Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:38 -0400 (Sat, 06 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" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 4.7.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlpsNMR_4.7.1.tar.gz |
StartedAt: 2024-07-05 20:20:51 -0400 (Fri, 05 Jul 2024) |
EndedAt: 2024-07-05 20:25:02 -0400 (Fri, 05 Jul 2024) |
EllapsedTime: 251.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings AlpsNMR_4.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘4.7.1’ * 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 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 8.217 1.748 4.497 SummarizedExperiment_to_nmr_data_1r 6.417 0.657 6.549 print.nmr_dataset 3.423 2.868 2.775 nmr_pca_outliers_robust 4.830 0.696 4.831 permutation_test_plot 3.700 1.769 1.384 * 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-3.20-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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) 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 24.745 10.320 22.879
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.622 | 0.376 | 1.467 | |
HMDB_blood | 0.006 | 0.000 | 0.006 | |
HMDB_cell | 0.002 | 0.000 | 0.002 | |
HMDB_urine | 0.004 | 0.000 | 0.004 | |
Parameters_blood | 0.002 | 0.000 | 0.001 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.001 | 0.000 | 0.001 | |
Peak_detection | 8.217 | 1.748 | 4.497 | |
Pipelines | 0.002 | 0.000 | 0.002 | |
ROI_blood | 0.000 | 0.003 | 0.003 | |
ROI_cell | 0.002 | 0.001 | 0.002 | |
ROI_urine | 0.002 | 0.000 | 0.002 | |
SummarizedExperiment_to_nmr_data_1r | 6.417 | 0.657 | 6.549 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.984 | 0.330 | 0.777 | |
bp_VIP_analysis | 1.288 | 0.724 | 0.772 | |
bp_kfold_VIP_analysis | 0.703 | 0.429 | 0.459 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.060 | 0.012 | 0.073 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 1.503 | 0.801 | 1.552 | |
format.nmr_dataset | 0.593 | 0.355 | 0.415 | |
format.nmr_dataset_1D | 0.743 | 0.389 | 0.531 | |
format.nmr_dataset_peak_table | 0.780 | 0.311 | 0.544 | |
get_integration_with_metadata | 0.018 | 0.003 | 0.022 | |
hmdb | 0.047 | 0.000 | 0.047 | |
is.nmr_dataset | 0.668 | 0.361 | 0.439 | |
is.nmr_dataset_1D | 0.709 | 0.449 | 0.582 | |
is.nmr_dataset_peak_table | 0.826 | 0.352 | 0.571 | |
load_and_save_functions | 1.336 | 0.718 | 1.313 | |
models_stability_plot_bootstrap | 0.001 | 0.000 | 0.002 | |
models_stability_plot_plsda | 0.346 | 0.433 | 0.321 | |
new_nmr_dataset | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.735 | 0.553 | 0.642 | |
nmr_autophase | 0.191 | 0.083 | 0.305 | |
nmr_baseline_estimation | 0.017 | 0.046 | 0.010 | |
nmr_baseline_removal | 0.004 | 0.000 | 0.005 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.204 | 0.035 | 0.239 | |
nmr_batman | 0.004 | 0.000 | 0.004 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.039 | 0.020 | 0.059 | |
nmr_data | 0.043 | 0.012 | 0.055 | |
nmr_data_1r_to_SummarizedExperiment | 0.884 | 0.564 | 0.827 | |
nmr_data_analysis | 0.360 | 0.457 | 0.349 | |
nmr_dataset | 0 | 0 | 0 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.908 | 0.434 | 0.773 | |
nmr_exclude_region | 0.004 | 0.009 | 0.013 | |
nmr_export_data_1r | 0.762 | 0.501 | 0.627 | |
nmr_get_peak_distances | 0.003 | 0.004 | 0.008 | |
nmr_identify_regions_blood | 0.014 | 0.000 | 0.013 | |
nmr_identify_regions_cell | 0.009 | 0.000 | 0.009 | |
nmr_identify_regions_urine | 0.010 | 0.004 | 0.013 | |
nmr_integrate_regions | 0.01 | 0.00 | 0.01 | |
nmr_interpolate_1D | 1.435 | 1.118 | 1.159 | |
nmr_meta_add | 1.576 | 0.905 | 1.320 | |
nmr_meta_export | 0.567 | 0.420 | 0.426 | |
nmr_meta_get | 0.674 | 0.476 | 0.510 | |
nmr_meta_get_column | 0.582 | 0.434 | 0.445 | |
nmr_meta_groups | 0.713 | 0.430 | 0.527 | |
nmr_normalize | 0.203 | 0.024 | 0.227 | |
nmr_pca_build_model | 1.508 | 0.934 | 1.244 | |
nmr_pca_outliers | 0.923 | 0.406 | 0.669 | |
nmr_pca_outliers_filter | 0.918 | 0.597 | 0.792 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 4.830 | 0.696 | 4.831 | |
nmr_pca_plots | 0.335 | 0.016 | 0.351 | |
nmr_peak_clustering | 0.055 | 0.004 | 0.060 | |
nmr_ppm_resolution | 0.007 | 0.000 | 0.007 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.302 | 0.944 | 0.958 | |
nmr_zip_bruker_samples | 0.284 | 0.004 | 0.289 | |
peaklist_accept_peaks | 0.006 | 0.000 | 0.005 | |
permutation_test_model | 0.578 | 0.643 | 1.378 | |
permutation_test_plot | 3.700 | 1.769 | 1.384 | |
plot.nmr_dataset_1D | 0.002 | 0.000 | 0.003 | |
plot_bootstrap_multimodel | 0.003 | 0.000 | 0.003 | |
plot_interactive | 2.221 | 1.063 | 0.569 | |
plot_plsda_multimodel | 0.182 | 0.348 | 0.255 | |
plot_plsda_samples | 0.107 | 0.127 | 0.181 | |
plot_vip_scores | 0.000 | 0.002 | 0.002 | |
plot_webgl | 0.000 | 0.001 | 0.002 | |
plsda_auroc_vip_compare | 0.407 | 0.261 | 0.574 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.000 | 0.003 | |
print.nmr_dataset | 3.423 | 2.868 | 2.775 | |
print.nmr_dataset_1D | 0.661 | 0.391 | 0.481 | |
print.nmr_dataset_peak_table | 0.764 | 0.467 | 0.590 | |
random_subsampling | 0.000 | 0.002 | 0.002 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.705 | 0.511 | 0.532 | |
sub-.nmr_dataset_1D | 0.690 | 0.443 | 0.553 | |
sub-.nmr_dataset_peak_table | 0.713 | 0.501 | 0.620 | |
tidy.nmr_dataset_1D | 0.731 | 0.623 | 0.672 | |
to_ASICS | 0.868 | 0.137 | 1.005 | |
to_ChemoSpec | 0.748 | 0.582 | 0.707 | |
validate_nmr_dataset | 1.621 | 1.386 | 1.353 | |
validate_nmr_dataset_family | 0.799 | 0.435 | 0.587 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.000 | |
zzz | 0.001 | 0.000 | 2.002 | |