Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:52 -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 |
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To the developers/maintainers of the structToolbox package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/structToolbox.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 1979/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.11.0 (landing page) Gavin Rhys Lloyd
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: structToolbox |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings structToolbox_1.11.0.tar.gz |
StartedAt: 2023-02-28 16:58:45 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 17:23:23 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1478.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: structToolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings structToolbox_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/structToolbox.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 ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.11.0’ * 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 ‘structToolbox’ 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fold_change_int 24.703 0.068 24.773 fold_change 16.533 0.036 16.571 fisher_exact 13.736 0.036 13.774 fs_line 9.348 0.060 9.409 forward_selection_by_rank 8.464 0.064 8.529 compare_dist 5.762 0.036 5.799 grid_search_1d 5.531 0.012 5.543 kfoldxcv_grid 4.986 0.023 5.010 * 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 ... ‘data_analysis_omics_using_the_structtoolbox.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘structToolbox’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (structToolbox)
structToolbox.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(ggplot2) > library(structToolbox) Loading required package: struct > > test_check("structToolbox") [ FAIL 0 | WARN 7 | SKIP 0 | PASS 124 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 124 ] > > proc.time() user system elapsed 239.489 2.798 242.294
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.236 | 0.000 | 0.236 | |
AUC | 2.395 | 0.124 | 2.519 | |
DFA | 0.248 | 0.001 | 0.248 | |
DatasetExperiment_boxplot | 1.658 | 0.031 | 1.690 | |
DatasetExperiment_dist | 2.172 | 0.028 | 2.199 | |
DatasetExperiment_factor_boxplot | 0.265 | 0.000 | 0.265 | |
DatasetExperiment_heatmap | 0.343 | 0.012 | 0.355 | |
HCA | 0.07 | 0.00 | 0.07 | |
HSD | 0.491 | 0.004 | 0.501 | |
HSDEM | 0.483 | 0.008 | 0.491 | |
MTBLS79_DatasetExperiment | 0.002 | 0.000 | 0.001 | |
PCA | 0.006 | 0.000 | 0.005 | |
PLSDA | 0.02 | 0.00 | 0.02 | |
PLSR | 0.006 | 0.000 | 0.006 | |
SVM | 0.014 | 0.000 | 0.015 | |
as_data_frame | 0.158 | 0.000 | 0.158 | |
autoscale | 0.089 | 0.000 | 0.089 | |
balanced_accuracy | 2.382 | 0.012 | 2.395 | |
blank_filter | 0.437 | 0.016 | 0.453 | |
blank_filter_hist | 0.000 | 0.001 | 0.001 | |
bootstrap | 0.006 | 0.001 | 0.007 | |
calculate | 0.007 | 0.000 | 0.007 | |
chart_plot | 0.037 | 0.000 | 0.037 | |
classical_lsq | 0.391 | 0.000 | 0.391 | |
compare_dist | 5.762 | 0.036 | 5.799 | |
confounders_clsq | 3.802 | 0.040 | 3.843 | |
confounders_lsq_barchart | 3.963 | 0.012 | 3.975 | |
confounders_lsq_boxplot | 3.981 | 0.060 | 4.042 | |
constant_sum_norm | 0.006 | 0.000 | 0.006 | |
corr_coef | 0.335 | 0.004 | 0.338 | |
dfa_scores_plot | 0.885 | 0.000 | 0.886 | |
dratio_filter | 0.817 | 0.004 | 0.821 | |
equal_split | 0.171 | 0.004 | 0.175 | |
feature_boxplot | 0.023 | 0.000 | 0.022 | |
feature_profile | 0.532 | 0.000 | 0.531 | |
feature_profile_array | 0.796 | 0.004 | 0.799 | |
filter_by_name | 0.036 | 0.000 | 0.035 | |
filter_na_count | 1.425 | 0.000 | 1.424 | |
filter_smeta | 0.079 | 0.000 | 0.079 | |
fisher_exact | 13.736 | 0.036 | 13.774 | |
fold_change | 16.533 | 0.036 | 16.571 | |
fold_change_int | 24.703 | 0.068 | 24.773 | |
fold_change_plot | 0.005 | 0.000 | 0.006 | |
forward_selection_by_rank | 8.464 | 0.064 | 8.529 | |
fs_line | 9.348 | 0.060 | 9.409 | |
glog_opt_plot | 0.641 | 0.000 | 0.640 | |
glog_transform | 0.392 | 0.000 | 0.391 | |
grid_search_1d | 5.531 | 0.012 | 5.543 | |
gs_line | 0.001 | 0.000 | 0.001 | |
hca_dendrogram | 0.001 | 0.000 | 0.001 | |
kfold_xval | 4.566 | 0.044 | 4.610 | |
kfoldxcv_grid | 4.986 | 0.023 | 5.010 | |
kfoldxcv_metric | 0.001 | 0.000 | 0.001 | |
knn_impute | 0.008 | 0.000 | 0.007 | |
kw_p_hist | 0.000 | 0.000 | 0.001 | |
kw_rank_sum | 0.09 | 0.00 | 0.09 | |
linear_model | 0.031 | 0.000 | 0.031 | |
log_transform | 0.005 | 0.000 | 0.006 | |
mean_centre | 0.002 | 0.000 | 0.002 | |
mean_of_medians | 0.148 | 0.004 | 0.152 | |
mixed_effect | 0.186 | 0.000 | 0.186 | |
model_apply | 0.029 | 0.000 | 0.030 | |
model_predict | 0.070 | 0.000 | 0.069 | |
model_reverse | 0.053 | 0.000 | 0.052 | |
model_train | 0.063 | 0.000 | 0.063 | |
mv_boxplot | 0.372 | 0.000 | 0.373 | |
mv_feature_filter | 0.137 | 0.000 | 0.137 | |
mv_feature_filter_hist | 0.001 | 0.000 | 0.001 | |
mv_histogram | 0.339 | 0.000 | 0.339 | |
mv_sample_filter | 0.007 | 0.000 | 0.006 | |
mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
nroot_transform | 0.005 | 0.000 | 0.006 | |
ontology_cache | 0.000 | 0.001 | 0.001 | |
pairs_filter | 0.004 | 0.003 | 0.007 | |
pareto_scale | 0.075 | 0.000 | 0.075 | |
pca_biplot | 0.011 | 0.000 | 0.011 | |
pca_correlation_plot | 0.006 | 0.000 | 0.005 | |
pca_dstat_plot | 0.007 | 0.000 | 0.007 | |
pca_loadings_plot | 0.007 | 0.000 | 0.007 | |
pca_scores_plot | 0.741 | 0.000 | 0.740 | |
pca_scree_plot | 0.001 | 0.000 | 0.001 | |
permutation_test | 0.007 | 0.000 | 0.007 | |
permutation_test_plot | 0.004 | 0.000 | 0.003 | |
permute_sample_order | 0.006 | 0.000 | 0.006 | |
pls_regcoeff_plot | 0.454 | 0.000 | 0.455 | |
pls_scores_plot | 0.946 | 0.000 | 0.947 | |
pls_vip_plot | 0.495 | 0.000 | 0.495 | |
plsda_feature_importance_plot | 0.841 | 0.004 | 0.845 | |
plsda_predicted_plot | 0.667 | 0.000 | 0.667 | |
plsda_roc_plot | 1.566 | 0.004 | 1.570 | |
plsr_cook_dist | 0.006 | 0.000 | 0.005 | |
plsr_prediction_plot | 0.005 | 0.000 | 0.006 | |
plsr_qq_plot | 0.005 | 0.000 | 0.006 | |
plsr_residual_hist | 0.005 | 0.000 | 0.006 | |
pqn_norm | 0.471 | 0.004 | 0.476 | |
pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
prop_na | 0.007 | 0.000 | 0.008 | |
r_squared | 0.001 | 0.000 | 0.001 | |
resample | 0.011 | 0.000 | 0.011 | |
resample_chart | 0.004 | 0.000 | 0.004 | |
rsd_filter | 0.011 | 0.000 | 0.010 | |
rsd_filter_hist | 0.000 | 0.000 | 0.001 | |
run | 0.042 | 0.000 | 0.042 | |
sb_corr | 0.019 | 0.000 | 0.019 | |
scatter_chart | 0.499 | 0.000 | 0.500 | |
split_data | 0.006 | 0.000 | 0.005 | |
stratified_split | 0.168 | 0.000 | 0.168 | |
svm_plot_2d | 0.869 | 0.004 | 0.872 | |
tSNE | 0.017 | 0.000 | 0.016 | |
tSNE_scatter | 0.006 | 0.000 | 0.005 | |
tic_chart | 0.308 | 0.016 | 0.324 | |
ttest | 0.013 | 0.000 | 0.013 | |
vec_norm | 0.001 | 0.000 | 0.001 | |
wilcox_p_hist | 0.000 | 0.000 | 0.001 | |
wilcox_test | 0.033 | 0.000 | 0.032 | |