Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 | |||||||||
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: 2024-12-19 22:51:05 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:01:15 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 609.9 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 4.4.2 (2024-10-31 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 7.54 0.33 12.91 nmr_pca_outliers_robust 6.69 0.19 11.18 Peak_detection 3.27 0.24 31.34 plsda_auroc_vip_compare 3.22 0.06 18.43 nmr_meta_add 2.39 0.05 11.14 permutation_test_model 2.32 0.07 16.31 nmr_pca_build_model 2.14 0.18 10.79 bp_VIP_analysis 2.24 0.05 15.04 validate_nmr_dataset 2.15 0.07 10.79 permutation_test_plot 2.17 0.04 16.08 nmr_interpolate_1D 1.98 0.03 10.67 nmr_read_samples 1.74 0.05 10.28 models_stability_plot_plsda 1.64 0.06 10.09 nmr_data_analysis 1.57 0.05 9.95 plot_plsda_samples 1.52 0.06 9.12 bp_kfold_VIP_analysis 1.54 0.00 10.00 nmr_data_1r_to_SummarizedExperiment 1.47 0.05 6.13 plot_plsda_multimodel 1.50 0.00 11.18 AlpsNMR-package 1.30 0.11 5.98 nmr_dataset_peak_table_to_SummarizedExperiment 1.33 0.05 6.08 nmr_pca_outliers_filter 1.33 0.04 5.77 to_ChemoSpec 1.35 0.00 5.63 SummarizedExperiment_to_nmr_dataset_peak_table 1.28 0.06 6.23 format.nmr_dataset_peak_table 1.19 0.05 5.51 nmr_pca_outliers 1.11 0.07 5.62 print.nmr_dataset_peak_table 1.11 0.07 5.56 is.nmr_dataset_peak_table 1.08 0.05 5.50 tidy.nmr_dataset_1D 1.05 0.07 5.31 sub-.nmr_dataset_peak_table 1.05 0.05 5.47 validate_nmr_dataset_family 1.05 0.03 5.72 nmr_autophase 1.06 0.01 5.52 plot_interactive 0.97 0.10 5.26 print.nmr_dataset_1D 1.04 0.01 5.25 new_nmr_dataset_peak_table 1.02 0.02 5.61 format.nmr_dataset_1D 0.93 0.09 5.59 print.nmr_dataset 0.99 0.02 5.43 sub-.nmr_dataset_1D 0.98 0.03 5.56 nmr_meta_groups 0.98 0.02 5.36 nmr_meta_get_column 0.91 0.05 5.33 is.nmr_dataset_1D 0.88 0.08 5.28 filter.nmr_dataset_family 0.92 0.03 5.44 sub-.nmr_dataset 0.91 0.04 5.44 nmr_export_data_1r 0.89 0.06 5.25 format.nmr_dataset 0.88 0.05 5.61 nmr_meta_export 0.91 0.02 5.20 is.nmr_dataset 0.89 0.02 5.45 load_and_save_functions 0.90 0.01 5.32 nmr_meta_get 0.87 0.01 5.33 * 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 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 24.29 1.29 83.89
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.30 | 0.11 | 5.98 | |
HMDB_blood | 0 | 0 | 0 | |
HMDB_cell | 0.00 | 0.02 | 0.02 | |
HMDB_urine | 0.01 | 0.00 | 0.01 | |
Parameters_blood | 0 | 0 | 0 | |
Parameters_cell | 0.00 | 0.01 | 0.02 | |
Parameters_urine | 0 | 0 | 0 | |
Peak_detection | 3.27 | 0.24 | 31.34 | |
Pipelines | 0 | 0 | 0 | |
ROI_blood | 0.00 | 0.01 | 0.02 | |
ROI_cell | 0.02 | 0.00 | 0.01 | |
ROI_urine | 0 | 0 | 0 | |
SummarizedExperiment_to_nmr_data_1r | 7.54 | 0.33 | 12.91 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.28 | 0.06 | 6.23 | |
bp_VIP_analysis | 2.24 | 0.05 | 15.04 | |
bp_kfold_VIP_analysis | 1.54 | 0.00 | 10.00 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.10 | 0.00 | 0.09 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.92 | 0.03 | 5.44 | |
format.nmr_dataset | 0.88 | 0.05 | 5.61 | |
format.nmr_dataset_1D | 0.93 | 0.09 | 5.59 | |
format.nmr_dataset_peak_table | 1.19 | 0.05 | 5.51 | |
get_integration_with_metadata | 0.03 | 0.02 | 0.05 | |
hmdb | 0.06 | 0.10 | 0.17 | |
is.nmr_dataset | 0.89 | 0.02 | 5.45 | |
is.nmr_dataset_1D | 0.88 | 0.08 | 5.28 | |
is.nmr_dataset_peak_table | 1.08 | 0.05 | 5.50 | |
load_and_save_functions | 0.90 | 0.01 | 5.32 | |
models_stability_plot_bootstrap | 0 | 0 | 0 | |
models_stability_plot_plsda | 1.64 | 0.06 | 10.09 | |
new_nmr_dataset | 0 | 0 | 0 | |
new_nmr_dataset_1D | 0 | 0 | 0 | |
new_nmr_dataset_peak_table | 1.02 | 0.02 | 5.61 | |
nmr_autophase | 1.06 | 0.01 | 5.52 | |
nmr_baseline_estimation | 0.02 | 0.00 | 0.01 | |
nmr_baseline_removal | 0.01 | 0.00 | 0.02 | |
nmr_baseline_threshold | 0 | 0 | 0 | |
nmr_baseline_threshold_plot | 0.25 | 0.00 | 0.25 | |
nmr_batman | 0.02 | 0.00 | 0.01 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.03 | 0.00 | 0.03 | |
nmr_data | 0.05 | 0.00 | 0.05 | |
nmr_data_1r_to_SummarizedExperiment | 1.47 | 0.05 | 6.13 | |
nmr_data_analysis | 1.57 | 0.05 | 9.95 | |
nmr_dataset | 0 | 0 | 0 | |
nmr_dataset_1D | 0 | 0 | 0 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.33 | 0.05 | 6.08 | |
nmr_exclude_region | 0.00 | 0.01 | 0.01 | |
nmr_export_data_1r | 0.89 | 0.06 | 5.25 | |
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 | 0.01 | |
nmr_identify_regions_urine | 0.02 | 0.00 | 0.02 | |
nmr_integrate_regions | 0.02 | 0.00 | 0.02 | |
nmr_interpolate_1D | 1.98 | 0.03 | 10.67 | |
nmr_meta_add | 2.39 | 0.05 | 11.14 | |
nmr_meta_export | 0.91 | 0.02 | 5.20 | |
nmr_meta_get | 0.87 | 0.01 | 5.33 | |
nmr_meta_get_column | 0.91 | 0.05 | 5.33 | |
nmr_meta_groups | 0.98 | 0.02 | 5.36 | |
nmr_normalize | 0.33 | 0.00 | 0.32 | |
nmr_pca_build_model | 2.14 | 0.18 | 10.79 | |
nmr_pca_outliers | 1.11 | 0.07 | 5.62 | |
nmr_pca_outliers_filter | 1.33 | 0.04 | 5.77 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 6.69 | 0.19 | 11.18 | |
nmr_pca_plots | 0.56 | 0.00 | 0.57 | |
nmr_peak_clustering | 0.11 | 0.00 | 0.11 | |
nmr_ppm_resolution | 0.01 | 0.00 | 0.01 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.74 | 0.05 | 10.28 | |
nmr_zip_bruker_samples | 0.01 | 0.04 | 0.47 | |
peaklist_accept_peaks | 0 | 0 | 0 | |
permutation_test_model | 2.32 | 0.07 | 16.31 | |
permutation_test_plot | 2.17 | 0.04 | 16.08 | |
plot.nmr_dataset_1D | 0.01 | 0.00 | 0.02 | |
plot_bootstrap_multimodel | 0 | 0 | 0 | |
plot_interactive | 0.97 | 0.10 | 5.26 | |
plot_plsda_multimodel | 1.50 | 0.00 | 11.18 | |
plot_plsda_samples | 1.52 | 0.06 | 9.12 | |
plot_vip_scores | 0 | 0 | 0 | |
plot_webgl | 0 | 0 | 0 | |
plsda_auroc_vip_compare | 3.22 | 0.06 | 18.43 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0 | 0 | 0 | |
print.nmr_dataset | 0.99 | 0.02 | 5.43 | |
print.nmr_dataset_1D | 1.04 | 0.01 | 5.25 | |
print.nmr_dataset_peak_table | 1.11 | 0.07 | 5.56 | |
random_subsampling | 0 | 0 | 0 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.91 | 0.04 | 5.44 | |
sub-.nmr_dataset_1D | 0.98 | 0.03 | 5.56 | |
sub-.nmr_dataset_peak_table | 1.05 | 0.05 | 5.47 | |
tidy.nmr_dataset_1D | 1.05 | 0.07 | 5.31 | |
to_ASICS | 1.12 | 0.14 | 1.27 | |
to_ChemoSpec | 1.35 | 0.00 | 5.63 | |
validate_nmr_dataset | 2.15 | 0.07 | 10.79 | |
validate_nmr_dataset_family | 1.05 | 0.03 | 5.72 | |
validate_nmr_dataset_peak_table | 0 | 0 | 0 | |
zzz | 0.00 | 0.00 | 2.03 | |