| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:25 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 54/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.3.0 (landing page) Sergio Oller Moreno
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: AlpsNMR |
| Version: 4.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings AlpsNMR_4.3.0.tar.gz |
| StartedAt: 2023-05-09 08:24:53 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 08:30:45 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 351.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings AlpsNMR_4.3.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* 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 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 10.602 2.128 8.961
SummarizedExperiment_to_nmr_data_1r 8.711 0.608 8.916
nmr_pca_outliers_robust 7.443 1.041 8.006
plot_interactive 4.647 1.335 1.054
permutation_test_plot 4.099 1.270 2.687
* 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/bbs-3.17-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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
19.106 6.791 20.134
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 2.388 | 0.493 | 2.525 | |
| HMDB_blood | 0.002 | 0.008 | 0.010 | |
| HMDB_cell | 0.000 | 0.003 | 0.003 | |
| HMDB_urine | 0.006 | 0.000 | 0.007 | |
| Parameters_blood | 0.003 | 0.000 | 0.003 | |
| Parameters_cell | 0.001 | 0.001 | 0.002 | |
| Parameters_urine | 0.000 | 0.002 | 0.002 | |
| Peak_detection | 10.602 | 2.128 | 8.961 | |
| Pipelines | 0.002 | 0.000 | 0.002 | |
| ROI_blood | 0.004 | 0.000 | 0.004 | |
| ROI_cell | 0.003 | 0.000 | 0.004 | |
| ROI_urine | 0.004 | 0.000 | 0.004 | |
| SummarizedExperiment_to_nmr_data_1r | 8.711 | 0.608 | 8.916 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.986 | 0.697 | 2.280 | |
| bp_VIP_analysis | 1.026 | 0.551 | 1.330 | |
| bp_kfold_VIP_analysis | 1.657 | 0.694 | 0.819 | |
| download_MTBLS242 | 0.001 | 0.000 | 0.000 | |
| file_lister | 0.071 | 0.020 | 0.091 | |
| files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
| filter.nmr_dataset_family | 1.010 | 0.445 | 1.077 | |
| format.nmr_dataset | 0.940 | 0.445 | 0.937 | |
| format.nmr_dataset_1D | 0.997 | 0.630 | 1.093 | |
| format.nmr_dataset_peak_table | 1.106 | 0.554 | 1.205 | |
| get_integration_with_metadata | 0.038 | 0.000 | 0.039 | |
| hmdb | 0.063 | 0.004 | 0.066 | |
| is.nmr_dataset | 0.849 | 0.662 | 1.026 | |
| is.nmr_dataset_1D | 0.986 | 0.604 | 1.141 | |
| is.nmr_dataset_peak_table | 1.085 | 0.514 | 1.109 | |
| load_and_save_functions | 0.958 | 0.492 | 0.962 | |
| models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
| models_stability_plot_plsda | 0.419 | 0.401 | 0.522 | |
| new_nmr_dataset | 0.043 | 0.077 | 0.002 | |
| new_nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
| new_nmr_dataset_peak_table | 1.186 | 0.503 | 1.215 | |
| nmr_baseline_estimation | 0.180 | 0.031 | 0.210 | |
| nmr_baseline_removal | 0.006 | 0.000 | 0.006 | |
| nmr_baseline_threshold | 0.002 | 0.000 | 0.001 | |
| nmr_baseline_threshold_plot | 0.233 | 0.024 | 0.257 | |
| nmr_batman | 0.004 | 0.000 | 0.004 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.054 | 0.004 | 0.057 | |
| nmr_data | 0.060 | 0.004 | 0.064 | |
| nmr_data_1r_to_SummarizedExperiment | 1.270 | 0.481 | 1.308 | |
| nmr_data_analysis | 0.466 | 0.432 | 0.503 | |
| nmr_dataset | 0.001 | 0.000 | 0.001 | |
| nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.288 | 0.561 | 1.410 | |
| nmr_exclude_region | 0.008 | 0.000 | 0.008 | |
| nmr_export_data_1r | 0.945 | 0.697 | 1.168 | |
| nmr_get_peak_distances | 0.010 | 0.004 | 0.013 | |
| nmr_identify_regions_blood | 0.012 | 0.008 | 0.020 | |
| nmr_identify_regions_cell | 0.009 | 0.004 | 0.013 | |
| nmr_identify_regions_urine | 0.019 | 0.000 | 0.019 | |
| nmr_integrate_regions | 0.02 | 0.00 | 0.02 | |
| nmr_interpolate_1D | 2.769 | 1.438 | 3.258 | |
| nmr_meta_add | 2.253 | 1.389 | 2.725 | |
| nmr_meta_export | 0.921 | 0.546 | 1.005 | |
| nmr_meta_get | 0.911 | 0.503 | 0.964 | |
| nmr_meta_get_column | 0.918 | 0.538 | 1.001 | |
| nmr_meta_groups | 0.938 | 0.556 | 1.016 | |
| nmr_normalize | 0.318 | 0.128 | 0.446 | |
| nmr_pca_build_model | 2.212 | 1.372 | 2.610 | |
| nmr_pca_outliers | 1.115 | 0.614 | 1.247 | |
| nmr_pca_outliers_filter | 1.227 | 0.714 | 1.459 | |
| nmr_pca_outliers_plot | 0.000 | 0.000 | 0.001 | |
| nmr_pca_outliers_robust | 7.443 | 1.041 | 8.006 | |
| nmr_pca_plots | 0.526 | 0.063 | 0.590 | |
| nmr_peak_clustering | 0.102 | 0.009 | 0.111 | |
| nmr_ppm_resolution | 0.008 | 0.004 | 0.012 | |
| nmr_read_bruker_fid | 0.001 | 0.000 | 0.000 | |
| nmr_read_samples | 1.775 | 1.091 | 1.942 | |
| nmr_zip_bruker_samples | 0.241 | 0.012 | 0.254 | |
| peaklist_accept_peaks | 0.003 | 0.003 | 0.005 | |
| permutation_test_model | 0.513 | 0.585 | 2.787 | |
| permutation_test_plot | 4.099 | 1.270 | 2.687 | |
| plot.nmr_dataset_1D | 0.000 | 0.002 | 0.002 | |
| plot_bootstrap_multimodel | 0.002 | 0.000 | 0.003 | |
| plot_interactive | 4.647 | 1.335 | 1.054 | |
| plot_plsda_multimodel | 0.213 | 0.298 | 0.326 | |
| plot_plsda_samples | 0.146 | 0.176 | 0.250 | |
| plot_vip_scores | 0.030 | 0.055 | 0.002 | |
| plot_webgl | 0.003 | 0.000 | 0.003 | |
| plsda_auroc_vip_compare | 0.627 | 0.397 | 0.876 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0.003 | 0.000 | 0.004 | |
| print.nmr_dataset | 0.893 | 0.501 | 0.945 | |
| print.nmr_dataset_1D | 1.022 | 0.605 | 1.154 | |
| print.nmr_dataset_peak_table | 1.027 | 0.561 | 1.128 | |
| random_subsampling | 0.000 | 0.002 | 0.003 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 0.877 | 0.506 | 0.937 | |
| sub-.nmr_dataset_1D | 1.187 | 0.537 | 1.212 | |
| sub-.nmr_dataset_peak_table | 1.073 | 0.646 | 1.207 | |
| tidy.nmr_dataset_1D | 1.173 | 0.861 | 1.498 | |
| to_ChemoSpec | 1.166 | 0.733 | 1.392 | |
| validate_nmr_dataset | 1.948 | 1.391 | 2.321 | |
| validate_nmr_dataset_family | 1.132 | 0.710 | 1.286 | |
| validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.001 | |
| zzz | 0.000 | 0.000 | 2.002 | |