Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:28:37 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 57/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.7.0 (landing page) Sergio Oller Moreno
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 4.7.0 |
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_4.7.0.tar.gz |
StartedAt: 2024-05-31 01:21:28 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:25:42 -0400 (Fri, 31 May 2024) |
EllapsedTime: 253.4 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_4.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 ‘4.7.0’ * 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 7.280 1.480 6.160 SummarizedExperiment_to_nmr_data_1r 6.548 0.819 7.061 nmr_pca_outliers_robust 4.893 0.696 5.204 * 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 4.4.0 RC (2024-04-16 r86468) -- "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 13.475 4.052 13.620
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.661 | 0.282 | 1.676 | |
HMDB_blood | 0.006 | 0.000 | 0.006 | |
HMDB_cell | 0.003 | 0.000 | 0.002 | |
HMDB_urine | 0.004 | 0.000 | 0.004 | |
Parameters_blood | 0.001 | 0.000 | 0.001 | |
Parameters_cell | 0.002 | 0.000 | 0.001 | |
Parameters_urine | 0.002 | 0.000 | 0.002 | |
Peak_detection | 7.28 | 1.48 | 6.16 | |
Pipelines | 0.001 | 0.000 | 0.001 | |
ROI_blood | 0.003 | 0.000 | 0.003 | |
ROI_cell | 0.002 | 0.000 | 0.003 | |
ROI_urine | 0.002 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 6.548 | 0.819 | 7.061 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.584 | 0.483 | 1.724 | |
bp_VIP_analysis | 1.164 | 0.471 | 0.893 | |
bp_kfold_VIP_analysis | 0.670 | 0.310 | 0.551 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.051 | 0.015 | 0.067 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 0.618 | 0.328 | 0.687 | |
format.nmr_dataset | 0.618 | 0.382 | 0.668 | |
format.nmr_dataset_1D | 0.681 | 0.375 | 0.745 | |
format.nmr_dataset_peak_table | 0.794 | 0.428 | 0.838 | |
get_integration_with_metadata | 0.023 | 0.000 | 0.023 | |
hmdb | 0.049 | 0.000 | 0.049 | |
is.nmr_dataset | 0.685 | 0.478 | 0.811 | |
is.nmr_dataset_1D | 0.762 | 0.480 | 0.853 | |
is.nmr_dataset_peak_table | 0.716 | 0.381 | 0.753 | |
load_and_save_functions | 0.593 | 0.388 | 0.655 | |
models_stability_plot_bootstrap | 0.002 | 0.001 | 0.001 | |
models_stability_plot_plsda | 0.308 | 0.311 | 0.325 | |
new_nmr_dataset | 0.002 | 0.000 | 0.001 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.767 | 0.497 | 0.822 | |
nmr_baseline_estimation | 0.145 | 0.027 | 0.172 | |
nmr_baseline_removal | 0.005 | 0.001 | 0.006 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.230 | 0.039 | 0.269 | |
nmr_batman | 0.004 | 0.000 | 0.003 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.042 | 0.003 | 0.046 | |
nmr_data | 0.057 | 0.008 | 0.064 | |
nmr_data_1r_to_SummarizedExperiment | 0.859 | 0.387 | 0.933 | |
nmr_data_analysis | 0.387 | 0.385 | 0.427 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.697 | 0.596 | 1.912 | |
nmr_exclude_region | 0.006 | 0.000 | 0.006 | |
nmr_export_data_1r | 0.649 | 0.390 | 0.722 | |
nmr_get_peak_distances | 0.014 | 0.004 | 0.018 | |
nmr_identify_regions_blood | 0.016 | 0.000 | 0.016 | |
nmr_identify_regions_cell | 0.008 | 0.000 | 0.009 | |
nmr_identify_regions_urine | 0.014 | 0.000 | 0.014 | |
nmr_integrate_regions | 0.009 | 0.004 | 0.013 | |
nmr_interpolate_1D | 1.302 | 0.726 | 1.359 | |
nmr_meta_add | 1.65 | 0.85 | 1.78 | |
nmr_meta_export | 0.647 | 0.560 | 0.721 | |
nmr_meta_get | 0.611 | 0.357 | 0.641 | |
nmr_meta_get_column | 0.654 | 0.542 | 0.825 | |
nmr_meta_groups | 0.666 | 0.435 | 0.715 | |
nmr_normalize | 0.235 | 0.020 | 0.254 | |
nmr_pca_build_model | 1.601 | 0.923 | 1.794 | |
nmr_pca_outliers | 0.749 | 0.434 | 0.832 | |
nmr_pca_outliers_filter | 0.747 | 0.541 | 0.940 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 4.893 | 0.696 | 5.204 | |
nmr_pca_plots | 0.303 | 0.008 | 0.311 | |
nmr_peak_clustering | 0.050 | 0.012 | 0.062 | |
nmr_ppm_resolution | 0.007 | 0.000 | 0.007 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.485 | 0.885 | 1.552 | |
nmr_zip_bruker_samples | 0.263 | 0.000 | 0.265 | |
peaklist_accept_peaks | 0.001 | 0.003 | 0.004 | |
permutation_test_model | 0.294 | 0.344 | 1.788 | |
permutation_test_plot | 2.795 | 0.952 | 1.883 | |
plot.nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
plot_bootstrap_multimodel | 0.000 | 0.002 | 0.002 | |
plot_interactive | 3.078 | 1.016 | 0.741 | |
plot_plsda_multimodel | 0.288 | 0.480 | 0.457 | |
plot_plsda_samples | 0.164 | 0.206 | 0.259 | |
plot_vip_scores | 0.001 | 0.001 | 0.002 | |
plot_webgl | 0.028 | 0.060 | 0.002 | |
plsda_auroc_vip_compare | 0.398 | 0.253 | 0.552 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.002 | 0.000 | 0.002 | |
print.nmr_dataset | 0.574 | 0.456 | 0.667 | |
print.nmr_dataset_1D | 0.716 | 0.455 | 0.839 | |
print.nmr_dataset_peak_table | 0.757 | 0.513 | 0.864 | |
random_subsampling | 0.002 | 0.000 | 0.001 | |
save_files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.828 | 0.760 | 0.917 | |
sub-.nmr_dataset_1D | 0.659 | 0.427 | 0.750 | |
sub-.nmr_dataset_peak_table | 0.867 | 0.455 | 0.867 | |
tidy.nmr_dataset_1D | 0.839 | 0.564 | 0.932 | |
to_ChemoSpec | 0.931 | 0.661 | 1.047 | |
validate_nmr_dataset | 1.379 | 1.050 | 1.675 | |
validate_nmr_dataset_family | 0.785 | 0.513 | 0.886 | |
validate_nmr_dataset_peak_table | 0.001 | 0.000 | 0.002 | |
zzz | 0.001 | 0.000 | 2.002 | |