Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2079/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.18.0 (landing page) Gavin Rhys Lloyd
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the structToolbox package: - 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 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: structToolbox |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.18.0.tar.gz |
StartedAt: 2024-12-21 11:10:54 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 11:19:27 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 513.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: structToolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings structToolbox_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/structToolbox.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.18.0’ * 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 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 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 15.958 0.059 16.159 fold_change 10.618 0.058 10.709 fisher_exact 10.415 0.043 10.493 fs_line 7.120 0.121 7.259 forward_selection_by_rank 6.292 0.108 6.414 compare_dist 4.866 0.192 5.070 * 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
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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(ggplot2) > library(structToolbox) Loading required package: struct > > test_check("structToolbox") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 166 ] > > proc.time() user system elapsed 189.381 2.024 192.573
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.240 | 0.006 | 0.247 | |
AUC | 2.048 | 0.076 | 2.136 | |
DFA | 0.204 | 0.002 | 0.207 | |
DatasetExperiment_boxplot | 1.858 | 0.034 | 1.898 | |
DatasetExperiment_dist | 1.459 | 0.065 | 1.532 | |
DatasetExperiment_factor_boxplot | 0.214 | 0.002 | 0.218 | |
DatasetExperiment_heatmap | 0.428 | 0.016 | 0.445 | |
HCA | 0.075 | 0.005 | 0.080 | |
HSD | 0.319 | 0.017 | 0.344 | |
HSDEM | 0.494 | 0.020 | 0.518 | |
MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
OPLSDA | 0.010 | 0.001 | 0.011 | |
OPLSR | 0.014 | 0.000 | 0.014 | |
PCA | 0.004 | 0.000 | 0.005 | |
PLSDA | 0.024 | 0.001 | 0.025 | |
PLSR | 0.011 | 0.001 | 0.011 | |
SVM | 0.027 | 0.001 | 0.028 | |
as_data_frame | 0.132 | 0.002 | 0.134 | |
autoscale | 0.079 | 0.002 | 0.081 | |
balanced_accuracy | 1.791 | 0.016 | 1.810 | |
blank_filter | 0.396 | 0.017 | 0.415 | |
blank_filter_hist | 0.001 | 0.000 | 0.001 | |
bootstrap | 0.019 | 0.001 | 0.020 | |
calculate | 0.005 | 0.001 | 0.006 | |
chart_plot | 0.027 | 0.001 | 0.028 | |
classical_lsq | 0.329 | 0.003 | 0.335 | |
compare_dist | 4.866 | 0.192 | 5.070 | |
confounders_clsq | 2.924 | 0.022 | 2.952 | |
confounders_lsq_barchart | 3.046 | 0.021 | 3.079 | |
confounders_lsq_boxplot | 2.950 | 0.019 | 2.979 | |
constant_sum_norm | 0.016 | 0.001 | 0.016 | |
corr_coef | 0.284 | 0.003 | 0.287 | |
dfa_scores_plot | 0.731 | 0.009 | 0.741 | |
dratio_filter | 0.278 | 0.007 | 0.287 | |
equal_split | 0.139 | 0.002 | 0.142 | |
feature_boxplot | 0.031 | 0.001 | 0.032 | |
feature_profile | 0.390 | 0.008 | 0.399 | |
feature_profile_array | 0.477 | 0.006 | 0.484 | |
filter_by_name | 0.031 | 0.001 | 0.032 | |
filter_na_count | 1.095 | 0.043 | 1.141 | |
filter_smeta | 0.063 | 0.000 | 0.066 | |
fisher_exact | 10.415 | 0.043 | 10.493 | |
fold_change | 10.618 | 0.058 | 10.709 | |
fold_change_int | 15.958 | 0.059 | 16.159 | |
fold_change_plot | 0.012 | 0.000 | 0.012 | |
forward_selection_by_rank | 6.292 | 0.108 | 6.414 | |
fs_line | 7.120 | 0.121 | 7.259 | |
glog_opt_plot | 0.477 | 0.005 | 0.484 | |
glog_transform | 0.281 | 0.002 | 0.283 | |
grid_search_1d | 3.793 | 0.127 | 3.931 | |
gs_line | 0.001 | 0.000 | 0.001 | |
hca_dendrogram | 0.001 | 0.000 | 0.000 | |
kfold_xval | 3.475 | 0.027 | 3.515 | |
kfoldxcv_grid | 3.795 | 0.031 | 3.854 | |
kfoldxcv_metric | 0.001 | 0.001 | 0.001 | |
knn_impute | 0.012 | 0.000 | 0.011 | |
kw_p_hist | 0.001 | 0.000 | 0.001 | |
kw_rank_sum | 0.100 | 0.001 | 0.102 | |
linear_model | 0.028 | 0.000 | 0.029 | |
log_transform | 0.013 | 0.000 | 0.014 | |
mean_centre | 0.003 | 0.000 | 0.003 | |
mean_of_medians | 0.121 | 0.001 | 0.123 | |
mixed_effect | 0.183 | 0.003 | 0.190 | |
model_apply | 0.023 | 0.001 | 0.024 | |
model_predict | 0.053 | 0.001 | 0.054 | |
model_reverse | 0.043 | 0.000 | 0.044 | |
model_train | 0.049 | 0.000 | 0.050 | |
mv_boxplot | 0.300 | 0.009 | 0.310 | |
mv_feature_filter | 0.119 | 0.002 | 0.122 | |
mv_feature_filter_hist | 0.001 | 0.001 | 0.001 | |
mv_histogram | 0.250 | 0.003 | 0.256 | |
mv_sample_filter | 0.015 | 0.000 | 0.016 | |
mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
nroot_transform | 0.013 | 0.000 | 0.013 | |
ontology_cache | 0.000 | 0.000 | 0.001 | |
pairs_filter | 0.015 | 0.000 | 0.015 | |
pareto_scale | 0.054 | 0.001 | 0.054 | |
pca_biplot | 0.019 | 0.000 | 0.019 | |
pca_correlation_plot | 0.011 | 0.000 | 0.012 | |
pca_dstat_plot | 0.014 | 0.000 | 0.013 | |
pca_loadings_plot | 0.014 | 0.000 | 0.014 | |
pca_scores_plot | 0.521 | 0.009 | 0.531 | |
pca_scree_plot | 0.014 | 0.000 | 0.014 | |
permutation_test | 0.018 | 0.001 | 0.018 | |
permutation_test_plot | 0.004 | 0.000 | 0.004 | |
permute_sample_order | 0.016 | 0.000 | 0.016 | |
pls_regcoeff_plot | 0.396 | 0.009 | 0.408 | |
pls_scores_plot | 0.664 | 0.006 | 0.671 | |
pls_vip_plot | 0.373 | 0.004 | 0.379 | |
plsda_feature_importance_plot | 0.626 | 0.007 | 0.636 | |
plsda_predicted_plot | 0.439 | 0.006 | 0.446 | |
plsda_roc_plot | 1.136 | 0.012 | 1.153 | |
plsr_cook_dist | 0.011 | 0.000 | 0.011 | |
plsr_prediction_plot | 0.011 | 0.000 | 0.013 | |
plsr_qq_plot | 0.011 | 0.001 | 0.011 | |
plsr_residual_hist | 0.010 | 0.000 | 0.011 | |
pqn_norm | 0.342 | 0.003 | 0.346 | |
pqn_norm_hist | 0.001 | 0.000 | 0.001 | |
prop_na | 0.016 | 0.001 | 0.016 | |
r_squared | 0.001 | 0.000 | 0.001 | |
resample | 0.023 | 0.000 | 0.024 | |
resample_chart | 0.003 | 0.000 | 0.003 | |
rsd_filter | 0.036 | 0.001 | 0.037 | |
rsd_filter_hist | 0.001 | 0.000 | 0.001 | |
run | 0.032 | 0.000 | 0.033 | |
sb_corr | 0.033 | 0.001 | 0.034 | |
scatter_chart | 0.324 | 0.004 | 0.329 | |
split_data | 0.013 | 0.000 | 0.013 | |
stratified_split | 0.121 | 0.001 | 0.123 | |
svm_plot_2d | 0.703 | 0.018 | 0.748 | |
tSNE | 0.031 | 0.001 | 0.033 | |
tSNE_scatter | 0.014 | 0.001 | 0.015 | |
tic_chart | 0.212 | 0.004 | 0.219 | |
ttest | 0.021 | 0.000 | 0.022 | |
vec_norm | 0.001 | 0.001 | 0.001 | |
wilcox_p_hist | 0.000 | 0.000 | 0.001 | |
wilcox_test | 0.024 | 0.001 | 0.025 | |