Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-09 12:04 -0400 (Thu, 09 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 59/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.11.1 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 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: 4.11.1 |
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_4.11.1.tar.gz |
StartedAt: 2025-10-08 20:03:33 -0400 (Wed, 08 Oct 2025) |
EndedAt: 2025-10-08 20:07:29 -0400 (Wed, 08 Oct 2025) |
EllapsedTime: 236.2 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_4.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 ‘4.11.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'reexports.Rd': ‘[magrittr:pipe]{%>%}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: filter.nmr_dataset_family.Rd: dplyr Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 10.440 3.125 9.764 SummarizedExperiment_to_nmr_data_1r 7.983 1.048 8.098 filter.nmr_dataset_family 4.504 3.829 3.928 nmr_pca_outliers_robust 6.294 1.169 6.154 permutation_test_plot 4.631 2.638 2.391 plot_bootstrap_multimodel 3.601 1.761 0.067 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck/00check.log’ for details.
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘AlpsNMR’ ... ** this is package ‘AlpsNMR’ version ‘4.11.1’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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 27.749 11.390 27.877
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.194 | 0.565 | 2.022 | |
HMDB_blood | 0.006 | 0.002 | 0.008 | |
HMDB_cell | 0.003 | 0.001 | 0.004 | |
HMDB_urine | 0.005 | 0.002 | 0.008 | |
Parameters_blood | 0.002 | 0.002 | 0.003 | |
Parameters_cell | 0.002 | 0.001 | 0.003 | |
Parameters_urine | 0.002 | 0.001 | 0.003 | |
Peak_detection | 10.440 | 3.125 | 9.764 | |
Pipelines | 0.002 | 0.001 | 0.003 | |
ROI_blood | 0.003 | 0.001 | 0.004 | |
ROI_cell | 0.003 | 0.002 | 0.005 | |
ROI_urine | 0.004 | 0.001 | 0.006 | |
SummarizedExperiment_to_nmr_data_1r | 7.983 | 1.048 | 8.098 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.716 | 1.191 | 1.591 | |
bp_VIP_analysis | 1.964 | 1.220 | 1.288 | |
bp_kfold_VIP_analysis | 1.209 | 0.765 | 0.886 | |
download_MTBLS242 | 0.000 | 0.000 | 0.001 | |
file_lister | 0.076 | 0.018 | 0.096 | |
files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
filter.nmr_dataset_family | 4.504 | 3.829 | 3.928 | |
format.nmr_dataset | 0.746 | 0.625 | 0.887 | |
format.nmr_dataset_1D | 1.065 | 0.854 | 0.972 | |
format.nmr_dataset_peak_table | 1.199 | 0.992 | 1.181 | |
get_integration_with_metadata | 0.039 | 0.020 | 0.061 | |
hmdb | 0.071 | 0.024 | 0.096 | |
is.nmr_dataset | 1.275 | 1.222 | 0.928 | |
is.nmr_dataset_1D | 0.981 | 0.689 | 0.811 | |
is.nmr_dataset_peak_table | 1.125 | 0.685 | 0.936 | |
load_and_save_functions | 1.062 | 0.857 | 0.842 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.003 | |
models_stability_plot_plsda | 0.637 | 0.777 | 0.666 | |
new_nmr_dataset | 0.001 | 0.001 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
new_nmr_dataset_peak_table | 0.858 | 0.563 | 0.987 | |
nmr_autophase | 0.285 | 0.189 | 0.469 | |
nmr_baseline_estimation | 0.011 | 0.005 | 0.016 | |
nmr_baseline_removal | 0.005 | 0.002 | 0.006 | |
nmr_baseline_threshold | 0.001 | 0.001 | 0.001 | |
nmr_baseline_threshold_plot | 0.615 | 0.297 | 0.523 | |
nmr_batman | 0.003 | 0.001 | 0.004 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.040 | 0.006 | 0.047 | |
nmr_data | 0.062 | 0.010 | 0.071 | |
nmr_data_1r_to_SummarizedExperiment | 1.106 | 0.679 | 1.264 | |
nmr_data_analysis | 0.907 | 1.001 | 0.741 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.000 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.143 | 0.685 | 1.284 | |
nmr_exclude_region | 0.006 | 0.002 | 0.009 | |
nmr_export_data_1r | 1.373 | 1.178 | 0.999 | |
nmr_get_peak_distances | 0.010 | 0.001 | 0.012 | |
nmr_identify_regions_blood | 0.016 | 0.004 | 0.020 | |
nmr_identify_regions_cell | 0.012 | 0.002 | 0.014 | |
nmr_identify_regions_urine | 0.017 | 0.003 | 0.020 | |
nmr_integrate_regions | 0.009 | 0.001 | 0.011 | |
nmr_interpolate_1D | 2.292 | 1.678 | 1.993 | |
nmr_meta_add | 2.657 | 1.651 | 2.382 | |
nmr_meta_export | 1.043 | 0.829 | 0.861 | |
nmr_meta_get | 1.242 | 1.068 | 1.081 | |
nmr_meta_get_column | 1.073 | 0.888 | 0.923 | |
nmr_meta_groups | 0.996 | 0.663 | 0.817 | |
nmr_normalize | 0.443 | 0.088 | 0.547 | |
nmr_pca_build_model | 2.371 | 1.604 | 2.163 | |
nmr_pca_outliers | 2.007 | 1.333 | 2.439 | |
nmr_pca_outliers_filter | 0.989 | 0.599 | 1.172 | |
nmr_pca_outliers_plot | 0.000 | 0.000 | 0.001 | |
nmr_pca_outliers_robust | 6.294 | 1.169 | 6.154 | |
nmr_pca_plots | 0.636 | 0.023 | 0.666 | |
nmr_peak_clustering | 0.101 | 0.002 | 0.104 | |
nmr_ppm_resolution | 0.010 | 0.002 | 0.012 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.972 | 1.494 | 1.583 | |
nmr_zip_bruker_samples | 0.237 | 0.045 | 0.299 | |
peaklist_accept_peaks | 0.005 | 0.001 | 0.006 | |
permutation_test_model | 0.994 | 0.837 | 2.336 | |
permutation_test_plot | 4.631 | 2.638 | 2.391 | |
plot.nmr_dataset_1D | 0.002 | 0.002 | 0.004 | |
plot_bootstrap_multimodel | 3.601 | 1.761 | 0.067 | |
plot_interactive | 1.036 | 0.694 | 0.896 | |
plot_plsda_multimodel | 0.343 | 0.481 | 0.452 | |
plot_plsda_samples | 0.170 | 0.249 | 0.406 | |
plot_vip_scores | 0.003 | 0.007 | 0.014 | |
plot_webgl | 0.001 | 0.001 | 0.002 | |
plsda_auroc_vip_compare | 0.705 | 0.560 | 1.240 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.002 | 0.002 | 0.003 | |
print.nmr_dataset | 1.143 | 0.946 | 0.921 | |
print.nmr_dataset_1D | 1.229 | 0.993 | 1.051 | |
print.nmr_dataset_peak_table | 1.134 | 0.769 | 1.081 | |
random_subsampling | 0.002 | 0.004 | 0.006 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 1.063 | 0.888 | 0.878 | |
sub-.nmr_dataset_1D | 1.023 | 0.758 | 0.875 | |
sub-.nmr_dataset_peak_table | 1.191 | 0.961 | 1.063 | |
tidy.nmr_dataset_1D | 1.251 | 0.890 | 1.096 | |
to_ASICS | 1.108 | 0.198 | 1.317 | |
to_ChemoSpec | 1.156 | 0.623 | 1.059 | |
validate_nmr_dataset | 2.330 | 2.002 | 2.043 | |
validate_nmr_dataset_family | 1.679 | 1.664 | 1.577 | |
validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.002 | |
zzz | 0.000 | 0.000 | 2.137 | |