Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:36:10 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 57/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.5.0 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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: 4.5.0 |
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_4.5.0.tar.gz |
StartedAt: 2024-03-27 20:11:14 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 20:15:40 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 265.7 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_4.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘4.5.0’ * 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 8.108 1.463 6.714 SummarizedExperiment_to_nmr_data_1r 6.726 0.952 7.350 permutation_test_plot 3.952 1.375 1.962 nmr_pca_outliers_robust 4.716 0.563 4.959 nmr_pca_build_model 3.001 2.020 4.255 * 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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 13.402 3.957 13.367
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.612 | 0.340 | 1.634 | |
HMDB_blood | 0.003 | 0.004 | 0.007 | |
HMDB_cell | 0.002 | 0.000 | 0.002 | |
HMDB_urine | 0.004 | 0.000 | 0.004 | |
Parameters_blood | 0.002 | 0.000 | 0.002 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.002 | 0.000 | 0.002 | |
Peak_detection | 8.108 | 1.463 | 6.714 | |
Pipelines | 0.002 | 0.000 | 0.002 | |
ROI_blood | 0.003 | 0.000 | 0.003 | |
ROI_cell | 0.003 | 0.000 | 0.003 | |
ROI_urine | 0.003 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 6.726 | 0.952 | 7.350 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 0.982 | 0.323 | 1.028 | |
bp_VIP_analysis | 1.388 | 0.700 | 1.191 | |
bp_kfold_VIP_analysis | 0.664 | 0.426 | 0.594 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.062 | 0.004 | 0.066 | |
files_to_rDolphin | 0.001 | 0.000 | 0.001 | |
filter.nmr_dataset_family | 0.759 | 0.306 | 0.779 | |
format.nmr_dataset | 0.705 | 0.310 | 0.677 | |
format.nmr_dataset_1D | 0.768 | 0.388 | 0.793 | |
format.nmr_dataset_peak_table | 1.368 | 0.530 | 1.545 | |
get_integration_with_metadata | 0.019 | 0.003 | 0.021 | |
hmdb | 0.042 | 0.004 | 0.046 | |
is.nmr_dataset | 0.613 | 0.388 | 0.695 | |
is.nmr_dataset_1D | 0.743 | 0.334 | 0.763 | |
is.nmr_dataset_peak_table | 0.810 | 0.432 | 0.800 | |
load_and_save_functions | 0.670 | 0.401 | 0.730 | |
models_stability_plot_bootstrap | 0.000 | 0.002 | 0.002 | |
models_stability_plot_plsda | 0.327 | 0.344 | 0.358 | |
new_nmr_dataset | 0.001 | 0.000 | 0.002 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.821 | 0.469 | 0.891 | |
nmr_baseline_estimation | 0.125 | 0.028 | 0.152 | |
nmr_baseline_removal | 0.005 | 0.000 | 0.005 | |
nmr_baseline_threshold | 0.000 | 0.002 | 0.001 | |
nmr_baseline_threshold_plot | 0.342 | 0.058 | 0.400 | |
nmr_batman | 0.004 | 0.000 | 0.004 | |
nmr_batman_options | 0.000 | 0.000 | 0.001 | |
nmr_build_peak_table | 0.038 | 0.004 | 0.042 | |
nmr_data | 0.046 | 0.004 | 0.050 | |
nmr_data_1r_to_SummarizedExperiment | 0.947 | 0.390 | 1.041 | |
nmr_data_analysis | 0.434 | 0.324 | 0.412 | |
nmr_dataset | 0.000 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.000 | 0.001 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.941 | 0.396 | 1.008 | |
nmr_exclude_region | 0.006 | 0.000 | 0.006 | |
nmr_export_data_1r | 0.585 | 0.461 | 0.722 | |
nmr_get_peak_distances | 0.003 | 0.004 | 0.007 | |
nmr_identify_regions_blood | 0.005 | 0.008 | 0.013 | |
nmr_identify_regions_cell | 0.008 | 0.000 | 0.008 | |
nmr_identify_regions_urine | 0.009 | 0.003 | 0.013 | |
nmr_integrate_regions | 0.009 | 0.000 | 0.010 | |
nmr_interpolate_1D | 1.412 | 0.788 | 1.475 | |
nmr_meta_add | 1.688 | 0.775 | 1.809 | |
nmr_meta_export | 0.714 | 0.474 | 0.792 | |
nmr_meta_get | 0.765 | 0.543 | 0.797 | |
nmr_meta_get_column | 0.688 | 0.375 | 0.723 | |
nmr_meta_groups | 0.732 | 0.442 | 0.771 | |
nmr_normalize | 0.274 | 0.040 | 0.314 | |
nmr_pca_build_model | 3.001 | 2.020 | 4.255 | |
nmr_pca_outliers | 0.758 | 0.491 | 0.859 | |
nmr_pca_outliers_filter | 0.841 | 0.492 | 0.977 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 4.716 | 0.563 | 4.959 | |
nmr_pca_plots | 0.396 | 0.024 | 0.419 | |
nmr_peak_clustering | 0.063 | 0.004 | 0.066 | |
nmr_ppm_resolution | 0.004 | 0.004 | 0.009 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.387 | 1.017 | 1.539 | |
nmr_zip_bruker_samples | 0.257 | 0.010 | 0.269 | |
peaklist_accept_peaks | 0.003 | 0.000 | 0.004 | |
permutation_test_model | 0.334 | 0.391 | 1.904 | |
permutation_test_plot | 3.952 | 1.375 | 1.962 | |
plot.nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
plot_bootstrap_multimodel | 0.002 | 0.000 | 0.003 | |
plot_interactive | 2.031 | 1.091 | 1.042 | |
plot_plsda_multimodel | 0.170 | 0.250 | 0.265 | |
plot_plsda_samples | 0.097 | 0.162 | 0.205 | |
plot_vip_scores | 0.002 | 0.001 | 0.002 | |
plot_webgl | 0.022 | 0.048 | 0.002 | |
plsda_auroc_vip_compare | 0.513 | 0.346 | 0.741 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.000 | 0.003 | |
print.nmr_dataset | 0.688 | 0.454 | 0.717 | |
print.nmr_dataset_1D | 0.779 | 0.511 | 0.807 | |
print.nmr_dataset_peak_table | 0.741 | 0.516 | 0.856 | |
random_subsampling | 0.003 | 0.000 | 0.003 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.685 | 0.492 | 0.783 | |
sub-.nmr_dataset_1D | 0.746 | 0.495 | 0.847 | |
sub-.nmr_dataset_peak_table | 0.842 | 0.631 | 1.058 | |
tidy.nmr_dataset_1D | 0.901 | 0.437 | 0.947 | |
to_ChemoSpec | 0.780 | 0.520 | 0.917 | |
validate_nmr_dataset | 1.595 | 1.180 | 1.870 | |
validate_nmr_dataset_family | 0.734 | 0.489 | 0.811 | |
validate_nmr_dataset_peak_table | 0.000 | 0.001 | 0.001 | |
zzz | 0.000 | 0.001 | 2.003 | |