| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:37:57 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 55/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.2.0 (landing page) Sergio Oller Moreno
| kjohnson2 | macOS 12.6.1 Monterey / 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: 4.2.0 |
| 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_4.2.0.tar.gz |
| StartedAt: 2023-10-17 01:57:02 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 02:02:25 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 323.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_4.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/AlpsNMR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.2.0’
* 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 9.255 1.678 13.009
SummarizedExperiment_to_nmr_data_1r 6.431 0.515 10.539
nmr_pca_outliers_robust 6.038 0.482 9.881
* 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-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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
15.883 3.855 27.181
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 1.917 | 0.322 | 3.348 | |
| HMDB_blood | 0.007 | 0.002 | 0.014 | |
| HMDB_cell | 0.003 | 0.001 | 0.005 | |
| HMDB_urine | 0.005 | 0.002 | 0.015 | |
| Parameters_blood | 0.002 | 0.002 | 0.004 | |
| Parameters_cell | 0.003 | 0.002 | 0.008 | |
| Parameters_urine | 0.003 | 0.002 | 0.004 | |
| Peak_detection | 9.255 | 1.678 | 13.009 | |
| Pipelines | 0.002 | 0.001 | 0.003 | |
| ROI_blood | 0.003 | 0.001 | 0.008 | |
| ROI_cell | 0.003 | 0.001 | 0.006 | |
| ROI_urine | 0.004 | 0.001 | 0.007 | |
| SummarizedExperiment_to_nmr_data_1r | 6.431 | 0.515 | 10.539 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 2.195 | 0.483 | 3.877 | |
| bp_VIP_analysis | 1.614 | 0.502 | 2.225 | |
| bp_kfold_VIP_analysis | 0.865 | 0.312 | 1.257 | |
| download_MTBLS242 | 0.000 | 0.000 | 0.001 | |
| file_lister | 0.076 | 0.018 | 0.142 | |
| files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
| filter.nmr_dataset_family | 0.811 | 0.253 | 1.569 | |
| format.nmr_dataset | 0.803 | 0.425 | 1.653 | |
| format.nmr_dataset_1D | 0.821 | 0.311 | 1.648 | |
| format.nmr_dataset_peak_table | 0.876 | 0.372 | 1.771 | |
| get_integration_with_metadata | 0.032 | 0.003 | 0.046 | |
| hmdb | 0.067 | 0.006 | 0.107 | |
| is.nmr_dataset | 0.795 | 0.360 | 1.661 | |
| is.nmr_dataset_1D | 0.904 | 0.400 | 1.849 | |
| is.nmr_dataset_peak_table | 0.942 | 0.395 | 1.921 | |
| load_and_save_functions | 0.769 | 0.358 | 1.612 | |
| models_stability_plot_bootstrap | 0.002 | 0.001 | 0.004 | |
| models_stability_plot_plsda | 0.419 | 0.245 | 0.733 | |
| new_nmr_dataset | 0.002 | 0.000 | 0.006 | |
| new_nmr_dataset_1D | 0.001 | 0.001 | 0.003 | |
| new_nmr_dataset_peak_table | 0.941 | 0.394 | 1.917 | |
| nmr_baseline_estimation | 0.164 | 0.039 | 0.310 | |
| nmr_baseline_removal | 0.005 | 0.001 | 0.007 | |
| nmr_baseline_threshold | 0.001 | 0.000 | 0.002 | |
| nmr_baseline_threshold_plot | 0.220 | 0.022 | 0.375 | |
| nmr_batman | 0.003 | 0.001 | 0.006 | |
| nmr_batman_options | 0.001 | 0.000 | 0.003 | |
| nmr_build_peak_table | 0.050 | 0.002 | 0.081 | |
| nmr_data | 0.052 | 0.002 | 0.085 | |
| nmr_data_1r_to_SummarizedExperiment | 1.154 | 0.496 | 2.323 | |
| nmr_data_analysis | 0.474 | 0.321 | 0.910 | |
| nmr_dataset | 0.001 | 0.000 | 0.002 | |
| nmr_dataset_1D | 0.002 | 0.001 | 0.001 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.070 | 0.347 | 2.067 | |
| nmr_exclude_region | 0.007 | 0.002 | 0.016 | |
| nmr_export_data_1r | 0.909 | 0.485 | 1.889 | |
| nmr_get_peak_distances | 0.011 | 0.002 | 0.019 | |
| nmr_identify_regions_blood | 0.015 | 0.004 | 0.030 | |
| nmr_identify_regions_cell | 0.010 | 0.002 | 0.018 | |
| nmr_identify_regions_urine | 0.016 | 0.003 | 0.030 | |
| nmr_integrate_regions | 0.016 | 0.003 | 0.028 | |
| nmr_interpolate_1D | 1.792 | 0.866 | 3.720 | |
| nmr_meta_add | 2.182 | 0.914 | 4.363 | |
| nmr_meta_export | 0.823 | 0.323 | 1.676 | |
| nmr_meta_get | 0.848 | 0.371 | 1.663 | |
| nmr_meta_get_column | 0.872 | 0.464 | 1.741 | |
| nmr_meta_groups | 0.773 | 0.341 | 1.626 | |
| nmr_normalize | 0.291 | 0.034 | 0.503 | |
| nmr_pca_build_model | 2.032 | 1.016 | 4.120 | |
| nmr_pca_outliers | 1.532 | 0.497 | 2.979 | |
| nmr_pca_outliers_filter | 0.972 | 0.349 | 1.941 | |
| nmr_pca_outliers_plot | 0.000 | 0.000 | 0.001 | |
| nmr_pca_outliers_robust | 6.038 | 0.482 | 9.881 | |
| nmr_pca_plots | 0.429 | 0.015 | 0.672 | |
| nmr_peak_clustering | 0.097 | 0.005 | 0.157 | |
| nmr_ppm_resolution | 0.010 | 0.003 | 0.019 | |
| nmr_read_bruker_fid | 0.001 | 0.001 | 0.001 | |
| nmr_read_samples | 1.651 | 0.826 | 3.453 | |
| nmr_zip_bruker_samples | 0.306 | 0.048 | 0.562 | |
| peaklist_accept_peaks | 0.005 | 0.002 | 0.008 | |
| permutation_test_model | 2.086 | 0.586 | 4.285 | |
| permutation_test_plot | 3.767 | 0.891 | 4.324 | |
| plot.nmr_dataset_1D | 0.002 | 0.002 | 0.003 | |
| plot_bootstrap_multimodel | 0.002 | 0.002 | 0.005 | |
| plot_interactive | 0.927 | 0.463 | 1.973 | |
| plot_plsda_multimodel | 0.236 | 0.218 | 0.538 | |
| plot_plsda_samples | 0.150 | 0.152 | 0.454 | |
| plot_vip_scores | 0.002 | 0.002 | 0.007 | |
| plot_webgl | 0.002 | 0.001 | 0.005 | |
| plsda_auroc_vip_compare | 0.531 | 0.337 | 1.311 | |
| plsda_auroc_vip_method | 0.000 | 0.000 | 0.002 | |
| ppm_resolution | 0.003 | 0.002 | 0.007 | |
| print.nmr_dataset | 0.927 | 0.504 | 1.810 | |
| print.nmr_dataset_1D | 0.873 | 0.400 | 1.798 | |
| print.nmr_dataset_peak_table | 0.978 | 0.423 | 1.997 | |
| random_subsampling | 0.002 | 0.004 | 0.010 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0.000 | 0.000 | 0.001 | |
| sub-.nmr_dataset | 0.920 | 0.481 | 1.911 | |
| sub-.nmr_dataset_1D | 0.821 | 0.390 | 1.731 | |
| sub-.nmr_dataset_peak_table | 1.017 | 0.487 | 2.037 | |
| tidy.nmr_dataset_1D | 1.059 | 0.494 | 2.117 | |
| to_ChemoSpec | 1.043 | 0.431 | 2.125 | |
| validate_nmr_dataset | 1.740 | 0.858 | 3.667 | |
| validate_nmr_dataset_family | 0.918 | 0.421 | 1.740 | |
| validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.004 | |
| zzz | 0.000 | 0.001 | 2.146 | |