Sergio Oller Moreno
| Snapshot Date: 2025-03-24 13:00 -0400 (Mon, 24 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/AlpsNMR |
| git_branch: RELEASE_3_20 |
| git_last_commit: ab34115 |
| git_last_commit_date: 2024-10-29 10:53:23 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-27 12:06 -0400 (Thu, 27 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4420 |
| 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 58/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.8.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 4.8.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz |
| StartedAt: 2025-03-24 22:51:00 -0400 (Mon, 24 Mar 2025) |
| EndedAt: 2025-03-24 23:01:01 -0400 (Mon, 24 Mar 2025) |
| EllapsedTime: 601.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AlpsNMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AlpsNMR' version '4.8.0'
* 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 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 code 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
SummarizedExperiment_to_nmr_data_1r 7.21 0.28 12.13
nmr_pca_outliers_robust 6.45 0.23 11.06
Peak_detection 3.35 0.21 30.55
plsda_auroc_vip_compare 3.17 0.03 18.70
permutation_test_plot 2.56 0.03 16.66
nmr_meta_add 2.34 0.08 11.19
permutation_test_model 2.32 0.00 16.43
bp_VIP_analysis 2.26 0.05 15.16
nmr_pca_build_model 2.17 0.11 10.97
validate_nmr_dataset 2.10 0.06 11.20
nmr_interpolate_1D 2.03 0.06 10.53
nmr_read_samples 1.95 0.03 10.98
nmr_data_analysis 1.66 0.03 10.19
AlpsNMR-package 1.50 0.07 6.04
plot_plsda_samples 1.52 0.05 9.04
plot_plsda_multimodel 1.47 0.06 9.67
bp_kfold_VIP_analysis 1.52 0.00 10.25
SummarizedExperiment_to_nmr_dataset_peak_table 1.41 0.08 5.79
nmr_data_1r_to_SummarizedExperiment 1.39 0.08 6.08
nmr_dataset_peak_table_to_SummarizedExperiment 1.41 0.03 5.95
models_stability_plot_plsda 1.42 0.01 10.05
to_ChemoSpec 1.24 0.09 5.52
nmr_pca_outliers_filter 1.16 0.09 5.61
new_nmr_dataset_peak_table 1.12 0.05 5.50
validate_nmr_dataset_family 1.15 0.02 5.59
sub-.nmr_dataset_peak_table 1.14 0.02 5.45
nmr_autophase 1.06 0.06 5.54
is.nmr_dataset_peak_table 1.05 0.06 5.55
plot_interactive 1.04 0.05 6.98
print.nmr_dataset_peak_table 1.06 0.03 5.44
filter.nmr_dataset_family 0.97 0.09 5.33
format.nmr_dataset_peak_table 1.02 0.03 5.39
nmr_pca_outliers 1.03 0.02 5.36
nmr_export_data_1r 1.00 0.03 5.63
print.nmr_dataset_1D 1.01 0.02 5.34
load_and_save_functions 0.97 0.05 5.28
nmr_meta_groups 0.94 0.05 5.36
nmr_meta_get 0.95 0.03 5.19
tidy.nmr_dataset_1D 0.97 0.01 5.28
sub-.nmr_dataset_1D 0.90 0.06 5.21
is.nmr_dataset_1D 0.92 0.02 5.21
sub-.nmr_dataset 0.91 0.03 5.17
format.nmr_dataset_1D 0.87 0.05 5.22
nmr_meta_export 0.91 0.01 5.23
format.nmr_dataset 0.89 0.00 5.22
nmr_meta_get_column 0.87 0.02 5.17
is.nmr_dataset 0.87 0.00 5.25
print.nmr_dataset 0.80 0.03 5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
Attaching package: 'AlpsNMR'
The following object is masked from 'package:stats':
filter
>
> test_check("AlpsNMR")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_rDolphin.R:2:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 93 ]
>
> proc.time()
user system elapsed
24.14 1.50 83.93
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 1.50 | 0.07 | 6.04 | |
| HMDB_blood | 0 | 0 | 0 | |
| HMDB_cell | 0 | 0 | 0 | |
| HMDB_urine | 0.00 | 0.01 | 0.01 | |
| Parameters_blood | 0 | 0 | 0 | |
| Parameters_cell | 0.02 | 0.00 | 0.00 | |
| Parameters_urine | 0.01 | 0.00 | 0.01 | |
| Peak_detection | 3.35 | 0.21 | 30.55 | |
| Pipelines | 0 | 0 | 0 | |
| ROI_blood | 0.00 | 0.01 | 0.01 | |
| ROI_cell | 0 | 0 | 0 | |
| ROI_urine | 0 | 0 | 0 | |
| SummarizedExperiment_to_nmr_data_1r | 7.21 | 0.28 | 12.13 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.41 | 0.08 | 5.79 | |
| bp_VIP_analysis | 2.26 | 0.05 | 15.16 | |
| bp_kfold_VIP_analysis | 1.52 | 0.00 | 10.25 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.03 | 0.03 | 0.06 | |
| files_to_rDolphin | 0 | 0 | 0 | |
| filter.nmr_dataset_family | 0.97 | 0.09 | 5.33 | |
| format.nmr_dataset | 0.89 | 0.00 | 5.22 | |
| format.nmr_dataset_1D | 0.87 | 0.05 | 5.22 | |
| format.nmr_dataset_peak_table | 1.02 | 0.03 | 5.39 | |
| get_integration_with_metadata | 0.03 | 0.02 | 0.04 | |
| hmdb | 0.05 | 0.12 | 0.18 | |
| is.nmr_dataset | 0.87 | 0.00 | 5.25 | |
| is.nmr_dataset_1D | 0.92 | 0.02 | 5.21 | |
| is.nmr_dataset_peak_table | 1.05 | 0.06 | 5.55 | |
| load_and_save_functions | 0.97 | 0.05 | 5.28 | |
| models_stability_plot_bootstrap | 0 | 0 | 0 | |
| models_stability_plot_plsda | 1.42 | 0.01 | 10.05 | |
| new_nmr_dataset | 0 | 0 | 0 | |
| new_nmr_dataset_1D | 0.02 | 0.00 | 0.02 | |
| new_nmr_dataset_peak_table | 1.12 | 0.05 | 5.50 | |
| nmr_autophase | 1.06 | 0.06 | 5.54 | |
| nmr_baseline_estimation | 0.00 | 0.00 | 0.03 | |
| nmr_baseline_removal | 0.02 | 0.00 | 0.02 | |
| nmr_baseline_threshold | 0 | 0 | 0 | |
| nmr_baseline_threshold_plot | 0.28 | 0.00 | 0.28 | |
| nmr_batman | 0 | 0 | 0 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.03 | 0.01 | 0.04 | |
| nmr_data | 0.03 | 0.02 | 0.05 | |
| nmr_data_1r_to_SummarizedExperiment | 1.39 | 0.08 | 6.08 | |
| nmr_data_analysis | 1.66 | 0.03 | 10.19 | |
| nmr_dataset | 0 | 0 | 0 | |
| nmr_dataset_1D | 0 | 0 | 0 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.41 | 0.03 | 5.95 | |
| nmr_exclude_region | 0 | 0 | 0 | |
| nmr_export_data_1r | 1.00 | 0.03 | 5.63 | |
| nmr_get_peak_distances | 0 | 0 | 0 | |
| nmr_identify_regions_blood | 0.02 | 0.00 | 0.02 | |
| nmr_identify_regions_cell | 0.01 | 0.00 | 0.02 | |
| nmr_identify_regions_urine | 0.02 | 0.00 | 0.01 | |
| nmr_integrate_regions | 0.02 | 0.00 | 0.02 | |
| nmr_interpolate_1D | 2.03 | 0.06 | 10.53 | |
| nmr_meta_add | 2.34 | 0.08 | 11.19 | |
| nmr_meta_export | 0.91 | 0.01 | 5.23 | |
| nmr_meta_get | 0.95 | 0.03 | 5.19 | |
| nmr_meta_get_column | 0.87 | 0.02 | 5.17 | |
| nmr_meta_groups | 0.94 | 0.05 | 5.36 | |
| nmr_normalize | 0.33 | 0.01 | 0.34 | |
| nmr_pca_build_model | 2.17 | 0.11 | 10.97 | |
| nmr_pca_outliers | 1.03 | 0.02 | 5.36 | |
| nmr_pca_outliers_filter | 1.16 | 0.09 | 5.61 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 6.45 | 0.23 | 11.06 | |
| nmr_pca_plots | 0.56 | 0.00 | 0.56 | |
| nmr_peak_clustering | 0.09 | 0.00 | 0.09 | |
| nmr_ppm_resolution | 0.02 | 0.02 | 0.04 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 1.95 | 0.03 | 10.98 | |
| nmr_zip_bruker_samples | 0.00 | 0.03 | 0.77 | |
| peaklist_accept_peaks | 0 | 0 | 0 | |
| permutation_test_model | 2.32 | 0.00 | 16.43 | |
| permutation_test_plot | 2.56 | 0.03 | 16.66 | |
| plot.nmr_dataset_1D | 0 | 0 | 0 | |
| plot_bootstrap_multimodel | 0 | 0 | 0 | |
| plot_interactive | 1.04 | 0.05 | 6.98 | |
| plot_plsda_multimodel | 1.47 | 0.06 | 9.67 | |
| plot_plsda_samples | 1.52 | 0.05 | 9.04 | |
| plot_vip_scores | 0 | 0 | 0 | |
| plot_webgl | 0.01 | 0.00 | 0.02 | |
| plsda_auroc_vip_compare | 3.17 | 0.03 | 18.70 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0.02 | 0.00 | 0.02 | |
| print.nmr_dataset | 0.80 | 0.03 | 5.14 | |
| print.nmr_dataset_1D | 1.01 | 0.02 | 5.34 | |
| print.nmr_dataset_peak_table | 1.06 | 0.03 | 5.44 | |
| random_subsampling | 0 | 0 | 0 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 0.91 | 0.03 | 5.17 | |
| sub-.nmr_dataset_1D | 0.90 | 0.06 | 5.21 | |
| sub-.nmr_dataset_peak_table | 1.14 | 0.02 | 5.45 | |
| tidy.nmr_dataset_1D | 0.97 | 0.01 | 5.28 | |
| to_ASICS | 1.00 | 0.15 | 1.14 | |
| to_ChemoSpec | 1.24 | 0.09 | 5.52 | |
| validate_nmr_dataset | 2.10 | 0.06 | 11.20 | |
| validate_nmr_dataset_family | 1.15 | 0.02 | 5.59 | |
| validate_nmr_dataset_peak_table | 0 | 0 | 0 | |
| zzz | 0.00 | 0.00 | 2.02 | |