| Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-09-27 11:36:10 -0400 (Wed, 27 Sep 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" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 | | ||||||||
|
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: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings AlpsNMR_4.2.0.tar.gz |
| StartedAt: 2023-09-26 23:25:18 -0400 (Tue, 26 Sep 2023) |
| EndedAt: 2023-09-26 23:33:03 -0400 (Tue, 26 Sep 2023) |
| EllapsedTime: 465.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AlpsNMR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings AlpsNMR_4.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* 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 '4.2.0'
* 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 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
nmr_pca_outliers_robust 4.88 0.25 8.53
SummarizedExperiment_to_nmr_data_1r 4.78 0.23 8.61
plsda_auroc_vip_compare 2.83 0.01 14.50
Peak_detection 2.18 0.20 23.05
nmr_meta_add 1.83 0.06 9.00
permutation_test_plot 1.86 0.03 12.47
bp_VIP_analysis 1.86 0.00 11.79
permutation_test_model 1.81 0.04 12.33
nmr_pca_build_model 1.63 0.03 8.49
nmr_read_samples 1.61 0.00 8.27
nmr_interpolate_1D 1.47 0.11 8.41
validate_nmr_dataset 1.50 0.03 8.39
nmr_data_analysis 1.30 0.02 7.57
models_stability_plot_plsda 1.22 0.07 7.22
plot_plsda_samples 1.26 0.03 7.09
plot_plsda_multimodel 1.27 0.01 7.06
bp_kfold_VIP_analysis 1.23 0.01 7.86
nmr_dataset_peak_table_to_SummarizedExperiment 1.13 0.01 5.11
* 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-3.17-bioc\R\bin\R.exe CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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
9.75 0.84 53.62
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
| name | user | system | elapsed | |
| AlpsNMR-package | 1.13 | 0.08 | 4.62 | |
| HMDB_blood | 0 | 0 | 0 | |
| HMDB_cell | 0 | 0 | 0 | |
| HMDB_urine | 0.01 | 0.00 | 0.01 | |
| Parameters_blood | 0 | 0 | 0 | |
| Parameters_cell | 0.02 | 0.00 | 0.02 | |
| Parameters_urine | 0 | 0 | 0 | |
| Peak_detection | 2.18 | 0.20 | 23.05 | |
| Pipelines | 0 | 0 | 0 | |
| ROI_blood | 0 | 0 | 0 | |
| ROI_cell | 0 | 0 | 0 | |
| ROI_urine | 0 | 0 | 0 | |
| SummarizedExperiment_to_nmr_data_1r | 4.78 | 0.23 | 8.61 | |
| SummarizedExperiment_to_nmr_dataset_peak_table | 1.11 | 0.05 | 4.68 | |
| bp_VIP_analysis | 1.86 | 0.00 | 11.79 | |
| bp_kfold_VIP_analysis | 1.23 | 0.01 | 7.86 | |
| download_MTBLS242 | 0 | 0 | 0 | |
| file_lister | 0.08 | 0.00 | 0.09 | |
| files_to_rDolphin | 0 | 0 | 0 | |
| filter.nmr_dataset_family | 0.80 | 0.02 | 4.30 | |
| format.nmr_dataset | 0.70 | 0.01 | 4.22 | |
| format.nmr_dataset_1D | 0.82 | 0.00 | 4.10 | |
| format.nmr_dataset_peak_table | 0.82 | 0.02 | 4.66 | |
| get_integration_with_metadata | 0.04 | 0.00 | 0.03 | |
| hmdb | 0.06 | 0.09 | 0.15 | |
| is.nmr_dataset | 0.86 | 0.05 | 4.75 | |
| is.nmr_dataset_1D | 0.74 | 0.05 | 4.31 | |
| is.nmr_dataset_peak_table | 0.86 | 0.03 | 4.36 | |
| load_and_save_functions | 0.73 | 0.01 | 4.69 | |
| models_stability_plot_bootstrap | 0 | 0 | 0 | |
| models_stability_plot_plsda | 1.22 | 0.07 | 7.22 | |
| new_nmr_dataset | 0 | 0 | 0 | |
| new_nmr_dataset_1D | 0 | 0 | 0 | |
| new_nmr_dataset_peak_table | 0.83 | 0.01 | 4.81 | |
| nmr_baseline_estimation | 0.11 | 0.05 | 0.16 | |
| nmr_baseline_removal | 0 | 0 | 0 | |
| nmr_baseline_threshold | 0 | 0 | 0 | |
| nmr_baseline_threshold_plot | 0.25 | 0.05 | 0.29 | |
| nmr_batman | 0 | 0 | 0 | |
| nmr_batman_options | 0 | 0 | 0 | |
| nmr_build_peak_table | 0.04 | 0.00 | 0.05 | |
| nmr_data | 0.07 | 0.00 | 0.06 | |
| nmr_data_1r_to_SummarizedExperiment | 1.04 | 0.01 | 4.67 | |
| nmr_data_analysis | 1.30 | 0.02 | 7.57 | |
| nmr_dataset | 0 | 0 | 0 | |
| nmr_dataset_1D | 0 | 0 | 0 | |
| nmr_dataset_peak_table_to_SummarizedExperiment | 1.13 | 0.01 | 5.11 | |
| nmr_exclude_region | 0.01 | 0.00 | 0.01 | |
| nmr_export_data_1r | 0.83 | 0.00 | 4.42 | |
| nmr_get_peak_distances | 0 | 0 | 0 | |
| nmr_identify_regions_blood | 0 | 0 | 0 | |
| nmr_identify_regions_cell | 0.00 | 0.02 | 0.02 | |
| nmr_identify_regions_urine | 0.04 | 0.00 | 0.02 | |
| nmr_integrate_regions | 0.01 | 0.00 | 0.01 | |
| nmr_interpolate_1D | 1.47 | 0.11 | 8.41 | |
| nmr_meta_add | 1.83 | 0.06 | 9.00 | |
| nmr_meta_export | 0.73 | 0.02 | 4.36 | |
| nmr_meta_get | 0.94 | 0.00 | 4.40 | |
| nmr_meta_get_column | 0.73 | 0.01 | 4.47 | |
| nmr_meta_groups | 0.80 | 0.03 | 4.17 | |
| nmr_normalize | 0.22 | 0.00 | 0.22 | |
| nmr_pca_build_model | 1.63 | 0.03 | 8.49 | |
| nmr_pca_outliers | 0.86 | 0.03 | 4.22 | |
| nmr_pca_outliers_filter | 0.88 | 0.07 | 4.24 | |
| nmr_pca_outliers_plot | 0 | 0 | 0 | |
| nmr_pca_outliers_robust | 4.88 | 0.25 | 8.53 | |
| nmr_pca_plots | 0.35 | 0.00 | 0.34 | |
| nmr_peak_clustering | 0.09 | 0.00 | 0.10 | |
| nmr_ppm_resolution | 0.00 | 0.01 | 0.01 | |
| nmr_read_bruker_fid | 0 | 0 | 0 | |
| nmr_read_samples | 1.61 | 0.00 | 8.27 | |
| nmr_zip_bruker_samples | 0.01 | 0.03 | 0.39 | |
| peaklist_accept_peaks | 0.02 | 0.00 | 0.01 | |
| permutation_test_model | 1.81 | 0.04 | 12.33 | |
| permutation_test_plot | 1.86 | 0.03 | 12.47 | |
| plot.nmr_dataset_1D | 0 | 0 | 0 | |
| plot_bootstrap_multimodel | 0 | 0 | 0 | |
| plot_interactive | 0.78 | 0.00 | 4.27 | |
| plot_plsda_multimodel | 1.27 | 0.01 | 7.06 | |
| plot_plsda_samples | 1.26 | 0.03 | 7.09 | |
| plot_vip_scores | 0 | 0 | 0 | |
| plot_webgl | 0.00 | 0.02 | 0.02 | |
| plsda_auroc_vip_compare | 2.83 | 0.01 | 14.50 | |
| plsda_auroc_vip_method | 0 | 0 | 0 | |
| ppm_resolution | 0 | 0 | 0 | |
| print.nmr_dataset | 0.83 | 0.02 | 4.51 | |
| print.nmr_dataset_1D | 0.89 | 0.05 | 4.47 | |
| print.nmr_dataset_peak_table | 0.88 | 0.04 | 4.47 | |
| random_subsampling | 0 | 0 | 0 | |
| save_files_to_rDolphin | 0 | 0 | 0 | |
| save_profiling_output | 0 | 0 | 0 | |
| sub-.nmr_dataset | 0.75 | 0.04 | 4.31 | |
| sub-.nmr_dataset_1D | 0.82 | 0.01 | 4.69 | |
| sub-.nmr_dataset_peak_table | 0.86 | 0.02 | 4.60 | |
| tidy.nmr_dataset_1D | 0.85 | 0.03 | 4.37 | |
| to_ChemoSpec | 0.92 | 0.06 | 4.36 | |
| validate_nmr_dataset | 1.50 | 0.03 | 8.39 | |
| validate_nmr_dataset_family | 0.84 | 0.00 | 4.48 | |
| validate_nmr_dataset_peak_table | 0.02 | 0.00 | 0.02 | |
| zzz | 0.00 | 0.00 | 2.05 | |