Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:48 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 57/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.6.0 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | 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: 4.6.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AlpsNMR_4.6.0.tar.gz |
StartedAt: 2024-05-31 01:09:56 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:14:08 -0400 (Fri, 31 May 2024) |
EllapsedTime: 251.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings AlpsNMR_4.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.6.0’ * 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 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Peak_detection 7.363 1.399 5.941 SummarizedExperiment_to_nmr_data_1r 6.430 0.539 6.683 nmr_pca_outliers_robust 4.655 0.546 4.847 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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) Loading required package: future Attaching package: 'AlpsNMR' The following object is masked from 'package:stats': filter > > test_check("AlpsNMR") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_rDolphin.R:2:5' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ] > > proc.time() user system elapsed 12.599 3.757 12.729
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.608 | 0.317 | 1.657 | |
HMDB_blood | 0.006 | 0.000 | 0.007 | |
HMDB_cell | 0.003 | 0.000 | 0.002 | |
HMDB_urine | 0.002 | 0.003 | 0.004 | |
Parameters_blood | 0.001 | 0.001 | 0.002 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.001 | 0.000 | 0.002 | |
Peak_detection | 7.363 | 1.399 | 5.941 | |
Pipelines | 0.002 | 0.000 | 0.001 | |
ROI_blood | 0.000 | 0.003 | 0.003 | |
ROI_cell | 0.003 | 0.001 | 0.003 | |
ROI_urine | 0.003 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 6.430 | 0.539 | 6.683 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.620 | 0.393 | 1.722 | |
bp_VIP_analysis | 1.139 | 0.478 | 0.904 | |
bp_kfold_VIP_analysis | 0.646 | 0.367 | 0.573 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.060 | 0.004 | 0.065 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.671 | 0.276 | 0.700 | |
format.nmr_dataset | 0.644 | 0.442 | 0.744 | |
format.nmr_dataset_1D | 0.712 | 0.357 | 0.751 | |
format.nmr_dataset_peak_table | 0.749 | 0.420 | 0.847 | |
get_integration_with_metadata | 0.023 | 0.000 | 0.024 | |
hmdb | 0.047 | 0.004 | 0.051 | |
is.nmr_dataset | 0.627 | 0.482 | 0.734 | |
is.nmr_dataset_1D | 0.785 | 0.344 | 0.780 | |
is.nmr_dataset_peak_table | 0.775 | 0.371 | 0.770 | |
load_and_save_functions | 0.583 | 0.363 | 0.635 | |
models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
models_stability_plot_plsda | 0.302 | 0.232 | 0.291 | |
new_nmr_dataset | 0.000 | 0.001 | 0.002 | |
new_nmr_dataset_1D | 0.000 | 0.001 | 0.001 | |
new_nmr_dataset_peak_table | 0.747 | 0.387 | 0.785 | |
nmr_baseline_estimation | 0.124 | 0.032 | 0.156 | |
nmr_baseline_removal | 0.004 | 0.000 | 0.004 | |
nmr_baseline_threshold | 0.002 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.179 | 0.032 | 0.211 | |
nmr_batman | 0.004 | 0.000 | 0.003 | |
nmr_batman_options | 0.000 | 0.000 | 0.001 | |
nmr_build_peak_table | 0.032 | 0.004 | 0.036 | |
nmr_data | 0.041 | 0.004 | 0.045 | |
nmr_data_1r_to_SummarizedExperiment | 0.879 | 0.382 | 0.939 | |
nmr_data_analysis | 0.360 | 0.286 | 0.353 | |
nmr_dataset | 0.001 | 0.000 | 0.000 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.633 | 0.527 | 1.835 | |
nmr_exclude_region | 0.001 | 0.004 | 0.005 | |
nmr_export_data_1r | 0.611 | 0.400 | 0.697 | |
nmr_get_peak_distances | 0.008 | 0.000 | 0.008 | |
nmr_identify_regions_blood | 0.007 | 0.008 | 0.015 | |
nmr_identify_regions_cell | 0.010 | 0.000 | 0.009 | |
nmr_identify_regions_urine | 0.015 | 0.000 | 0.014 | |
nmr_integrate_regions | 0.011 | 0.000 | 0.011 | |
nmr_interpolate_1D | 1.424 | 0.730 | 1.489 | |
nmr_meta_add | 1.579 | 0.914 | 1.781 | |
nmr_meta_export | 0.637 | 0.412 | 0.697 | |
nmr_meta_get | 0.596 | 0.423 | 0.667 | |
nmr_meta_get_column | 0.622 | 0.482 | 0.726 | |
nmr_meta_groups | 0.607 | 0.434 | 0.672 | |
nmr_normalize | 0.226 | 0.011 | 0.237 | |
nmr_pca_build_model | 1.703 | 0.769 | 1.739 | |
nmr_pca_outliers | 0.736 | 0.528 | 0.923 | |
nmr_pca_outliers_filter | 0.795 | 0.514 | 0.969 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 4.655 | 0.546 | 4.847 | |
nmr_pca_plots | 0.294 | 0.009 | 0.302 | |
nmr_peak_clustering | 0.055 | 0.003 | 0.058 | |
nmr_ppm_resolution | 0.011 | 0.000 | 0.011 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 1.385 | 0.976 | 1.486 | |
nmr_zip_bruker_samples | 0.256 | 0.009 | 0.264 | |
peaklist_accept_peaks | 0.004 | 0.000 | 0.004 | |
permutation_test_model | 0.293 | 0.338 | 1.788 | |
permutation_test_plot | 2.630 | 0.967 | 1.762 | |
plot.nmr_dataset_1D | 0.000 | 0.002 | 0.001 | |
plot_bootstrap_multimodel | 0.002 | 0.001 | 0.002 | |
plot_interactive | 2.945 | 1.032 | 0.726 | |
plot_plsda_multimodel | 0.362 | 0.576 | 0.515 | |
plot_plsda_samples | 0.124 | 0.137 | 0.287 | |
plot_vip_scores | 0.016 | 0.072 | 0.002 | |
plot_webgl | 0.002 | 0.000 | 0.001 | |
plsda_auroc_vip_compare | 0.411 | 0.256 | 0.567 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.000 | 0.003 | |
print.nmr_dataset | 0.604 | 0.503 | 0.713 | |
print.nmr_dataset_1D | 0.679 | 0.441 | 0.795 | |
print.nmr_dataset_peak_table | 0.808 | 0.457 | 0.910 | |
random_subsampling | 0.000 | 0.004 | 0.004 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.804 | 0.666 | 0.952 | |
sub-.nmr_dataset_1D | 0.662 | 0.453 | 0.781 | |
sub-.nmr_dataset_peak_table | 0.848 | 0.485 | 0.903 | |
tidy.nmr_dataset_1D | 0.863 | 0.610 | 1.009 | |
to_ChemoSpec | 0.919 | 0.434 | 0.942 | |
validate_nmr_dataset | 1.372 | 0.883 | 1.560 | |
validate_nmr_dataset_family | 0.712 | 0.421 | 0.784 | |
validate_nmr_dataset_peak_table | 0.002 | 0.000 | 0.001 | |
zzz | 0.001 | 0.000 | 2.002 | |