| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:25 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 54/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.3.0 (landing page) Sergio Oller Moreno
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: AlpsNMR |
| Version: 4.3.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings AlpsNMR_4.3.0.tar.gz |
| StartedAt: 2023-06-05 17:03:52 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 17:10:05 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 373.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings AlpsNMR_4.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AlpsNMR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘AlpsNMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AlpsNMR’ version ‘4.3.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Peak_detection 11.735 2.011 9.676
SummarizedExperiment_to_nmr_data_1r 9.162 0.644 9.449
nmr_pca_outliers_robust 8.147 0.725 8.439
plot_interactive 5.226 1.105 1.095
bp_kfold_VIP_analysis 4.143 1.853 0.801
nmr_pca_build_model 4.189 1.738 4.935
filter.nmr_dataset_family 3.350 1.874 3.443
* 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 ...
‘Vig01-introduction-to-alpsnmr.Rmd’ using ‘UTF-8’... OK
‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using ‘UTF-8’... OK
‘Vig02-handling-metadata-and-annotations.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ]
>
> proc.time()
user system elapsed
20.536 5.088 19.800
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 2.381 | 0.334 | 2.383 | |
| HMDB_blood | 0.008 | 0.000 | 0.008 | |
| HMDB_cell | 0.004 | 0.000 | 0.004 | |
| HMDB_urine | 0.005 | 0.000 | 0.005 | |
| Parameters_blood | 0.002 | 0.000 | 0.002 | |
| Parameters_cell | 0.001 | 0.001 | 0.002 | |
| Parameters_urine | 0.000 | 0.002 | 0.002 | |
| Peak_detection | 11.735 | 2.011 | 9.676 | |
| Pipelines | 0.002 | 0.000 | 0.002 | |
| ROI_blood | 0.004 | 0.000 | 0.005 | |
| ROI_cell | 0.000 | 0.004 | 0.004 | |
| ROI_urine | 0.004 | 0.000 | 0.004 | |
| SummarizedExperiment_to_nmr_data_1r | 9.162 | 0.644 | 9.449 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.454 | 0.419 | 1.435 | |
| bp_VIP_analysis | 0.373 | 0.318 | 2.700 | |
| bp_kfold_VIP_analysis | 4.143 | 1.853 | 0.801 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.085 | 0.008 | 0.094 | |
| files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
| filter.nmr_dataset_family | 3.350 | 1.874 | 3.443 | |
| format.nmr_dataset | 0.917 | 0.397 | 0.885 | |
| format.nmr_dataset_1D | 1.014 | 0.462 | 0.994 | |
| format.nmr_dataset_peak_table | 1.133 | 0.404 | 1.086 | |
| get_integration_with_metadata | 0.033 | 0.004 | 0.037 | |
| hmdb | 0.062 | 0.000 | 0.062 | |
| is.nmr_dataset | 0.908 | 0.410 | 0.879 | |
| is.nmr_dataset_1D | 1.039 | 0.453 | 1.041 | |
| is.nmr_dataset_peak_table | 1.140 | 0.475 | 1.160 | |
| load_and_save_functions | 0.957 | 0.422 | 0.945 | |
| models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
| models_stability_plot_plsda | 0.476 | 0.358 | 0.469 | |
| new_nmr_dataset | 0.002 | 0.000 | 0.002 | |
| new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
| new_nmr_dataset_peak_table | 1.066 | 0.475 | 1.115 | |
| nmr_baseline_estimation | 0.152 | 0.036 | 0.190 | |
| nmr_baseline_removal | 0.006 | 0.000 | 0.005 | |
| nmr_baseline_threshold | 0.001 | 0.000 | 0.002 | |
| nmr_baseline_threshold_plot | 0.270 | 0.016 | 0.286 | |
| nmr_batman | 0.004 | 0.000 | 0.003 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.062 | 0.000 | 0.062 | |
| nmr_data | 0.069 | 0.004 | 0.073 | |
| nmr_data_1r_to_SummarizedExperiment | 1.385 | 0.370 | 1.368 | |
| nmr_data_analysis | 0.476 | 0.447 | 0.513 | |
| nmr_dataset | 0.001 | 0.000 | 0.002 | |
| nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.388 | 0.509 | 1.420 | |
| nmr_exclude_region | 0.007 | 0.000 | 0.008 | |
| nmr_export_data_1r | 1.037 | 0.520 | 1.084 | |
| nmr_get_peak_distances | 0.014 | 0.000 | 0.014 | |
| nmr_identify_regions_blood | 0.018 | 0.003 | 0.021 | |
| nmr_identify_regions_cell | 0.014 | 0.000 | 0.014 | |
| nmr_identify_regions_urine | 0.020 | 0.000 | 0.021 | |
| nmr_integrate_regions | 0.02 | 0.00 | 0.02 | |
| nmr_interpolate_1D | 2.243 | 0.885 | 2.180 | |
| nmr_meta_add | 2.520 | 1.132 | 2.723 | |
| nmr_meta_export | 0.920 | 0.461 | 0.952 | |
| nmr_meta_get | 1.013 | 0.509 | 1.038 | |
| nmr_meta_get_column | 0.945 | 0.584 | 1.036 | |
| nmr_meta_groups | 1.024 | 0.483 | 0.984 | |
| nmr_normalize | 0.335 | 0.056 | 0.392 | |
| nmr_pca_build_model | 4.189 | 1.738 | 4.935 | |
| nmr_pca_outliers | 1.236 | 0.455 | 1.235 | |
| nmr_pca_outliers_filter | 1.257 | 0.469 | 1.268 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 8.147 | 0.725 | 8.439 | |
| nmr_pca_plots | 0.538 | 0.040 | 0.578 | |
| nmr_peak_clustering | 0.099 | 0.004 | 0.103 | |
| nmr_ppm_resolution | 0.000 | 0.008 | 0.009 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 1.983 | 0.923 | 1.947 | |
| nmr_zip_bruker_samples | 0.229 | 0.020 | 0.252 | |
| peaklist_accept_peaks | 0.004 | 0.000 | 0.005 | |
| permutation_test_model | 2.487 | 0.739 | 2.915 | |
| permutation_test_plot | 2.592 | 0.784 | 2.853 | |
| plot.nmr_dataset_1D | 0.002 | 0.000 | 0.002 | |
| plot_bootstrap_multimodel | 0.003 | 0.000 | 0.003 | |
| plot_interactive | 5.226 | 1.105 | 1.095 | |
| plot_plsda_multimodel | 0.225 | 0.275 | 0.317 | |
| plot_plsda_samples | 0.137 | 0.186 | 0.244 | |
| plot_vip_scores | 0.031 | 0.055 | 0.003 | |
| plot_webgl | 0.002 | 0.000 | 0.002 | |
| plsda_auroc_vip_compare | 0.616 | 0.400 | 0.854 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0.003 | 0.000 | 0.003 | |
| print.nmr_dataset | 0.949 | 0.492 | 0.984 | |
| print.nmr_dataset_1D | 1.131 | 0.566 | 1.225 | |
| print.nmr_dataset_peak_table | 1.169 | 0.549 | 1.195 | |
| random_subsampling | 0.003 | 0.000 | 0.002 | |
| save_files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 1.029 | 0.511 | 0.986 | |
| sub-.nmr_dataset_1D | 1.019 | 0.586 | 1.130 | |
| sub-.nmr_dataset_peak_table | 1.215 | 0.666 | 1.311 | |
| tidy.nmr_dataset_1D | 1.226 | 0.597 | 1.328 | |
| to_ChemoSpec | 1.215 | 0.667 | 1.373 | |
| validate_nmr_dataset | 2.159 | 0.901 | 2.100 | |
| validate_nmr_dataset_family | 1.191 | 0.546 | 1.193 | |
| validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.001 | |
| zzz | 0.000 | 0.000 | 2.002 | |