Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-05 11:41 -0400 (Sat, 05 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 57/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.7.2 (landing page) Sergio Oller Moreno
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | 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: 4.7.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.7.2.tar.gz |
StartedAt: 2024-10-04 18:52:50 -0400 (Fri, 04 Oct 2024) |
EndedAt: 2024-10-04 18:56:26 -0400 (Fri, 04 Oct 2024) |
EllapsedTime: 215.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AlpsNMR_4.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.7.2’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Peak_detection 11.615 3.503 10.588 SummarizedExperiment_to_nmr_data_1r 8.817 1.705 8.475 filter.nmr_dataset_family 4.483 3.505 3.530 is.nmr_dataset_peak_table 4.160 3.338 3.590 nmr_pca_outliers_robust 6.574 0.810 6.656 permutation_test_plot 4.549 2.639 2.246 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-apple-darwin20 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 26.181 9.049 25.453
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.103 | 0.600 | 1.968 | |
HMDB_blood | 0.008 | 0.003 | 0.011 | |
HMDB_cell | 0.002 | 0.001 | 0.004 | |
HMDB_urine | 0.004 | 0.001 | 0.007 | |
Parameters_blood | 0.002 | 0.001 | 0.003 | |
Parameters_cell | 0.002 | 0.002 | 0.003 | |
Parameters_urine | 0.002 | 0.001 | 0.003 | |
Peak_detection | 11.615 | 3.503 | 10.588 | |
Pipelines | 0.001 | 0.001 | 0.003 | |
ROI_blood | 0.003 | 0.001 | 0.005 | |
ROI_cell | 0.003 | 0.001 | 0.004 | |
ROI_urine | 0.004 | 0.002 | 0.005 | |
SummarizedExperiment_to_nmr_data_1r | 8.817 | 1.705 | 8.475 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.223 | 0.625 | 1.077 | |
bp_VIP_analysis | 1.423 | 0.730 | 1.142 | |
bp_kfold_VIP_analysis | 1.119 | 0.646 | 0.693 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.079 | 0.026 | 0.107 | |
files_to_rDolphin | 0.000 | 0.001 | 0.000 | |
filter.nmr_dataset_family | 4.483 | 3.505 | 3.530 | |
format.nmr_dataset | 0.877 | 0.636 | 0.714 | |
format.nmr_dataset_1D | 0.779 | 0.571 | 0.875 | |
format.nmr_dataset_peak_table | 1.149 | 0.881 | 1.094 | |
get_integration_with_metadata | 0.043 | 0.008 | 0.052 | |
hmdb | 0.058 | 0.011 | 0.070 | |
is.nmr_dataset | 1.097 | 0.774 | 0.647 | |
is.nmr_dataset_1D | 0.969 | 0.748 | 0.844 | |
is.nmr_dataset_peak_table | 4.160 | 3.338 | 3.590 | |
load_and_save_functions | 0.960 | 0.777 | 0.766 | |
models_stability_plot_bootstrap | 0.001 | 0.001 | 0.002 | |
models_stability_plot_plsda | 0.700 | 0.823 | 0.651 | |
new_nmr_dataset | 0.001 | 0.002 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
new_nmr_dataset_peak_table | 1.103 | 0.720 | 0.909 | |
nmr_autophase | 0.279 | 0.151 | 0.420 | |
nmr_baseline_estimation | 0.011 | 0.006 | 0.018 | |
nmr_baseline_removal | 0.006 | 0.001 | 0.007 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.259 | 0.030 | 0.293 | |
nmr_batman | 0.003 | 0.001 | 0.004 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.042 | 0.005 | 0.047 | |
nmr_data | 0.066 | 0.010 | 0.077 | |
nmr_data_1r_to_SummarizedExperiment | 1.149 | 0.511 | 0.989 | |
nmr_data_analysis | 0.563 | 0.534 | 0.549 | |
nmr_dataset | 0.001 | 0.000 | 0.002 | |
nmr_dataset_1D | 0.001 | 0.001 | 0.002 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.236 | 0.647 | 1.084 | |
nmr_exclude_region | 0.007 | 0.002 | 0.009 | |
nmr_export_data_1r | 0.941 | 0.618 | 0.811 | |
nmr_get_peak_distances | 0.010 | 0.002 | 0.013 | |
nmr_identify_regions_blood | 0.016 | 0.004 | 0.021 | |
nmr_identify_regions_cell | 0.012 | 0.002 | 0.014 | |
nmr_identify_regions_urine | 0.016 | 0.003 | 0.018 | |
nmr_integrate_regions | 0.013 | 0.002 | 0.016 | |
nmr_interpolate_1D | 1.885 | 1.176 | 1.546 | |
nmr_meta_add | 2.390 | 1.345 | 2.059 | |
nmr_meta_export | 1.006 | 0.780 | 0.815 | |
nmr_meta_get | 0.895 | 0.593 | 0.701 | |
nmr_meta_get_column | 0.726 | 0.480 | 0.801 | |
nmr_meta_groups | 1.358 | 1.066 | 0.966 | |
nmr_normalize | 0.315 | 0.053 | 0.369 | |
nmr_pca_build_model | 2.432 | 1.579 | 2.118 | |
nmr_pca_outliers | 1.106 | 0.662 | 0.973 | |
nmr_pca_outliers_filter | 1.151 | 0.671 | 1.041 | |
nmr_pca_outliers_plot | 0.000 | 0.001 | 0.001 | |
nmr_pca_outliers_robust | 6.574 | 0.810 | 6.656 | |
nmr_pca_plots | 0.413 | 0.012 | 0.430 | |
nmr_peak_clustering | 0.073 | 0.001 | 0.074 | |
nmr_ppm_resolution | 0.009 | 0.002 | 0.011 | |
nmr_read_bruker_fid | 0.001 | 0.000 | 0.001 | |
nmr_read_samples | 1.868 | 1.239 | 1.462 | |
nmr_zip_bruker_samples | 0.243 | 0.043 | 0.306 | |
peaklist_accept_peaks | 0.003 | 0.001 | 0.005 | |
permutation_test_model | 0.975 | 0.755 | 2.153 | |
permutation_test_plot | 4.549 | 2.639 | 2.246 | |
plot.nmr_dataset_1D | 0.002 | 0.002 | 0.004 | |
plot_bootstrap_multimodel | 3.308 | 1.452 | 0.045 | |
plot_interactive | 1.136 | 0.939 | 0.983 | |
plot_plsda_multimodel | 0.329 | 0.443 | 0.427 | |
plot_plsda_samples | 0.162 | 0.212 | 0.361 | |
plot_vip_scores | 0.002 | 0.001 | 0.003 | |
plot_webgl | 0.001 | 0.004 | 0.005 | |
plsda_auroc_vip_compare | 0.575 | 0.478 | 1.029 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.004 | 0.001 | 0.005 | |
print.nmr_dataset | 0.878 | 0.606 | 0.712 | |
print.nmr_dataset_1D | 1.173 | 0.976 | 1.009 | |
print.nmr_dataset_peak_table | 1.032 | 0.622 | 0.894 | |
random_subsampling | 0.001 | 0.004 | 0.006 | |
save_files_to_rDolphin | 0.000 | 0.000 | 0.001 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.862 | 0.551 | 0.675 | |
sub-.nmr_dataset_1D | 1.143 | 0.845 | 0.946 | |
sub-.nmr_dataset_peak_table | 1.096 | 0.671 | 0.982 | |
tidy.nmr_dataset_1D | 1.150 | 0.774 | 0.973 | |
to_ASICS | 1.123 | 0.204 | 1.340 | |
to_ChemoSpec | 1.245 | 1.120 | 1.623 | |
validate_nmr_dataset | 2.479 | 2.301 | 1.909 | |
validate_nmr_dataset_family | 1.162 | 0.926 | 0.995 | |
validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.002 | |
zzz | 0.000 | 0.000 | 2.127 | |