Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 59/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.11.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | 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: 4.11.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AlpsNMR_4.11.0.tar.gz |
StartedAt: 2025-09-21 20:53:41 -0400 (Sun, 21 Sep 2025) |
EndedAt: 2025-09-21 20:58:28 -0400 (Sun, 21 Sep 2025) |
EllapsedTime: 287.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: AlpsNMR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AlpsNMR_4.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.11.0’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Peak_detection 7.461 1.871 6.843 SummarizedExperiment_to_nmr_data_1r 6.629 0.826 6.819 nmr_interpolate_1D 4.179 3.080 3.440 nmr_pca_outliers_robust 4.946 1.155 5.247 permutation_test_plot 3.262 1.895 1.766 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: `expected`: TRUE ── Failure ('test-outliers.R:29:5'): nmr_pca_outliers_robust works ───────────── is.list(outliers_plot) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-outliers.R:30:5'): nmr_pca_outliers_robust works ───────────── is.list(plot) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 5 | WARN 0 | SKIP 1 | PASS 88 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/AlpsNMR.Rcheck/00check.log’ for details.
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘AlpsNMR’ ... ** this is package ‘AlpsNMR’ version ‘4.11.0’ ** 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.fail
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 5 | WARN 0 | SKIP 1 | PASS 88 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_rDolphin.R:2:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-outliers.R:26:5'): nmr_pca_outliers_robust works ───────────── is.list(plot_variance) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-outliers.R:27:5'): nmr_pca_outliers_robust works ───────────── is.list(score) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-outliers.R:28:5'): nmr_pca_outliers_robust works ───────────── is.list(loadings) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-outliers.R:29:5'): nmr_pca_outliers_robust works ───────────── is.list(outliers_plot) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-outliers.R:30:5'): nmr_pca_outliers_robust works ───────────── is.list(plot) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 5 | WARN 0 | SKIP 1 | PASS 88 ] Error: Test failures Execution halted
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.198 | 0.371 | 2.038 | |
HMDB_blood | 0.006 | 0.001 | 0.007 | |
HMDB_cell | 0.003 | 0.000 | 0.003 | |
HMDB_urine | 0.004 | 0.000 | 0.004 | |
Parameters_blood | 0.001 | 0.001 | 0.002 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.002 | 0.000 | 0.002 | |
Peak_detection | 7.461 | 1.871 | 6.843 | |
Pipelines | 0.001 | 0.001 | 0.002 | |
ROI_blood | 0.002 | 0.001 | 0.003 | |
ROI_cell | 0.002 | 0.001 | 0.003 | |
ROI_urine | 0.003 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 6.629 | 0.826 | 6.819 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.990 | 0.592 | 0.891 | |
bp_VIP_analysis | 1.391 | 0.877 | 0.844 | |
bp_kfold_VIP_analysis | 0.748 | 0.505 | 0.532 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.056 | 0.017 | 0.073 | |
files_to_rDolphin | 0.001 | 0.001 | 0.001 | |
filter.nmr_dataset_family | 1.632 | 0.740 | 1.568 | |
format.nmr_dataset | 0.649 | 0.421 | 0.482 | |
format.nmr_dataset_1D | 0.721 | 0.500 | 0.578 | |
format.nmr_dataset_peak_table | 0.806 | 0.490 | 0.660 | |
get_integration_with_metadata | 0.031 | 0.002 | 0.033 | |
hmdb | 0.053 | 0.023 | 0.076 | |
is.nmr_dataset | 0.654 | 0.492 | 0.508 | |
is.nmr_dataset_1D | 0.808 | 0.611 | 0.656 | |
is.nmr_dataset_peak_table | 0.847 | 0.478 | 0.644 | |
load_and_save_functions | 0.692 | 0.538 | 0.541 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.002 | |
models_stability_plot_plsda | 0.362 | 0.399 | 0.379 | |
new_nmr_dataset | 0.002 | 0.000 | 0.001 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.790 | 0.594 | 0.672 | |
nmr_autophase | 0.217 | 0.137 | 0.311 | |
nmr_baseline_estimation | 0.008 | 0.002 | 0.010 | |
nmr_baseline_removal | 0.003 | 0.001 | 0.005 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.299 | 0.047 | 0.347 | |
nmr_batman | 0.001 | 0.002 | 0.003 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.034 | 0.007 | 0.042 | |
nmr_data | 0.068 | 0.028 | 0.096 | |
nmr_data_1r_to_SummarizedExperiment | 0.991 | 0.505 | 0.862 | |
nmr_data_analysis | 0.396 | 0.510 | 0.430 | |
nmr_dataset | 0 | 0 | 0 | |
nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.950 | 0.547 | 0.821 | |
nmr_exclude_region | 0.006 | 0.000 | 0.006 | |
nmr_export_data_1r | 0.726 | 0.597 | 0.669 | |
nmr_get_peak_distances | 0.01 | 0.00 | 0.01 | |
nmr_identify_regions_blood | 0.015 | 0.000 | 0.015 | |
nmr_identify_regions_cell | 0.009 | 0.000 | 0.010 | |
nmr_identify_regions_urine | 0.013 | 0.001 | 0.014 | |
nmr_integrate_regions | 0.007 | 0.000 | 0.007 | |
nmr_interpolate_1D | 4.179 | 3.080 | 3.440 | |
nmr_meta_add | 1.683 | 0.932 | 1.398 | |
nmr_meta_export | 0.706 | 0.480 | 0.508 | |
nmr_meta_get | 0.653 | 0.477 | 0.506 | |
nmr_meta_get_column | 0.694 | 0.658 | 0.616 | |
nmr_meta_groups | 0.705 | 0.585 | 0.558 | |
nmr_normalize | 0.307 | 0.066 | 0.373 | |
nmr_pca_build_model | 1.661 | 1.246 | 1.414 | |
nmr_pca_outliers | 0.892 | 0.668 | 0.799 | |
nmr_pca_outliers_filter | 1.023 | 0.799 | 0.908 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 4.946 | 1.155 | 5.247 | |
nmr_pca_plots | 0.494 | 0.023 | 0.516 | |
nmr_peak_clustering | 0.069 | 0.005 | 0.074 | |
nmr_ppm_resolution | 0.006 | 0.001 | 0.008 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.390 | 1.248 | 1.138 | |
nmr_zip_bruker_samples | 0.253 | 0.012 | 0.265 | |
peaklist_accept_peaks | 0.004 | 0.000 | 0.004 | |
permutation_test_model | 2.393 | 1.496 | 1.724 | |
permutation_test_plot | 3.262 | 1.895 | 1.766 | |
plot.nmr_dataset_1D | 0.003 | 0.001 | 0.004 | |
plot_bootstrap_multimodel | 0.003 | 0.001 | 0.004 | |
plot_interactive | 1.735 | 1.048 | 0.698 | |
plot_plsda_multimodel | 0.198 | 0.419 | 0.320 | |
plot_plsda_samples | 0.107 | 0.157 | 0.210 | |
plot_vip_scores | 0.001 | 0.000 | 0.001 | |
plot_webgl | 0.001 | 0.000 | 0.001 | |
plsda_auroc_vip_compare | 0.550 | 0.442 | 0.792 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.000 | 0.003 | |
print.nmr_dataset | 0.819 | 0.887 | 0.793 | |
print.nmr_dataset_1D | 0.723 | 0.662 | 0.645 | |
print.nmr_dataset_peak_table | 0.838 | 0.703 | 0.838 | |
random_subsampling | 0.001 | 0.000 | 0.001 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.736 | 0.654 | 0.613 | |
sub-.nmr_dataset_1D | 0.732 | 0.705 | 0.680 | |
sub-.nmr_dataset_peak_table | 0.844 | 0.809 | 0.837 | |
tidy.nmr_dataset_1D | 0.935 | 0.751 | 0.797 | |
to_ASICS | 0.892 | 0.181 | 1.074 | |
to_ChemoSpec | 1.138 | 1.162 | 1.113 | |
validate_nmr_dataset | 1.889 | 1.968 | 1.708 | |
validate_nmr_dataset_family | 0.757 | 0.608 | 0.650 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.001 | |
zzz | 0.001 | 0.000 | 2.003 | |