Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 42/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AlpsNMR 4.1.6 (landing page) Sergio Oller Moreno
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | 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/library --timings AlpsNMR_4.1.6.tar.gz |
StartedAt: 2023-02-27 20:08:51 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:14:57 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 366.5 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/library --timings AlpsNMR_4.1.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AlpsNMR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-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 22.04.1 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 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 11.919 2.421 10.154 permutation_test_plot 6.979 1.889 3.343 SummarizedExperiment_to_nmr_data_1r 7.939 0.769 8.313 nmr_pca_outliers_robust 7.972 0.600 8.097 * 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/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) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 20.144 6.378 20.701
AlpsNMR.Rcheck/AlpsNMR-Ex.timings
name | user | system | elapsed | |
AlpsNMR-package | 2.358 | 0.369 | 2.373 | |
HMDB_blood | 0.036 | 0.008 | 0.044 | |
HMDB_cell | 0.003 | 0.000 | 0.003 | |
HMDB_urine | 0.006 | 0.000 | 0.006 | |
Parameters_blood | 0.003 | 0.000 | 0.003 | |
Parameters_cell | 0.003 | 0.000 | 0.002 | |
Parameters_urine | 0.003 | 0.000 | 0.003 | |
Peak_detection | 11.919 | 2.421 | 10.154 | |
Pipelines | 0.001 | 0.000 | 0.001 | |
ROI_blood | 0.004 | 0.000 | 0.004 | |
ROI_cell | 0.015 | 0.000 | 0.015 | |
ROI_urine | 0.004 | 0.000 | 0.004 | |
SummarizedExperiment_to_nmr_data_1r | 7.939 | 0.769 | 8.313 | |
SummarizedExperiment_to_nmr_dataset_peak_table | 1.401 | 0.444 | 1.415 | |
bp_VIP_analysis | 1.894 | 0.831 | 1.503 | |
bp_kfold_VIP_analysis | 1.021 | 0.570 | 0.890 | |
download_MTBLS242 | 0 | 0 | 0 | |
file_lister | 0.074 | 0.034 | 0.108 | |
files_to_rDolphin | 0 | 0 | 0 | |
filter.nmr_dataset_family | 1.118 | 0.590 | 1.237 | |
format.nmr_dataset | 0.965 | 0.579 | 1.028 | |
format.nmr_dataset_1D | 2.394 | 1.214 | 3.123 | |
format.nmr_dataset_peak_table | 1.149 | 0.487 | 1.199 | |
get_integration_with_metadata | 0.034 | 0.008 | 0.043 | |
hmdb | 0.071 | 0.016 | 0.087 | |
is.nmr_dataset | 0.974 | 0.564 | 1.032 | |
is.nmr_dataset_1D | 1.080 | 0.555 | 1.126 | |
is.nmr_dataset_peak_table | 1.218 | 0.429 | 1.188 | |
load_and_save_functions | 0.924 | 0.480 | 0.981 | |
models_stability_plot_bootstrap | 0.000 | 0.002 | 0.002 | |
models_stability_plot_plsda | 0.507 | 0.394 | 0.514 | |
new_nmr_dataset | 0.002 | 0.000 | 0.002 | |
new_nmr_dataset_1D | 0.002 | 0.000 | 0.002 | |
new_nmr_dataset_peak_table | 1.241 | 0.471 | 1.210 | |
nmr_baseline_estimation | 0.147 | 0.051 | 0.198 | |
nmr_baseline_removal | 0.006 | 0.001 | 0.006 | |
nmr_baseline_threshold | 0.001 | 0.000 | 0.002 | |
nmr_baseline_threshold_plot | 0.261 | 0.028 | 0.289 | |
nmr_batman | 0.000 | 0.003 | 0.003 | |
nmr_batman_options | 0.000 | 0.001 | 0.000 | |
nmr_build_peak_table | 0.071 | 0.004 | 0.075 | |
nmr_data | 0.073 | 0.011 | 0.085 | |
nmr_data_1r_to_SummarizedExperiment | 1.474 | 0.582 | 1.480 | |
nmr_data_analysis | 0.503 | 0.415 | 0.522 | |
nmr_dataset | 0.001 | 0.000 | 0.001 | |
nmr_dataset_1D | 0.001 | 0.000 | 0.002 | |
nmr_dataset_peak_table_to_SummarizedExperiment | 1.365 | 0.540 | 1.446 | |
nmr_exclude_region | 0.006 | 0.000 | 0.006 | |
nmr_export_data_1r | 1.131 | 0.538 | 1.200 | |
nmr_get_peak_distances | 0.006 | 0.008 | 0.014 | |
nmr_identify_regions_blood | 0.018 | 0.000 | 0.019 | |
nmr_identify_regions_cell | 0.009 | 0.004 | 0.012 | |
nmr_identify_regions_urine | 0.018 | 0.000 | 0.019 | |
nmr_integrate_regions | 0.016 | 0.000 | 0.017 | |
nmr_interpolate_1D | 2.006 | 1.169 | 2.205 | |
nmr_meta_add | 2.578 | 1.148 | 2.772 | |
nmr_meta_export | 0.987 | 0.637 | 1.093 | |
nmr_meta_get | 1.008 | 0.524 | 1.061 | |
nmr_meta_get_column | 0.883 | 0.523 | 0.955 | |
nmr_meta_groups | 1.006 | 0.550 | 1.064 | |
nmr_normalize | 0.346 | 0.051 | 0.397 | |
nmr_pca_build_model | 2.470 | 1.166 | 2.631 | |
nmr_pca_outliers | 1.242 | 0.705 | 1.455 | |
nmr_pca_outliers_filter | 2.041 | 0.820 | 2.383 | |
nmr_pca_outliers_plot | 0.001 | 0.000 | 0.001 | |
nmr_pca_outliers_robust | 7.972 | 0.600 | 8.097 | |
nmr_pca_plots | 0.542 | 0.012 | 0.555 | |
nmr_peak_clustering | 0.226 | 0.000 | 0.227 | |
nmr_ppm_resolution | 0.008 | 0.000 | 0.007 | |
nmr_read_bruker_fid | 0 | 0 | 0 | |
nmr_read_samples | 1.966 | 1.136 | 2.072 | |
nmr_zip_bruker_samples | 0.243 | 0.007 | 0.254 | |
peaklist_accept_peaks | 0.007 | 0.000 | 0.007 | |
permutation_test_model | 0.501 | 0.489 | 3.204 | |
permutation_test_plot | 6.979 | 1.889 | 3.343 | |
plot.nmr_dataset_1D | 0.002 | 0.000 | 0.001 | |
plot_bootstrap_multimodel | 0.003 | 0.000 | 0.003 | |
plot_interactive | 3.303 | 1.306 | 1.295 | |
plot_plsda_multimodel | 0.292 | 0.368 | 0.370 | |
plot_plsda_samples | 0.153 | 0.225 | 0.301 | |
plot_vip_scores | 0.002 | 0.001 | 0.003 | |
plot_webgl | 0.001 | 0.000 | 0.002 | |
plsda_auroc_vip_compare | 0.743 | 0.434 | 1.030 | |
plsda_auroc_vip_method | 0 | 0 | 0 | |
ppm_resolution | 0.003 | 0.000 | 0.003 | |
print.nmr_dataset | 0.993 | 0.617 | 1.079 | |
print.nmr_dataset_1D | 1.045 | 0.605 | 1.156 | |
print.nmr_dataset_peak_table | 1.170 | 0.622 | 1.280 | |
random_subsampling | 0.003 | 0.000 | 0.002 | |
save_files_to_rDolphin | 0.001 | 0.000 | 0.000 | |
save_profiling_output | 0 | 0 | 0 | |
sub-.nmr_dataset | 0.960 | 0.619 | 1.049 | |
sub-.nmr_dataset_1D | 1.167 | 0.545 | 1.244 | |
sub-.nmr_dataset_peak_table | 1.179 | 0.679 | 1.300 | |
tidy.nmr_dataset_1D | 1.319 | 0.581 | 1.330 | |
to_ChemoSpec | 1.290 | 0.669 | 1.440 | |
validate_nmr_dataset | 2.096 | 1.265 | 2.275 | |
validate_nmr_dataset_family | 1.158 | 0.631 | 1.199 | |
validate_nmr_dataset_peak_table | 0.001 | 0.001 | 0.001 | |
zzz | 0.000 | 0.000 | 2.002 | |