Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 57/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.7.1 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
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: 4.7.1 |
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_4.7.1.tar.gz |
StartedAt: 2024-07-15 18:50:04 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 18:53:35 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 211.6 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_4.7.1.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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.7.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 12.453 3.732 7.372 SummarizedExperiment_to_nmr_data_1r 7.737 0.831 7.873 nmr_pca_outliers_robust 5.994 0.706 5.980 nmr_read_samples 3.148 2.278 2.924 * 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 29.709 11.521 27.986
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.059 | 0.581 | 1.885 | |
HMDB_blood | 0.007 | 0.003 | 0.010 | |
HMDB_cell | 0.002 | 0.001 | 0.003 | |
HMDB_urine | 0.005 | 0.002 | 0.008 | |
Parameters_blood | 0.002 | 0.001 | 0.003 | |
Parameters_cell | 0.002 | 0.001 | 0.002 | |
Parameters_urine | 0.002 | 0.001 | 0.002 | |
Peak_detection | 12.453 | 3.732 | 7.372 | |
Pipelines | 0.001 | 0.001 | 0.002 | |
ROI_blood | 0.003 | 0.002 | 0.005 | |
ROI_cell | 0.003 | 0.002 | 0.005 | |
ROI_urine | 0.003 | 0.002 | 0.005 | |
SummarizedExperiment_to_nmr_data_1r | 7.737 | 0.831 | 7.873 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.332 | 0.816 | 1.253 | |
bp_VIP_analysis | 1.895 | 1.030 | 1.184 | |
bp_kfold_VIP_analysis | 1.068 | 0.579 | 0.725 | |
download_MTBLS242 | 0.000 | 0.001 | 0.000 | |
file_lister | 0.080 | 0.015 | 0.097 | |
files_to_rDolphin | 0.001 | 0.001 | 0.001 | |
filter.nmr_dataset_family | 1.216 | 0.879 | 1.043 | |
format.nmr_dataset | 1.065 | 0.831 | 0.873 | |
format.nmr_dataset_1D | 1.634 | 0.653 | 1.572 | |
format.nmr_dataset_peak_table | 0.995 | 0.537 | 0.815 | |
get_integration_with_metadata | 0.027 | 0.005 | 0.031 | |
hmdb | 0.057 | 0.009 | 0.066 | |
is.nmr_dataset | 0.951 | 0.674 | 0.741 | |
is.nmr_dataset_1D | 0.974 | 0.658 | 0.805 | |
is.nmr_dataset_peak_table | 0.969 | 0.533 | 0.788 | |
load_and_save_functions | 0.812 | 0.499 | 0.621 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.002 | |
models_stability_plot_plsda | 0.507 | 0.452 | 0.482 | |
new_nmr_dataset | 0.002 | 0.001 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_peak_table | 1.152 | 0.724 | 0.989 | |
nmr_autophase | 0.287 | 0.255 | 0.442 | |
nmr_baseline_estimation | 0.009 | 0.006 | 0.014 | |
nmr_baseline_removal | 0.006 | 0.001 | 0.007 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.263 | 0.030 | 0.296 | |
nmr_batman | 0.004 | 0.001 | 0.005 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_build_peak_table | 0.041 | 0.005 | 0.045 | |
nmr_data | 0.053 | 0.007 | 0.059 | |
nmr_data_1r_to_SummarizedExperiment | 1.096 | 0.450 | 0.949 | |
nmr_data_analysis | 0.560 | 0.517 | 0.531 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 2.118 | 1.003 | 2.069 | |
nmr_exclude_region | 0.007 | 0.002 | 0.013 | |
nmr_export_data_1r | 0.973 | 0.692 | 0.899 | |
nmr_get_peak_distances | 0.009 | 0.001 | 0.010 | |
nmr_identify_regions_blood | 0.014 | 0.004 | 0.018 | |
nmr_identify_regions_cell | 0.011 | 0.003 | 0.013 | |
nmr_identify_regions_urine | 0.017 | 0.003 | 0.019 | |
nmr_integrate_regions | 0.012 | 0.002 | 0.015 | |
nmr_interpolate_1D | 1.850 | 1.202 | 1.584 | |
nmr_meta_add | 3.142 | 1.611 | 2.890 | |
nmr_meta_export | 0.914 | 0.608 | 0.700 | |
nmr_meta_get | 0.896 | 0.530 | 0.694 | |
nmr_meta_get_column | 0.776 | 0.477 | 0.810 | |
nmr_meta_groups | 0.941 | 0.586 | 0.739 | |
nmr_normalize | 0.584 | 0.292 | 0.430 | |
nmr_pca_build_model | 2.294 | 1.443 | 1.916 | |
nmr_pca_outliers | 1.079 | 0.626 | 0.922 | |
nmr_pca_outliers_filter | 1.136 | 0.639 | 1.010 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 5.994 | 0.706 | 5.980 | |
nmr_pca_plots | 0.384 | 0.012 | 0.398 | |
nmr_peak_clustering | 0.083 | 0.002 | 0.085 | |
nmr_ppm_resolution | 0.009 | 0.003 | 0.012 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 3.148 | 2.278 | 2.924 | |
nmr_zip_bruker_samples | 0.244 | 0.037 | 0.299 | |
peaklist_accept_peaks | 0.004 | 0.000 | 0.005 | |
permutation_test_model | 1.976 | 1.079 | 2.009 | |
permutation_test_plot | 3.171 | 1.624 | 2.143 | |
plot.nmr_dataset_1D | 3.385 | 1.311 | 0.046 | |
plot_bootstrap_multimodel | 0.002 | 0.013 | 0.016 | |
plot_interactive | 0.892 | 0.577 | 0.751 | |
plot_plsda_multimodel | 0.327 | 0.424 | 0.399 | |
plot_plsda_samples | 0.154 | 0.211 | 0.349 | |
plot_vip_scores | 0.002 | 0.002 | 0.003 | |
plot_webgl | 0.001 | 0.002 | 0.004 | |
plsda_auroc_vip_compare | 0.593 | 0.493 | 1.067 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.001 | 0.004 | |
print.nmr_dataset | 0.763 | 0.566 | 0.840 | |
print.nmr_dataset_1D | 0.946 | 0.595 | 0.810 | |
print.nmr_dataset_peak_table | 1.305 | 1.014 | 0.982 | |
random_subsampling | 0.002 | 0.005 | 0.007 | |
save_files_to_rDolphin | 0.000 | 0.001 | 0.001 | |
save_profiling_output | 0.000 | 0.001 | 0.001 | |
sub-.nmr_dataset | 0.805 | 0.584 | 0.870 | |
sub-.nmr_dataset_1D | 1.268 | 0.853 | 0.858 | |
sub-.nmr_dataset_peak_table | 1.183 | 0.903 | 1.040 | |
tidy.nmr_dataset_1D | 1.168 | 0.824 | 1.037 | |
to_ASICS | 1.119 | 0.199 | 1.330 | |
to_ChemoSpec | 2.092 | 1.164 | 2.104 | |
validate_nmr_dataset | 1.815 | 1.229 | 1.476 | |
validate_nmr_dataset_family | 0.962 | 0.618 | 0.794 | |
validate_nmr_dataset_peak_table | 0.000 | 0.001 | 0.001 | |
zzz | 0.000 | 0.001 | 2.145 | |