Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz |
StartedAt: 2024-11-19 19:23:32 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 19:29:54 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 381.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 Peak_detection 8.466 2.654 7.954 SummarizedExperiment_to_nmr_data_1r 6.792 1.432 6.464 format.nmr_dataset 3.158 2.600 2.657 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 18.217 6.642 17.646
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.608 | 0.451 | 1.455 | |
HMDB_blood | 0.005 | 0.002 | 0.007 | |
HMDB_cell | 0.002 | 0.001 | 0.002 | |
HMDB_urine | 0.004 | 0.001 | 0.005 | |
Parameters_blood | 0.001 | 0.001 | 0.003 | |
Parameters_cell | 0.001 | 0.001 | 0.003 | |
Parameters_urine | 0.002 | 0.001 | 0.003 | |
Peak_detection | 8.466 | 2.654 | 7.954 | |
Pipelines | 0.001 | 0.001 | 0.002 | |
ROI_blood | 0.004 | 0.002 | 0.006 | |
ROI_cell | 0.004 | 0.001 | 0.005 | |
ROI_urine | 0.004 | 0.001 | 0.005 | |
SummarizedExperiment_to_nmr_data_1r | 6.792 | 1.432 | 6.464 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.890 | 0.452 | 0.775 | |
bp_VIP_analysis | 1.098 | 0.700 | 0.888 | |
bp_kfold_VIP_analysis | 0.719 | 0.387 | 0.474 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.056 | 0.018 | 0.076 | |
files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
filter.nmr_dataset_family | 1.189 | 0.874 | 0.785 | |
format.nmr_dataset | 3.158 | 2.600 | 2.657 | |
format.nmr_dataset_1D | 0.691 | 0.522 | 0.587 | |
format.nmr_dataset_peak_table | 0.614 | 0.415 | 0.701 | |
get_integration_with_metadata | 0.025 | 0.012 | 0.039 | |
hmdb | 0.049 | 0.018 | 0.068 | |
is.nmr_dataset | 0.690 | 0.541 | 0.534 | |
is.nmr_dataset_1D | 0.737 | 0.580 | 0.661 | |
is.nmr_dataset_peak_table | 0.701 | 0.417 | 0.593 | |
load_and_save_functions | 0.86 | 0.74 | 0.56 | |
models_stability_plot_bootstrap | 0.002 | 0.003 | 0.004 | |
models_stability_plot_plsda | 0.384 | 0.415 | 0.383 | |
new_nmr_dataset | 0.001 | 0.000 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.647 | 0.454 | 0.740 | |
nmr_autophase | 0.196 | 0.135 | 0.328 | |
nmr_baseline_estimation | 0.007 | 0.005 | 0.013 | |
nmr_baseline_removal | 0.003 | 0.002 | 0.006 | |
nmr_baseline_threshold | 0.001 | 0.001 | 0.001 | |
nmr_baseline_threshold_plot | 0.186 | 0.036 | 0.222 | |
nmr_batman | 0.003 | 0.001 | 0.004 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.030 | 0.006 | 0.037 | |
nmr_data | 0.038 | 0.009 | 0.047 | |
nmr_data_1r_to_SummarizedExperiment | 0.985 | 0.747 | 0.970 | |
nmr_data_analysis | 0.620 | 0.712 | 0.565 | |
nmr_dataset | 0.000 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.161 | 0.871 | 0.889 | |
nmr_exclude_region | 0.005 | 0.002 | 0.006 | |
nmr_export_data_1r | 0.693 | 0.455 | 0.570 | |
nmr_get_peak_distances | 0.007 | 0.001 | 0.007 | |
nmr_identify_regions_blood | 0.011 | 0.003 | 0.013 | |
nmr_identify_regions_cell | 0.008 | 0.001 | 0.008 | |
nmr_identify_regions_urine | 0.011 | 0.002 | 0.013 | |
nmr_integrate_regions | 0.008 | 0.001 | 0.010 | |
nmr_interpolate_1D | 1.494 | 1.020 | 1.214 | |
nmr_meta_add | 1.697 | 1.078 | 1.481 | |
nmr_meta_export | 0.621 | 0.407 | 0.479 | |
nmr_meta_get | 0.723 | 0.517 | 0.575 | |
nmr_meta_get_column | 0.704 | 0.521 | 0.586 | |
nmr_meta_groups | 0.772 | 0.592 | 0.627 | |
nmr_normalize | 0.201 | 0.021 | 0.223 | |
nmr_pca_build_model | 1.441 | 0.902 | 1.444 | |
nmr_pca_outliers | 0.795 | 0.476 | 0.692 | |
nmr_pca_outliers_filter | 1.578 | 0.879 | 1.409 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 3.943 | 0.498 | 3.900 | |
nmr_pca_plots | 0.260 | 0.010 | 0.272 | |
nmr_peak_clustering | 0.064 | 0.003 | 0.068 | |
nmr_ppm_resolution | 0.006 | 0.002 | 0.007 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 1.161 | 0.769 | 0.885 | |
nmr_zip_bruker_samples | 0.194 | 0.031 | 0.239 | |
peaklist_accept_peaks | 0.003 | 0.002 | 0.004 | |
permutation_test_model | 0.659 | 0.574 | 1.481 | |
permutation_test_plot | 3.071 | 1.830 | 1.671 | |
plot.nmr_dataset_1D | 0.002 | 0.001 | 0.002 | |
plot_bootstrap_multimodel | 0.002 | 0.001 | 0.003 | |
plot_interactive | 2.311 | 1.271 | 0.587 | |
plot_plsda_multimodel | 0.229 | 0.298 | 0.261 | |
plot_plsda_samples | 0.113 | 0.144 | 0.242 | |
plot_vip_scores | 0.001 | 0.002 | 0.002 | |
plot_webgl | 0.001 | 0.001 | 0.001 | |
plsda_auroc_vip_compare | 0.348 | 0.278 | 0.601 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.002 | 0.001 | 0.002 | |
print.nmr_dataset | 0.617 | 0.461 | 0.493 | |
print.nmr_dataset_1D | 0.586 | 0.450 | 0.654 | |
print.nmr_dataset_peak_table | 0.799 | 0.605 | 0.687 | |
random_subsampling | 0.001 | 0.002 | 0.003 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.902 | 0.863 | 0.582 | |
sub-.nmr_dataset_1D | 0.672 | 0.481 | 0.627 | |
sub-.nmr_dataset_peak_table | 0.783 | 0.561 | 0.670 | |
tidy.nmr_dataset_1D | 0.750 | 0.488 | 0.657 | |
to_ASICS | 0.757 | 0.126 | 0.888 | |
to_ChemoSpec | 0.723 | 0.454 | 0.656 | |
validate_nmr_dataset | 1.483 | 1.168 | 1.279 | |
validate_nmr_dataset_family | 0.701 | 0.548 | 0.590 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.001 | |
zzz | 0.000 | 0.000 | 2.144 | |