dataset_1D | 0.147 | 0.103 | 0.316 | |
to_ChemoSpec | 0.273 | 0.165 | 0.330 | |
validate_nmr_dataset | 0.438 | 0.323 | 0.538 | |
validate_nmr_dataset_family | 0.330 | 0.235 | 0.281 | |
validate_nmr_dataset_peak_table | 0 | 0 | 0 | |
zzz | 0.000 | 0.001 | 2.010 | |