Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 4.10.0 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | 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 | ![]() | ||||||||
kunpeng2 | 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: 4.10.0 |
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_4.10.0.tar.gz |
StartedAt: 2025-08-01 11:45:10 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 11:48:41 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 211.3 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_4.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.10.0’ * 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 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 11.130 3.068 10.457 SummarizedExperiment_to_nmr_data_1r 7.743 0.931 8.164 nmr_pca_outliers 4.389 2.442 3.414 permutation_test_plot 4.335 2.464 2.065 format.nmr_dataset_peak_table 4.148 2.438 3.551 * 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-3.21-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-arm64/Resources/library’ * installing *source* package ‘AlpsNMR’ ... ** this is package ‘AlpsNMR’ version ‘4.10.0’ ** 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
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-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 24.152 9.251 25.359
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.087 | 0.557 | 2.047 | |
HMDB_blood | 0.007 | 0.003 | 0.010 | |
HMDB_cell | 0.003 | 0.002 | 0.004 | |
HMDB_urine | 0.005 | 0.003 | 0.007 | |
Parameters_blood | 0.002 | 0.002 | 0.004 | |
Parameters_cell | 0.002 | 0.002 | 0.003 | |
Parameters_urine | 0.002 | 0.002 | 0.003 | |
Peak_detection | 11.130 | 3.068 | 10.457 | |
Pipelines | 0.002 | 0.001 | 0.002 | |
ROI_blood | 0.003 | 0.002 | 0.005 | |
ROI_cell | 0.002 | 0.002 | 0.004 | |
ROI_urine | 0.003 | 0.002 | 0.004 | |
SummarizedExperiment_to_nmr_data_1r | 7.743 | 0.931 | 8.164 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.195 | 0.762 | 1.422 | |
bp_VIP_analysis | 1.234 | 1.069 | 1.362 | |
bp_kfold_VIP_analysis | 0.869 | 0.849 | 0.815 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.060 | 0.045 | 0.115 | |
files_to_rDolphin | 0.001 | 0.000 | 0.001 | |
filter.nmr_dataset_family | 1.402 | 1.090 | 1.091 | |
format.nmr_dataset | 0.821 | 0.768 | 0.776 | |
format.nmr_dataset_1D | 0.920 | 0.845 | 0.920 | |
format.nmr_dataset_peak_table | 4.148 | 2.438 | 3.551 | |
get_integration_with_metadata | 0.030 | 0.011 | 0.043 | |
hmdb | 0.057 | 0.009 | 0.066 | |
is.nmr_dataset | 0.824 | 0.728 | 0.787 | |
is.nmr_dataset_1D | 0.784 | 0.534 | 0.832 | |
is.nmr_dataset_peak_table | 0.908 | 0.759 | 0.971 | |
load_and_save_functions | 0.782 | 0.643 | 0.721 | |
models_stability_plot_bootstrap | 0.002 | 0.003 | 0.005 | |
models_stability_plot_plsda | 0.422 | 0.526 | 0.475 | |
new_nmr_dataset | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_peak_table | 0.894 | 0.667 | 0.852 | |
nmr_autophase | 0.236 | 0.132 | 0.368 | |
nmr_baseline_estimation | 0.010 | 0.006 | 0.017 | |
nmr_baseline_removal | 0.006 | 0.002 | 0.008 | |
nmr_baseline_threshold | 0.002 | 0.001 | 0.002 | |
nmr_baseline_threshold_plot | 0.216 | 0.046 | 0.262 | |
nmr_batman | 0.004 | 0.002 | 0.005 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.037 | 0.009 | 0.047 | |
nmr_data | 0.046 | 0.008 | 0.054 | |
nmr_data_1r_to_SummarizedExperiment | 0.878 | 0.513 | 1.130 | |
nmr_data_analysis | 0.631 | 0.890 | 0.693 | |
nmr_dataset | 0.001 | 0.001 | 0.002 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.199 | 1.150 | 1.452 | |
nmr_exclude_region | 0.008 | 0.002 | 0.010 | |
nmr_export_data_1r | 0.878 | 0.821 | 0.917 | |
nmr_get_peak_distances | 0.010 | 0.005 | 0.018 | |
nmr_identify_regions_blood | 0.015 | 0.009 | 0.024 | |
nmr_identify_regions_cell | 0.010 | 0.002 | 0.011 | |
nmr_identify_regions_urine | 0.015 | 0.003 | 0.020 | |
nmr_integrate_regions | 0.008 | 0.002 | 0.011 | |
nmr_interpolate_1D | 1.657 | 1.353 | 1.771 | |
nmr_meta_add | 1.979 | 1.426 | 1.994 | |
nmr_meta_export | 0.759 | 0.801 | 0.759 | |
nmr_meta_get | 0.517 | 0.498 | 0.514 | |
nmr_meta_get_column | 0.505 | 0.386 | 0.479 | |
nmr_meta_groups | 0.841 | 0.728 | 0.868 | |
nmr_normalize | 0.253 | 0.058 | 0.358 | |
nmr_pca_build_model | 1.825 | 1.172 | 1.789 | |
nmr_pca_outliers | 4.389 | 2.442 | 3.414 | |
nmr_pca_outliers_filter | 1.723 | 0.670 | 1.816 | |
nmr_pca_outliers_plot | 0.000 | 0.000 | 0.001 | |
nmr_pca_outliers_robust | 4.293 | 0.580 | 4.356 | |
nmr_pca_plots | 0.363 | 0.021 | 0.385 | |
nmr_peak_clustering | 0.067 | 0.002 | 0.070 | |
nmr_ppm_resolution | 0.009 | 0.001 | 0.011 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 1.449 | 1.193 | 1.313 | |
nmr_zip_bruker_samples | 0.347 | 0.044 | 0.404 | |
peaklist_accept_peaks | 0.004 | 0.001 | 0.006 | |
permutation_test_model | 2.535 | 1.689 | 2.027 | |
permutation_test_plot | 4.335 | 2.464 | 2.065 | |
plot.nmr_dataset_1D | 0.002 | 0.002 | 0.003 | |
plot_bootstrap_multimodel | 0.002 | 0.004 | 0.006 | |
plot_interactive | 0.888 | 0.783 | 0.865 | |
plot_plsda_multimodel | 0.253 | 0.429 | 0.368 | |
plot_plsda_samples | 0.125 | 0.215 | 0.331 | |
plot_vip_scores | 0.001 | 0.001 | 0.004 | |
plot_webgl | 0.002 | 0.001 | 0.003 | |
plsda_auroc_vip_compare | 0.471 | 0.457 | 0.909 | |
plsda_auroc_vip_method | 0.000 | 0.000 | 0.001 | |
ppm_resolution | 0.003 | 0.001 | 0.005 | |
print.nmr_dataset | 0.835 | 0.874 | 0.874 | |
print.nmr_dataset_1D | 0.786 | 0.707 | 0.850 | |
print.nmr_dataset_peak_table | 0.961 | 0.893 | 1.090 | |
random_subsampling | 0.002 | 0.004 | 0.006 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0.000 | 0.001 | 0.000 | |
sub-.nmr_dataset | 0.823 | 0.906 | 0.901 | |
sub-.nmr_dataset_1D | 0.818 | 0.759 | 0.884 | |
sub-.nmr_dataset_peak_table | 1.263 | 1.272 | 1.425 | |
tidy.nmr_dataset_1D | 0.919 | 0.856 | 1.017 | |
to_ASICS | 1.097 | 0.195 | 1.328 | |
to_ChemoSpec | 0.978 | 0.744 | 1.033 | |
validate_nmr_dataset | 1.845 | 1.847 | 2.007 | |
validate_nmr_dataset_family | 0.857 | 0.840 | 0.914 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.002 | |
zzz | 0.001 | 0.000 | 2.151 | |