| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:36:49 -0400 (Mon, 16 Oct 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" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2023-10-15 22:27:12 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:35:13 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 481.2 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 20.131 4.918 23.267
nmr_pca_outliers_robust 15.814 1.429 21.087
SummarizedExperiment_to_nmr_data_1r 11.846 1.371 16.342
permutation_test_plot 8.126 3.365 8.222
tidy.nmr_dataset_1D 4.557 3.575 6.718
is.nmr_dataset 3.882 3.683 5.923
nmr_meta_export 4.053 3.178 5.864
permutation_test_model 4.521 1.947 8.172
nmr_meta_add 4.390 2.076 6.151
nmr_read_samples 3.565 2.410 5.081
nmr_pca_build_model 3.749 1.978 5.173
nmr_interpolate_1D 3.384 1.752 4.540
bp_VIP_analysis 3.419 1.689 3.641
validate_nmr_dataset 3.289 1.792 4.571
* 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
30.717 11.792 39.555
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 3.226 | 0.790 | 4.409 | |
| HMDB_blood | 0.012 | 0.005 | 0.058 | |
| HMDB_cell | 0.005 | 0.003 | 0.011 | |
| HMDB_urine | 0.008 | 0.005 | 0.014 | |
| Parameters_blood | 0.004 | 0.004 | 0.028 | |
| Parameters_cell | 0.004 | 0.003 | 0.020 | |
| Parameters_urine | 0.003 | 0.003 | 0.016 | |
| Peak_detection | 20.131 | 4.918 | 23.267 | |
| Pipelines | 0.002 | 0.002 | 0.004 | |
| ROI_blood | 0.007 | 0.003 | 0.016 | |
| ROI_cell | 0.007 | 0.003 | 0.014 | |
| ROI_urine | 0.006 | 0.003 | 0.010 | |
| SummarizedExperiment_to_nmr_data_1r | 11.846 | 1.371 | 16.342 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 2.195 | 0.865 | 3.052 | |
| bp_VIP_analysis | 3.419 | 1.689 | 3.641 | |
| bp_kfold_VIP_analysis | 1.963 | 1.068 | 2.158 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.167 | 0.030 | 0.233 | |
| files_to_rDolphin | 0.000 | 0.001 | 0.002 | |
| filter.nmr_dataset_family | 1.869 | 0.994 | 2.846 | |
| format.nmr_dataset | 1.666 | 0.972 | 2.419 | |
| format.nmr_dataset_1D | 1.807 | 0.991 | 2.499 | |
| format.nmr_dataset_peak_table | 1.887 | 0.887 | 2.491 | |
| get_integration_with_metadata | 0.058 | 0.004 | 0.086 | |
| hmdb | 0.105 | 0.010 | 0.148 | |
| is.nmr_dataset | 3.882 | 3.683 | 5.923 | |
| is.nmr_dataset_1D | 1.697 | 0.931 | 2.335 | |
| is.nmr_dataset_peak_table | 1.920 | 1.021 | 2.664 | |
| load_and_save_functions | 1.718 | 1.051 | 2.342 | |
| models_stability_plot_bootstrap | 0.019 | 0.028 | 0.063 | |
| models_stability_plot_plsda | 0.844 | 0.504 | 0.924 | |
| new_nmr_dataset | 0.003 | 0.001 | 0.004 | |
| new_nmr_dataset_1D | 0.002 | 0.001 | 0.004 | |
| new_nmr_dataset_peak_table | 1.827 | 0.883 | 2.678 | |
| nmr_baseline_estimation | 0.293 | 0.071 | 0.447 | |
| nmr_baseline_removal | 0.009 | 0.002 | 0.017 | |
| nmr_baseline_threshold | 0.002 | 0.001 | 0.003 | |
| nmr_baseline_threshold_plot | 0.414 | 0.026 | 0.545 | |
| nmr_batman | 0.005 | 0.001 | 0.008 | |
| nmr_batman_options | 0.000 | 0.000 | 0.001 | |
| nmr_build_peak_table | 0.084 | 0.005 | 0.130 | |
| nmr_data | 0.103 | 0.004 | 0.148 | |
| nmr_data_1r_to_SummarizedExperiment | 2.142 | 0.868 | 2.820 | |
| nmr_data_analysis | 0.819 | 0.509 | 1.047 | |
| nmr_dataset | 0.001 | 0.001 | 0.003 | |
| nmr_dataset_1D | 0.003 | 0.001 | 0.004 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 2.367 | 1.228 | 3.284 | |
| nmr_exclude_region | 0.011 | 0.003 | 0.022 | |
| nmr_export_data_1r | 1.790 | 0.961 | 2.399 | |
| nmr_get_peak_distances | 0.019 | 0.002 | 0.028 | |
| nmr_identify_regions_blood | 0.031 | 0.004 | 0.039 | |
| nmr_identify_regions_cell | 0.023 | 0.002 | 0.032 | |
| nmr_identify_regions_urine | 0.030 | 0.003 | 0.043 | |
| nmr_integrate_regions | 0.027 | 0.003 | 0.035 | |
| nmr_interpolate_1D | 3.384 | 1.752 | 4.540 | |
| nmr_meta_add | 4.390 | 2.076 | 6.151 | |
| nmr_meta_export | 4.053 | 3.178 | 5.864 | |
| nmr_meta_get | 1.663 | 0.877 | 2.257 | |
| nmr_meta_get_column | 1.638 | 0.880 | 2.149 | |
| nmr_meta_groups | 1.569 | 0.704 | 2.106 | |
| nmr_normalize | 0.591 | 0.100 | 0.881 | |
| nmr_pca_build_model | 3.749 | 1.978 | 5.173 | |
| nmr_pca_outliers | 1.968 | 0.945 | 2.709 | |
| nmr_pca_outliers_filter | 1.989 | 0.963 | 2.774 | |
| nmr_pca_outliers_plot | 0.001 | 0.001 | 0.001 | |
| nmr_pca_outliers_robust | 15.814 | 1.429 | 21.087 | |
| nmr_pca_plots | 0.839 | 0.024 | 1.140 | |
| nmr_peak_clustering | 0.161 | 0.006 | 0.216 | |
| nmr_ppm_resolution | 0.014 | 0.004 | 0.022 | |
| nmr_read_bruker_fid | 0.001 | 0.001 | 0.001 | |
| nmr_read_samples | 3.565 | 2.410 | 5.081 | |
| nmr_zip_bruker_samples | 0.327 | 0.078 | 0.460 | |
| peaklist_accept_peaks | 0.008 | 0.002 | 0.011 | |
| permutation_test_model | 4.521 | 1.947 | 8.172 | |
| permutation_test_plot | 8.126 | 3.365 | 8.222 | |
| plot.nmr_dataset_1D | 3.635 | 1.341 | 0.033 | |
| plot_bootstrap_multimodel | 0.005 | 0.020 | 0.025 | |
| plot_interactive | 1.871 | 1.169 | 3.037 | |
| plot_plsda_multimodel | 0.916 | 1.467 | 1.518 | |
| plot_plsda_samples | 0.561 | 0.849 | 1.500 | |
| plot_vip_scores | 0.004 | 0.005 | 0.010 | |
| plot_webgl | 0.003 | 0.002 | 0.004 | |
| plsda_auroc_vip_compare | 1.243 | 1.082 | 2.513 | |
| plsda_auroc_vip_method | 0.000 | 0.001 | 0.001 | |
| ppm_resolution | 0.005 | 0.002 | 0.009 | |
| print.nmr_dataset | 1.697 | 1.047 | 2.625 | |
| print.nmr_dataset_1D | 1.818 | 1.062 | 2.935 | |
| print.nmr_dataset_peak_table | 2.155 | 1.276 | 3.251 | |
| random_subsampling | 0.004 | 0.009 | 0.017 | |
| save_files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
| save_profiling_output | 0.000 | 0.001 | 0.001 | |
| sub-.nmr_dataset | 1.727 | 1.103 | 2.442 | |
| sub-.nmr_dataset_1D | 1.849 | 1.061 | 2.759 | |
| sub-.nmr_dataset_peak_table | 2.070 | 1.188 | 2.837 | |
| tidy.nmr_dataset_1D | 4.557 | 3.575 | 6.718 | |
| to_ChemoSpec | 1.984 | 0.955 | 2.858 | |
| validate_nmr_dataset | 3.289 | 1.792 | 4.571 | |
| validate_nmr_dataset_family | 1.736 | 0.945 | 2.393 | |
| validate_nmr_dataset_peak_table | 0.002 | 0.001 | 0.004 | |
| zzz | 0.001 | 0.001 | 2.106 | |