| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-09-26 11:37:07 -0400 (Tue, 26 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | 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: 4.2.0 |
| 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: 2023-09-25 22:30:31 -0400 (Mon, 25 Sep 2023) |
| EndedAt: 2023-09-25 22:38:39 -0400 (Mon, 25 Sep 2023) |
| EllapsedTime: 488.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_4.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 19.928 4.904 22.291
nmr_pca_outliers_robust 15.992 1.593 23.539
permutation_test_plot 11.562 4.459 7.570
SummarizedExperiment_to_nmr_data_1r 11.809 1.372 16.985
tidy.nmr_dataset_1D 4.591 3.577 6.676
nmr_meta_export 4.008 3.766 6.949
is.nmr_dataset 3.921 3.798 6.794
nmr_meta_add 4.418 2.123 6.642
nmr_read_samples 3.564 2.448 5.525
nmr_pca_build_model 3.760 2.041 5.843
nmr_interpolate_1D 3.398 1.751 4.877
bp_VIP_analysis 3.418 1.665 3.550
validate_nmr_dataset 3.316 1.763 4.518
permutation_test_model 0.890 0.653 7.416
* 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-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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
30.654 11.400 39.992
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 3.277 | 0.823 | 4.769 | |
| HMDB_blood | 0.012 | 0.005 | 0.028 | |
| HMDB_cell | 0.005 | 0.003 | 0.016 | |
| HMDB_urine | 0.009 | 0.004 | 0.014 | |
| Parameters_blood | 0.003 | 0.003 | 0.007 | |
| Parameters_cell | 0.003 | 0.003 | 0.011 | |
| Parameters_urine | 0.003 | 0.003 | 0.007 | |
| Peak_detection | 19.928 | 4.904 | 22.291 | |
| Pipelines | 0.003 | 0.002 | 0.007 | |
| ROI_blood | 0.007 | 0.003 | 0.014 | |
| ROI_cell | 0.007 | 0.003 | 0.014 | |
| ROI_urine | 0.007 | 0.003 | 0.013 | |
| SummarizedExperiment_to_nmr_data_1r | 11.809 | 1.372 | 16.985 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 2.205 | 0.885 | 3.167 | |
| bp_VIP_analysis | 3.418 | 1.665 | 3.550 | |
| bp_kfold_VIP_analysis | 1.945 | 1.031 | 2.117 | |
| download_MTBLS242 | 0.001 | 0.001 | 0.001 | |
| file_lister | 0.166 | 0.030 | 0.226 | |
| files_to_rDolphin | 0.000 | 0.002 | 0.004 | |
| filter.nmr_dataset_family | 1.898 | 1.148 | 3.033 | |
| format.nmr_dataset | 1.686 | 1.023 | 2.764 | |
| format.nmr_dataset_1D | 1.819 | 1.086 | 2.916 | |
| format.nmr_dataset_peak_table | 1.926 | 0.935 | 2.829 | |
| get_integration_with_metadata | 0.057 | 0.003 | 0.077 | |
| hmdb | 0.105 | 0.012 | 0.182 | |
| is.nmr_dataset | 3.921 | 3.798 | 6.794 | |
| is.nmr_dataset_1D | 1.716 | 0.960 | 2.688 | |
| is.nmr_dataset_peak_table | 1.947 | 1.003 | 2.770 | |
| load_and_save_functions | 1.712 | 1.043 | 2.470 | |
| models_stability_plot_bootstrap | 0.020 | 0.022 | 0.054 | |
| models_stability_plot_plsda | 0.827 | 0.517 | 0.937 | |
| new_nmr_dataset | 0.003 | 0.002 | 0.005 | |
| new_nmr_dataset_1D | 0.002 | 0.001 | 0.004 | |
| new_nmr_dataset_peak_table | 1.801 | 0.871 | 2.518 | |
| nmr_baseline_estimation | 0.291 | 0.071 | 0.477 | |
| nmr_baseline_removal | 0.009 | 0.002 | 0.013 | |
| nmr_baseline_threshold | 0.002 | 0.001 | 0.003 | |
| nmr_baseline_threshold_plot | 0.416 | 0.026 | 0.572 | |
| nmr_batman | 0.005 | 0.002 | 0.014 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.079 | 0.003 | 0.106 | |
| nmr_data | 0.102 | 0.005 | 0.146 | |
| nmr_data_1r_to_SummarizedExperiment | 2.132 | 0.850 | 2.933 | |
| nmr_data_analysis | 0.882 | 0.562 | 1.032 | |
| nmr_dataset | 0.001 | 0.001 | 0.002 | |
| nmr_dataset_1D | 0.002 | 0.001 | 0.003 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 2.278 | 1.058 | 3.581 | |
| nmr_exclude_region | 0.011 | 0.003 | 0.016 | |
| nmr_export_data_1r | 1.789 | 0.956 | 2.498 | |
| nmr_get_peak_distances | 0.019 | 0.002 | 0.029 | |
| nmr_identify_regions_blood | 0.031 | 0.005 | 0.048 | |
| nmr_identify_regions_cell | 0.021 | 0.002 | 0.030 | |
| nmr_identify_regions_urine | 0.031 | 0.003 | 0.042 | |
| nmr_integrate_regions | 0.027 | 0.003 | 0.038 | |
| nmr_interpolate_1D | 3.398 | 1.751 | 4.877 | |
| nmr_meta_add | 4.418 | 2.123 | 6.642 | |
| nmr_meta_export | 4.008 | 3.766 | 6.949 | |
| nmr_meta_get | 1.651 | 0.920 | 2.606 | |
| nmr_meta_get_column | 1.651 | 0.920 | 2.351 | |
| nmr_meta_groups | 1.571 | 0.733 | 2.161 | |
| nmr_normalize | 0.595 | 0.104 | 0.928 | |
| nmr_pca_build_model | 3.760 | 2.041 | 5.843 | |
| nmr_pca_outliers | 1.971 | 1.003 | 3.135 | |
| nmr_pca_outliers_filter | 1.991 | 1.007 | 3.186 | |
| nmr_pca_outliers_plot | 0.000 | 0.002 | 0.013 | |
| nmr_pca_outliers_robust | 15.992 | 1.593 | 23.539 | |
| nmr_pca_plots | 0.841 | 0.026 | 1.220 | |
| nmr_peak_clustering | 0.160 | 0.008 | 0.233 | |
| nmr_ppm_resolution | 0.014 | 0.004 | 0.023 | |
| nmr_read_bruker_fid | 0.001 | 0.000 | 0.001 | |
| nmr_read_samples | 3.564 | 2.448 | 5.525 | |
| nmr_zip_bruker_samples | 0.324 | 0.070 | 0.439 | |
| peaklist_accept_peaks | 0.008 | 0.003 | 0.009 | |
| permutation_test_model | 0.890 | 0.653 | 7.416 | |
| permutation_test_plot | 11.562 | 4.459 | 7.570 | |
| plot.nmr_dataset_1D | 3.575 | 1.268 | 0.020 | |
| plot_bootstrap_multimodel | 0.004 | 0.011 | 0.015 | |
| plot_interactive | 1.876 | 1.118 | 2.822 | |
| plot_plsda_multimodel | 0.922 | 1.489 | 1.500 | |
| plot_plsda_samples | 0.572 | 0.879 | 1.480 | |
| plot_vip_scores | 0.004 | 0.003 | 0.012 | |
| plot_webgl | 0.002 | 0.002 | 0.004 | |
| plsda_auroc_vip_compare | 1.268 | 1.104 | 2.517 | |
| plsda_auroc_vip_method | 0.000 | 0.001 | 0.005 | |
| ppm_resolution | 0.005 | 0.002 | 0.006 | |
| print.nmr_dataset | 1.678 | 0.989 | 2.364 | |
| print.nmr_dataset_1D | 1.803 | 0.986 | 2.636 | |
| print.nmr_dataset_peak_table | 2.139 | 1.294 | 3.280 | |
| random_subsampling | 0.004 | 0.010 | 0.019 | |
| save_files_to_rDolphin | 0.000 | 0.001 | 0.000 | |
| save_profiling_output | 0.000 | 0.001 | 0.001 | |
| sub-.nmr_dataset | 1.735 | 1.130 | 2.500 | |
| sub-.nmr_dataset_1D | 1.858 | 1.088 | 2.841 | |
| sub-.nmr_dataset_peak_table | 2.074 | 1.182 | 2.911 | |
| tidy.nmr_dataset_1D | 4.591 | 3.577 | 6.676 | |
| to_ChemoSpec | 1.993 | 0.955 | 2.901 | |
| validate_nmr_dataset | 3.316 | 1.763 | 4.518 | |
| validate_nmr_dataset_family | 1.741 | 0.914 | 2.458 | |
| validate_nmr_dataset_peak_table | 0.002 | 0.001 | 0.003 | |
| zzz | 0.000 | 0.001 | 2.001 | |