Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-28 11:45 -0500 (Tue, 28 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
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 58/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.9.0 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 4.9.0 |
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_4.9.0.tar.gz |
StartedAt: 2025-01-27 18:00:12 -0500 (Mon, 27 Jan 2025) |
EndedAt: 2025-01-27 18:01:23 -0500 (Mon, 27 Jan 2025) |
EllapsedTime: 70.9 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_4.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.9.0’ * 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 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 * 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 ‘4.9.0’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 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 9.877 3.925 9.259
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 0.666 | 0.177 | 0.686 | |
HMDB_blood | 0.002 | 0.001 | 0.004 | |
HMDB_cell | 0.001 | 0.001 | 0.002 | |
HMDB_urine | 0.002 | 0.001 | 0.002 | |
Parameters_blood | 0.000 | 0.001 | 0.001 | |
Parameters_cell | 0.001 | 0.000 | 0.001 | |
Parameters_urine | 0.000 | 0.000 | 0.001 | |
Peak_detection | 2.778 | 0.937 | 2.620 | |
Pipelines | 0.001 | 0.000 | 0.001 | |
ROI_blood | 0.001 | 0.001 | 0.001 | |
ROI_cell | 0.001 | 0.000 | 0.001 | |
ROI_urine | 0.001 | 0.001 | 0.002 | |
SummarizedExperiment_to_nmr_data_1r | 2.525 | 0.288 | 2.567 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.384 | 0.290 | 0.393 | |
bp_VIP_analysis | 0.492 | 0.439 | 0.457 | |
bp_kfold_VIP_analysis | 0.272 | 0.306 | 0.278 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.024 | 0.010 | 0.033 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.276 | 0.150 | 0.278 | |
format.nmr_dataset | 1.406 | 0.833 | 1.070 | |
format.nmr_dataset_1D | 0.275 | 0.237 | 0.253 | |
format.nmr_dataset_peak_table | 0.294 | 0.255 | 0.271 | |
get_integration_with_metadata | 0.009 | 0.007 | 0.016 | |
hmdb | 0.018 | 0.008 | 0.026 | |
is.nmr_dataset | 0.271 | 0.303 | 0.269 | |
is.nmr_dataset_1D | 0.275 | 0.221 | 0.259 | |
is.nmr_dataset_peak_table | 0.287 | 0.198 | 0.268 | |
load_and_save_functions | 0.234 | 0.190 | 0.216 | |
models_stability_plot_bootstrap | 0.001 | 0.001 | 0.001 | |
models_stability_plot_plsda | 0.136 | 0.178 | 0.152 | |
new_nmr_dataset | 0.001 | 0.001 | 0.001 | |
new_nmr_dataset_1D | 0.000 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.291 | 0.217 | 0.283 | |
nmr_autophase | 0.073 | 0.050 | 0.124 | |
nmr_baseline_estimation | 0.003 | 0.003 | 0.007 | |
nmr_baseline_removal | 0.002 | 0.001 | 0.002 | |
nmr_baseline_threshold | 0 | 0 | 0 | |
nmr_baseline_threshold_plot | 0.064 | 0.033 | 0.096 | |
nmr_batman | 0.001 | 0.001 | 0.002 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_build_peak_table | 0.010 | 0.004 | 0.014 | |
nmr_data | 0.015 | 0.004 | 0.019 | |
nmr_data_1r_to_SummarizedExperiment | 0.368 | 0.273 | 0.375 | |
nmr_data_analysis | 0.130 | 0.186 | 0.157 | |
nmr_dataset | 0.000 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.000 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.392 | 0.357 | 0.391 | |
nmr_exclude_region | 0.002 | 0.001 | 0.003 | |
nmr_export_data_1r | 0.290 | 0.285 | 0.283 | |
nmr_get_peak_distances | 0.002 | 0.002 | 0.004 | |
nmr_identify_regions_blood | 0.009 | 0.005 | 0.013 | |
nmr_identify_regions_cell | 0.002 | 0.000 | 0.003 | |
nmr_identify_regions_urine | 0.004 | 0.002 | 0.005 | |
nmr_integrate_regions | 0.003 | 0.000 | 0.004 | |
nmr_interpolate_1D | 0.525 | 0.416 | 0.496 | |
nmr_meta_add | 0.582 | 0.443 | 0.580 | |
nmr_meta_export | 0.222 | 0.184 | 0.192 | |
nmr_meta_get | 0.234 | 0.284 | 0.247 | |
nmr_meta_get_column | 0.254 | 0.259 | 0.235 | |
nmr_meta_groups | 0.231 | 0.279 | 0.236 | |
nmr_normalize | 0.072 | 0.014 | 0.085 | |
nmr_pca_build_model | 0.848 | 0.589 | 0.950 | |
nmr_pca_outliers | 0.327 | 0.262 | 0.318 | |
nmr_pca_outliers_filter | 0.304 | 0.219 | 0.298 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 1.669 | 0.258 | 1.724 | |
nmr_pca_plots | 0.099 | 0.003 | 0.102 | |
nmr_peak_clustering | 0.018 | 0.001 | 0.018 | |
nmr_ppm_resolution | 0.002 | 0.001 | 0.003 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 0.481 | 0.530 | 0.469 | |
nmr_zip_bruker_samples | 0.111 | 0.015 | 0.129 | |
peaklist_accept_peaks | 0.001 | 0.000 | 0.002 | |
permutation_test_model | 0.497 | 0.413 | 0.567 | |
permutation_test_plot | 1.225 | 0.899 | 0.595 | |
plot.nmr_dataset_1D | 0.001 | 0.001 | 0.001 | |
plot_bootstrap_multimodel | 0.001 | 0.001 | 0.002 | |
plot_interactive | 0.310 | 0.299 | 0.323 | |
plot_plsda_multimodel | 0.093 | 0.294 | 0.192 | |
plot_plsda_samples | 0.045 | 0.094 | 0.140 | |
plot_vip_scores | 0.001 | 0.001 | 0.002 | |
plot_webgl | 0.000 | 0.001 | 0.001 | |
plsda_auroc_vip_compare | 0.152 | 0.232 | 0.380 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.001 | 0.000 | 0.002 | |
print.nmr_dataset | 0.549 | 0.391 | 0.634 | |
print.nmr_dataset_1D | 0.235 | 0.174 | 0.204 | |
print.nmr_dataset_peak_table | 0.274 | 0.242 | 0.259 | |
random_subsampling | 0.000 | 0.001 | 0.002 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.238 | 0.239 | 0.222 | |
sub-.nmr_dataset_1D | 0.244 | 0.201 | 0.235 | |
sub-.nmr_dataset_peak_table | 0.262 | 0.214 | 0.282 | |
tidy.nmr_dataset_1D | 0.272 | 0.220 | 0.269 | |
to_ASICS | 0.328 | 0.076 | 0.410 | |
to_ChemoSpec | 0.319 | 0.239 | 0.327 | |
validate_nmr_dataset | 0.546 | 0.553 | 0.530 | |
validate_nmr_dataset_family | 1.674 | 1.067 | 1.381 | |
validate_nmr_dataset_peak_table | 0 | 0 | 0 | |
zzz | 0.00 | 0.00 | 2.01 | |