Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 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: 4.6.0 |
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: 2024-07-21 21:37:24 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 21:41:45 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 260.5 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 4.4.1 (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 ‘4.6.0’ * 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 7.611 1.696 6.651 SummarizedExperiment_to_nmr_data_1r 7.048 1.193 7.476 nmr_pca_outliers_robust 4.583 0.555 4.807 * 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 4.4.1 (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) 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 13.263 4.131 13.473
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.648 | 0.291 | 1.680 | |
HMDB_blood | 0.003 | 0.004 | 0.007 | |
HMDB_cell | 0.002 | 0.001 | 0.002 | |
HMDB_urine | 0.002 | 0.002 | 0.004 | |
Parameters_blood | 0.001 | 0.001 | 0.002 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.002 | 0.000 | 0.001 | |
Peak_detection | 7.611 | 1.696 | 6.651 | |
Pipelines | 0.000 | 0.002 | 0.002 | |
ROI_blood | 0.002 | 0.002 | 0.003 | |
ROI_cell | 0.003 | 0.000 | 0.003 | |
ROI_urine | 0.003 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 7.048 | 1.193 | 7.476 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.472 | 0.429 | 1.601 | |
bp_VIP_analysis | 1.088 | 0.642 | 0.947 | |
bp_kfold_VIP_analysis | 0.688 | 0.362 | 0.589 | |
download_MTBLS242 | 0.001 | 0.000 | 0.000 | |
file_lister | 0.054 | 0.015 | 0.069 | |
files_to_rDolphin | 0.001 | 0.001 | 0.000 | |
filter.nmr_dataset_family | 0.688 | 0.335 | 0.728 | |
format.nmr_dataset | 0.712 | 0.474 | 0.726 | |
format.nmr_dataset_1D | 0.833 | 0.369 | 0.858 | |
format.nmr_dataset_peak_table | 0.786 | 0.415 | 0.857 | |
get_integration_with_metadata | 0.025 | 0.000 | 0.024 | |
hmdb | 0.038 | 0.012 | 0.049 | |
is.nmr_dataset | 0.636 | 0.411 | 0.704 | |
is.nmr_dataset_1D | 0.741 | 0.437 | 0.814 | |
is.nmr_dataset_peak_table | 0.766 | 0.445 | 0.849 | |
load_and_save_functions | 0.620 | 0.467 | 0.721 | |
models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
models_stability_plot_plsda | 0.343 | 0.299 | 0.344 | |
new_nmr_dataset | 0.001 | 0.000 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
new_nmr_dataset_peak_table | 0.782 | 0.557 | 0.912 | |
nmr_baseline_estimation | 0.150 | 0.024 | 0.174 | |
nmr_baseline_removal | 0.004 | 0.000 | 0.004 | |
nmr_baseline_threshold | 0.002 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.204 | 0.016 | 0.219 | |
nmr_batman | 0.000 | 0.003 | 0.003 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_build_peak_table | 0.041 | 0.000 | 0.040 | |
nmr_data | 0.059 | 0.000 | 0.058 | |
nmr_data_1r_to_SummarizedExperiment | 0.928 | 0.411 | 1.018 | |
nmr_data_analysis | 0.356 | 0.505 | 0.461 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.002 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.734 | 0.513 | 1.873 | |
nmr_exclude_region | 0.003 | 0.004 | 0.006 | |
nmr_export_data_1r | 0.629 | 0.380 | 0.673 | |
nmr_get_peak_distances | 0.008 | 0.000 | 0.008 | |
nmr_identify_regions_blood | 0.009 | 0.003 | 0.013 | |
nmr_identify_regions_cell | 0.008 | 0.000 | 0.008 | |
nmr_identify_regions_urine | 0.005 | 0.007 | 0.013 | |
nmr_integrate_regions | 0.007 | 0.004 | 0.010 | |
nmr_interpolate_1D | 1.321 | 0.827 | 1.459 | |
nmr_meta_add | 1.613 | 0.780 | 1.722 | |
nmr_meta_export | 0.615 | 0.401 | 0.642 | |
nmr_meta_get | 0.582 | 0.334 | 0.607 | |
nmr_meta_get_column | 0.602 | 0.386 | 0.664 | |
nmr_meta_groups | 0.640 | 0.313 | 0.621 | |
nmr_normalize | 0.218 | 0.020 | 0.238 | |
nmr_pca_build_model | 1.478 | 0.712 | 1.565 | |
nmr_pca_outliers | 0.724 | 0.347 | 0.759 | |
nmr_pca_outliers_filter | 0.754 | 0.348 | 0.781 | |
nmr_pca_outliers_plot | 0.000 | 0.000 | 0.001 | |
nmr_pca_outliers_robust | 4.583 | 0.555 | 4.807 | |
nmr_pca_plots | 0.314 | 0.036 | 0.350 | |
nmr_peak_clustering | 0.059 | 0.008 | 0.067 | |
nmr_ppm_resolution | 0.007 | 0.000 | 0.008 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.465 | 0.853 | 1.521 | |
nmr_zip_bruker_samples | 0.257 | 0.012 | 0.271 | |
peaklist_accept_peaks | 0.004 | 0.000 | 0.004 | |
permutation_test_model | 1.701 | 0.974 | 2.225 | |
permutation_test_plot | 1.722 | 0.751 | 1.964 | |
plot.nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
plot_bootstrap_multimodel | 0.002 | 0.000 | 0.002 | |
plot_interactive | 3.329 | 0.995 | 0.762 | |
plot_plsda_multimodel | 0.183 | 0.242 | 0.277 | |
plot_plsda_samples | 0.095 | 0.157 | 0.186 | |
plot_vip_scores | 0.000 | 0.002 | 0.002 | |
plot_webgl | 0.025 | 0.042 | 0.001 | |
plsda_auroc_vip_compare | 0.410 | 0.313 | 0.620 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.000 | 0.004 | 0.003 | |
print.nmr_dataset | 0.667 | 0.439 | 0.734 | |
print.nmr_dataset_1D | 0.898 | 0.426 | 0.925 | |
print.nmr_dataset_peak_table | 0.776 | 0.404 | 0.822 | |
random_subsampling | 0.001 | 0.004 | 0.004 | |
save_files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.653 | 0.569 | 0.828 | |
sub-.nmr_dataset_1D | 0.778 | 0.505 | 0.912 | |
sub-.nmr_dataset_peak_table | 0.788 | 0.411 | 0.837 | |
tidy.nmr_dataset_1D | 2.363 | 1.591 | 3.552 | |
to_ChemoSpec | 0.743 | 0.465 | 0.842 | |
validate_nmr_dataset | 1.393 | 1.098 | 1.622 | |
validate_nmr_dataset_family | 0.638 | 0.485 | 0.757 | |
validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.001 | |
zzz | 0.000 | 0.000 | 2.002 | |