Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:21 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 55/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.1.6 (landing page) Sergio Oller Moreno
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: AlpsNMR |
Version: 4.1.6 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings AlpsNMR_4.1.6.tar.gz |
StartedAt: 2023-04-11 18:30:55 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 18:35:27 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 271.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AlpsNMR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AlpsNMR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings AlpsNMR_4.1.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘AlpsNMR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AlpsNMR’ version ‘4.1.6’ * 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 R 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 7.655 1.560 6.526 nmr_pca_outliers_robust 6.274 1.697 7.560 SummarizedExperiment_to_nmr_data_1r 5.672 0.862 6.186 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Vig01-introduction-to-alpsnmr.Rmd’ using ‘UTF-8’... OK ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using ‘UTF-8’... OK ‘Vig02-handling-metadata-and-annotations.Rmd’ using ‘UTF-8’... OK NONE * 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-3.17-bioc/R/bin/R CMD INSTALL AlpsNMR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154) Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 ═══════════════════════════════════════════════════════════════ • On Bioconductor (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 91 ] > > proc.time() user system elapsed 15.067 4.767 15.019
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 1.746 | 0.269 | 1.768 | |
HMDB_blood | 0.006 | 0.000 | 0.006 | |
HMDB_cell | 0.003 | 0.000 | 0.002 | |
HMDB_urine | 0.005 | 0.000 | 0.004 | |
Parameters_blood | 0.002 | 0.000 | 0.002 | |
Parameters_cell | 0.001 | 0.000 | 0.002 | |
Parameters_urine | 0.002 | 0.000 | 0.002 | |
Peak_detection | 7.655 | 1.560 | 6.526 | |
Pipelines | 0.002 | 0.000 | 0.002 | |
ROI_blood | 0.004 | 0.000 | 0.003 | |
ROI_cell | 0.004 | 0.000 | 0.004 | |
ROI_urine | 0.003 | 0.000 | 0.003 | |
SummarizedExperiment_to_nmr_data_1r | 5.672 | 0.862 | 6.186 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.844 | 0.426 | 1.923 | |
bp_VIP_analysis | 0.816 | 0.388 | 1.024 | |
bp_kfold_VIP_analysis | 1.154 | 0.549 | 0.574 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.058 | 0.016 | 0.074 | |
files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
filter.nmr_dataset_family | 0.911 | 0.453 | 0.907 | |
format.nmr_dataset | 0.638 | 0.355 | 0.653 | |
format.nmr_dataset_1D | 2.684 | 1.660 | 3.043 | |
format.nmr_dataset_peak_table | 0.765 | 0.448 | 0.875 | |
get_integration_with_metadata | 0.027 | 0.004 | 0.030 | |
hmdb | 0.046 | 0.004 | 0.049 | |
is.nmr_dataset | 0.632 | 0.357 | 0.669 | |
is.nmr_dataset_1D | 0.709 | 0.377 | 0.740 | |
is.nmr_dataset_peak_table | 0.774 | 0.426 | 0.864 | |
load_and_save_functions | 0.612 | 0.366 | 0.668 | |
models_stability_plot_bootstrap | 0.002 | 0.000 | 0.002 | |
models_stability_plot_plsda | 0.383 | 0.359 | 0.426 | |
new_nmr_dataset | 0.002 | 0.000 | 0.003 | |
new_nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
new_nmr_dataset_peak_table | 0.740 | 0.422 | 0.807 | |
nmr_baseline_estimation | 0.126 | 0.009 | 0.134 | |
nmr_baseline_removal | 0.005 | 0.000 | 0.005 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.001 | |
nmr_baseline_threshold_plot | 0.216 | 0.035 | 0.251 | |
nmr_batman | 0.003 | 0.000 | 0.003 | |
nmr_batman_options | 0 | 0 | 0 | |
nmr_build_peak_table | 0.045 | 0.003 | 0.048 | |
nmr_data | 0.039 | 0.016 | 0.054 | |
nmr_data_1r_to_SummarizedExperiment | 0.937 | 0.475 | 1.113 | |
nmr_data_analysis | 0.349 | 0.511 | 0.477 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.001 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 0.987 | 0.691 | 1.214 | |
nmr_exclude_region | 0.007 | 0.000 | 0.007 | |
nmr_export_data_1r | 0.767 | 0.533 | 0.860 | |
nmr_get_peak_distances | 0.012 | 0.000 | 0.011 | |
nmr_identify_regions_blood | 0.008 | 0.008 | 0.016 | |
nmr_identify_regions_cell | 0.009 | 0.000 | 0.010 | |
nmr_identify_regions_urine | 0.012 | 0.004 | 0.015 | |
nmr_integrate_regions | 0.004 | 0.012 | 0.016 | |
nmr_interpolate_1D | 1.450 | 0.891 | 1.575 | |
nmr_meta_add | 1.707 | 0.961 | 1.970 | |
nmr_meta_export | 0.629 | 0.547 | 0.771 | |
nmr_meta_get | 0.700 | 0.506 | 0.770 | |
nmr_meta_get_column | 0.709 | 0.452 | 0.819 | |
nmr_meta_groups | 0.782 | 0.482 | 0.864 | |
nmr_normalize | 0.248 | 0.116 | 0.364 | |
nmr_pca_build_model | 1.741 | 0.989 | 1.991 | |
nmr_pca_outliers | 0.965 | 0.608 | 1.102 | |
nmr_pca_outliers_filter | 0.926 | 0.485 | 0.994 | |
nmr_pca_outliers_plot | 0.001 | 0.000 | 0.000 | |
nmr_pca_outliers_robust | 6.274 | 1.697 | 7.560 | |
nmr_pca_plots | 0.388 | 0.024 | 0.412 | |
nmr_peak_clustering | 0.074 | 0.000 | 0.074 | |
nmr_ppm_resolution | 0.008 | 0.000 | 0.008 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.276 | 0.753 | 1.404 | |
nmr_zip_bruker_samples | 0.251 | 0.015 | 0.268 | |
peaklist_accept_peaks | 0.003 | 0.000 | 0.004 | |
permutation_test_model | 1.867 | 0.661 | 2.217 | |
permutation_test_plot | 1.970 | 0.758 | 2.230 | |
plot.nmr_dataset_1D | 0.002 | 0.001 | 0.001 | |
plot_bootstrap_multimodel | 0.003 | 0.000 | 0.002 | |
plot_interactive | 2.113 | 0.771 | 0.759 | |
plot_plsda_multimodel | 0.178 | 0.245 | 0.275 | |
plot_plsda_samples | 0.120 | 0.139 | 0.190 | |
plot_vip_scores | 0.030 | 0.032 | 0.002 | |
plot_webgl | 0.002 | 0.000 | 0.001 | |
plsda_auroc_vip_compare | 0.452 | 0.244 | 0.594 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.000 | 0.004 | 0.004 | |
print.nmr_dataset | 0.707 | 0.503 | 0.773 | |
print.nmr_dataset_1D | 0.856 | 0.633 | 1.019 | |
print.nmr_dataset_peak_table | 0.996 | 0.651 | 1.296 | |
random_subsampling | 0.000 | 0.004 | 0.005 | |
save_files_to_rDolphin | 0 | 0 | 0 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.797 | 0.484 | 0.855 | |
sub-.nmr_dataset_1D | 0.807 | 0.508 | 0.849 | |
sub-.nmr_dataset_peak_table | 0.923 | 0.585 | 1.040 | |
tidy.nmr_dataset_1D | 0.843 | 0.534 | 0.953 | |
to_ChemoSpec | 0.907 | 0.543 | 1.038 | |
validate_nmr_dataset | 1.561 | 1.199 | 1.854 | |
validate_nmr_dataset_family | 0.811 | 0.481 | 0.880 | |
validate_nmr_dataset_peak_table | 0.002 | 0.000 | 0.002 | |
zzz | 0.000 | 0.001 | 2.002 | |