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 11:40:18 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: AlpsNMR |
Version: 4.5.0 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings AlpsNMR_4.5.0.tar.gz |
StartedAt: 2024-03-28 02:43:01 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 02:46:40 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 218.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings AlpsNMR_4.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/AlpsNMR.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 12.337 2.254 10.271 SummarizedExperiment_to_nmr_data_1r 8.669 0.915 9.182 nmr_pca_outliers_robust 7.714 0.823 8.106 nmr_pca_build_model 3.954 1.942 4.920 permutation_test_plot 4.330 1.219 2.890 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
AlpsNMR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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) (2024-03-19 r86153) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 18.635 4.532 18.276
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.267 | 0.353 | 2.266 | |
HMDB_blood | 0.008 | 0.000 | 0.008 | |
HMDB_cell | 0.000 | 0.003 | 0.004 | |
HMDB_urine | 0.005 | 0.000 | 0.005 | |
Parameters_blood | 0.002 | 0.000 | 0.001 | |
Parameters_cell | 0.002 | 0.000 | 0.002 | |
Parameters_urine | 0.001 | 0.000 | 0.002 | |
Peak_detection | 12.337 | 2.254 | 10.271 | |
Pipelines | 0.002 | 0.000 | 0.002 | |
ROI_blood | 0.005 | 0.000 | 0.004 | |
ROI_cell | 0.004 | 0.000 | 0.004 | |
ROI_urine | 0.004 | 0.000 | 0.004 | |
SummarizedExperiment_to_nmr_data_1r | 8.669 | 0.915 | 9.182 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.359 | 0.370 | 1.365 | |
bp_VIP_analysis | 1.955 | 0.876 | 1.571 | |
bp_kfold_VIP_analysis | 1.078 | 0.550 | 0.924 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.080 | 0.032 | 0.113 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 1.035 | 0.447 | 1.087 | |
format.nmr_dataset | 0.943 | 0.513 | 1.005 | |
format.nmr_dataset_1D | 1.107 | 0.591 | 1.197 | |
format.nmr_dataset_peak_table | 1.909 | 0.731 | 2.147 | |
get_integration_with_metadata | 0.036 | 0.000 | 0.035 | |
hmdb | 0.066 | 0.000 | 0.067 | |
is.nmr_dataset | 0.852 | 0.428 | 0.864 | |
is.nmr_dataset_1D | 0.963 | 0.459 | 1.013 | |
is.nmr_dataset_peak_table | 1.083 | 0.400 | 1.059 | |
load_and_save_functions | 0.928 | 0.375 | 0.879 | |
models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
models_stability_plot_plsda | 0.458 | 0.353 | 0.444 | |
new_nmr_dataset | 0.000 | 0.002 | 0.002 | |
new_nmr_dataset_1D | 0.000 | 0.002 | 0.002 | |
new_nmr_dataset_peak_table | 1.079 | 0.583 | 1.184 | |
nmr_baseline_estimation | 0.141 | 0.044 | 0.187 | |
nmr_baseline_removal | 0.003 | 0.004 | 0.007 | |
nmr_baseline_threshold | 0.002 | 0.001 | 0.002 | |
nmr_baseline_threshold_plot | 0.516 | 0.059 | 0.577 | |
nmr_batman | 0.003 | 0.000 | 0.003 | |
nmr_batman_options | 0.001 | 0.000 | 0.000 | |
nmr_build_peak_table | 0.044 | 0.004 | 0.048 | |
nmr_data | 0.065 | 0.004 | 0.069 | |
nmr_data_1r_to_SummarizedExperiment | 1.248 | 0.461 | 1.335 | |
nmr_data_analysis | 0.531 | 0.413 | 0.518 | |
nmr_dataset | 0.001 | 0.000 | 0.002 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.261 | 0.527 | 1.342 | |
nmr_exclude_region | 0.007 | 0.000 | 0.006 | |
nmr_export_data_1r | 1.016 | 0.446 | 1.019 | |
nmr_get_peak_distances | 0.006 | 0.004 | 0.011 | |
nmr_identify_regions_blood | 0.011 | 0.008 | 0.020 | |
nmr_identify_regions_cell | 0.012 | 0.000 | 0.012 | |
nmr_identify_regions_urine | 0.018 | 0.000 | 0.018 | |
nmr_integrate_regions | 0.013 | 0.000 | 0.012 | |
nmr_interpolate_1D | 2.177 | 0.964 | 2.243 | |
nmr_meta_add | 2.422 | 0.973 | 2.502 | |
nmr_meta_export | 1.021 | 0.558 | 1.000 | |
nmr_meta_get | 1.015 | 0.788 | 1.166 | |
nmr_meta_get_column | 0.950 | 0.494 | 0.993 | |
nmr_meta_groups | 0.930 | 0.616 | 1.038 | |
nmr_normalize | 0.413 | 0.124 | 0.538 | |
nmr_pca_build_model | 3.954 | 1.942 | 4.920 | |
nmr_pca_outliers | 1.171 | 0.522 | 1.243 | |
nmr_pca_outliers_filter | 1.286 | 0.471 | 1.307 | |
nmr_pca_outliers_plot | 0 | 0 | 0 | |
nmr_pca_outliers_robust | 7.714 | 0.823 | 8.106 | |
nmr_pca_plots | 0.668 | 0.040 | 0.710 | |
nmr_peak_clustering | 0.087 | 0.016 | 0.103 | |
nmr_ppm_resolution | 0.006 | 0.003 | 0.009 | |
nmr_read_bruker_fid | 0.000 | 0.000 | 0.001 | |
nmr_read_samples | 1.815 | 1.000 | 1.842 | |
nmr_zip_bruker_samples | 0.231 | 0.023 | 0.257 | |
peaklist_accept_peaks | 0.005 | 0.000 | 0.006 | |
permutation_test_model | 2.277 | 0.839 | 2.701 | |
permutation_test_plot | 4.330 | 1.219 | 2.890 | |
plot.nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
plot_bootstrap_multimodel | 0.002 | 0.000 | 0.003 | |
plot_interactive | 2.922 | 1.117 | 1.115 | |
plot_plsda_multimodel | 0.183 | 0.343 | 0.319 | |
plot_plsda_samples | 0.128 | 0.189 | 0.236 | |
plot_vip_scores | 0.001 | 0.000 | 0.003 | |
plot_webgl | 0.002 | 0.000 | 0.002 | |
plsda_auroc_vip_compare | 0.708 | 0.511 | 0.966 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.004 | 0.000 | 0.003 | |
print.nmr_dataset | 0.945 | 0.530 | 0.932 | |
print.nmr_dataset_1D | 1.154 | 0.608 | 1.185 | |
print.nmr_dataset_peak_table | 1.132 | 0.594 | 1.204 | |
random_subsampling | 0.002 | 0.000 | 0.002 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0.000 | 0.000 | 0.001 | |
sub-.nmr_dataset | 0.965 | 0.516 | 0.972 | |
sub-.nmr_dataset_1D | 0.966 | 0.609 | 1.070 | |
sub-.nmr_dataset_peak_table | 1.161 | 0.566 | 1.263 | |
tidy.nmr_dataset_1D | 1.267 | 0.539 | 1.276 | |
to_ChemoSpec | 1.269 | 0.746 | 1.436 | |
validate_nmr_dataset | 2.080 | 1.458 | 2.452 | |
validate_nmr_dataset_family | 0.991 | 0.661 | 1.135 | |
validate_nmr_dataset_peak_table | 0.000 | 0.001 | 0.002 | |
zzz | 0.000 | 0.000 | 2.002 | |