| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:31 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 56/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AlpsNMR 4.4.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / 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: 4.4.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings AlpsNMR_4.4.0.tar.gz |
| StartedAt: 2024-04-15 22:13:27 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 22:21:58 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 511.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings AlpsNMR_4.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* 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 '4.4.0'
* 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 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
SummarizedExperiment_to_nmr_data_1r 6.63 0.23 10.74
nmr_pca_outliers_robust 5.86 0.18 9.96
plsda_auroc_vip_compare 2.90 0.03 14.41
Peak_detection 2.69 0.14 25.98
nmr_meta_add 2.28 0.04 10.20
permutation_test_plot 2.17 0.03 14.91
bp_VIP_analysis 2.07 0.02 12.57
permutation_test_model 1.97 0.07 13.72
nmr_pca_build_model 1.91 0.03 9.54
nmr_interpolate_1D 1.74 0.08 9.64
validate_nmr_dataset 1.70 0.05 9.08
nmr_read_samples 1.58 0.05 9.07
nmr_data_analysis 1.52 0.06 7.82
plot_plsda_samples 1.55 0.03 7.29
bp_kfold_VIP_analysis 1.48 0.00 8.81
models_stability_plot_plsda 1.44 0.03 7.90
plot_plsda_multimodel 1.45 0.00 8.21
nmr_data_1r_to_SummarizedExperiment 1.37 0.05 5.18
SummarizedExperiment_to_nmr_dataset_peak_table 1.37 0.03 5.04
nmr_dataset_peak_table_to_SummarizedExperiment 1.25 0.03 5.28
AlpsNMR-package 1.20 0.05 5.34
to_ChemoSpec 1.19 0.03 5.05
nmr_pca_outliers_filter 1.13 0.01 5.06
print.nmr_dataset_peak_table 1.00 0.03 5.02
sub-.nmr_dataset_peak_table 0.85 0.04 5.06
* 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: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
10.45 0.93 58.61
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 1.20 | 0.05 | 5.34 | |
| HMDB_blood | 0.00 | 0.02 | 0.02 | |
| HMDB_cell | 0.02 | 0.00 | 0.02 | |
| HMDB_urine | 0.01 | 0.00 | 0.01 | |
| Parameters_blood | 0 | 0 | 0 | |
| Parameters_cell | 0 | 0 | 0 | |
| Parameters_urine | 0 | 0 | 0 | |
| Peak_detection | 2.69 | 0.14 | 25.98 | |
| Pipelines | 0 | 0 | 0 | |
| ROI_blood | 0.00 | 0.02 | 0.02 | |
| ROI_cell | 0 | 0 | 0 | |
| ROI_urine | 0 | 0 | 0 | |
| SummarizedExperiment_to_nmr_data_1r | 6.63 | 0.23 | 10.74 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.37 | 0.03 | 5.04 | |
| bp_VIP_analysis | 2.07 | 0.02 | 12.57 | |
| bp_kfold_VIP_analysis | 1.48 | 0.00 | 8.81 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.08 | 0.04 | 0.11 | |
| files_to_rDolphin | 0 | 0 | 0 | |
| filter.nmr_dataset_family | 0.87 | 0.03 | 4.86 | |
| format.nmr_dataset | 0.82 | 0.02 | 4.91 | |
| format.nmr_dataset_1D | 0.83 | 0.02 | 4.75 | |
| format.nmr_dataset_peak_table | 0.87 | 0.03 | 4.47 | |
| get_integration_with_metadata | 0.03 | 0.00 | 0.03 | |
| hmdb | 0.05 | 0.14 | 0.19 | |
| is.nmr_dataset | 0.75 | 0.01 | 4.67 | |
| is.nmr_dataset_1D | 0.87 | 0.02 | 4.59 | |
| is.nmr_dataset_peak_table | 0.96 | 0.03 | 4.38 | |
| load_and_save_functions | 0.82 | 0.02 | 4.45 | |
| models_stability_plot_bootstrap | 0 | 0 | 0 | |
| models_stability_plot_plsda | 1.44 | 0.03 | 7.90 | |
| new_nmr_dataset | 0 | 0 | 0 | |
| new_nmr_dataset_1D | 0 | 0 | 0 | |
| new_nmr_dataset_peak_table | 0.98 | 0.05 | 4.86 | |
| nmr_baseline_estimation | 0.16 | 0.01 | 0.19 | |
| nmr_baseline_removal | 0 | 0 | 0 | |
| nmr_baseline_threshold | 0.01 | 0.00 | 0.01 | |
| nmr_baseline_threshold_plot | 0.41 | 0.05 | 0.45 | |
| nmr_batman | 0 | 0 | 0 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.04 | 0.00 | 0.05 | |
| nmr_data | 0.05 | 0.00 | 0.04 | |
| nmr_data_1r_to_SummarizedExperiment | 1.37 | 0.05 | 5.18 | |
| nmr_data_analysis | 1.52 | 0.06 | 7.82 | |
| nmr_dataset | 0 | 0 | 0 | |
| nmr_dataset_1D | 0 | 0 | 0 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.25 | 0.03 | 5.28 | |
| nmr_exclude_region | 0 | 0 | 0 | |
| nmr_export_data_1r | 0.94 | 0.00 | 4.75 | |
| nmr_get_peak_distances | 0 | 0 | 0 | |
| nmr_identify_regions_blood | 0.01 | 0.00 | 0.02 | |
| nmr_identify_regions_cell | 0.02 | 0.00 | 0.02 | |
| nmr_identify_regions_urine | 0.00 | 0.02 | 0.01 | |
| nmr_integrate_regions | 0.01 | 0.00 | 0.02 | |
| nmr_interpolate_1D | 1.74 | 0.08 | 9.64 | |
| nmr_meta_add | 2.28 | 0.04 | 10.20 | |
| nmr_meta_export | 0.81 | 0.03 | 4.94 | |
| nmr_meta_get | 0.86 | 0.02 | 4.50 | |
| nmr_meta_get_column | 0.86 | 0.00 | 4.70 | |
| nmr_meta_groups | 0.77 | 0.00 | 4.60 | |
| nmr_normalize | 0.26 | 0.02 | 0.28 | |
| nmr_pca_build_model | 1.91 | 0.03 | 9.54 | |
| nmr_pca_outliers | 1.01 | 0.03 | 4.97 | |
| nmr_pca_outliers_filter | 1.13 | 0.01 | 5.06 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 5.86 | 0.18 | 9.96 | |
| nmr_pca_plots | 0.45 | 0.00 | 0.46 | |
| nmr_peak_clustering | 0.06 | 0.00 | 0.06 | |
| nmr_ppm_resolution | 0.02 | 0.00 | 0.01 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 1.58 | 0.05 | 9.07 | |
| nmr_zip_bruker_samples | 0.01 | 0.01 | 0.39 | |
| peaklist_accept_peaks | 0 | 0 | 0 | |
| permutation_test_model | 1.97 | 0.07 | 13.72 | |
| permutation_test_plot | 2.17 | 0.03 | 14.91 | |
| plot.nmr_dataset_1D | 0 | 0 | 0 | |
| plot_bootstrap_multimodel | 0 | 0 | 0 | |
| plot_interactive | 0.93 | 0.02 | 4.83 | |
| plot_plsda_multimodel | 1.45 | 0.00 | 8.21 | |
| plot_plsda_samples | 1.55 | 0.03 | 7.29 | |
| plot_vip_scores | 0 | 0 | 0 | |
| plot_webgl | 0 | 0 | 0 | |
| plsda_auroc_vip_compare | 2.90 | 0.03 | 14.41 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0 | 0 | 0 | |
| print.nmr_dataset | 0.89 | 0.02 | 4.80 | |
| print.nmr_dataset_1D | 0.84 | 0.01 | 4.70 | |
| print.nmr_dataset_peak_table | 1.00 | 0.03 | 5.02 | |
| random_subsampling | 0 | 0 | 0 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 0.86 | 0.02 | 4.92 | |
| sub-.nmr_dataset_1D | 0.84 | 0.01 | 4.73 | |
| sub-.nmr_dataset_peak_table | 0.85 | 0.04 | 5.06 | |
| tidy.nmr_dataset_1D | 1.01 | 0.04 | 4.83 | |
| to_ChemoSpec | 1.19 | 0.03 | 5.05 | |
| validate_nmr_dataset | 1.70 | 0.05 | 9.08 | |
| validate_nmr_dataset_family | 0.88 | 0.04 | 4.71 | |
| validate_nmr_dataset_peak_table | 0 | 0 | 0 | |
| zzz | 0.00 | 0.00 | 2.03 | |