Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 2064/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.19.0 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.19.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings structToolbox_1.19.0.tar.gz |
StartedAt: 2024-12-23 02:41:45 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 02:59:35 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 1070.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: structToolbox.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings structToolbox_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/structToolbox.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.19.0’ * 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 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 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 16.043 0.204 16.247 fold_change 10.826 0.028 10.854 fisher_exact 10.022 0.092 10.115 fs_line 5.829 0.031 5.861 forward_selection_by_rank 5.785 0.048 5.835 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
structToolbox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL structToolbox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 175.561 1.717 177.303
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.214 | 0.000 | 0.214 | |
AUC | 2.021 | 0.109 | 2.131 | |
DFA | 0.194 | 0.000 | 0.194 | |
DatasetExperiment_boxplot | 1.692 | 0.017 | 1.710 | |
DatasetExperiment_dist | 1.322 | 0.098 | 1.420 | |
DatasetExperiment_factor_boxplot | 0.200 | 0.000 | 0.201 | |
DatasetExperiment_heatmap | 0.407 | 0.002 | 0.408 | |
HCA | 0.067 | 0.000 | 0.066 | |
HSD | 0.286 | 0.005 | 0.294 | |
HSDEM | 0.352 | 0.003 | 0.356 | |
MTBLS79_DatasetExperiment | 0.001 | 0.000 | 0.001 | |
OPLSDA | 0.011 | 0.000 | 0.011 | |
OPLSR | 0.016 | 0.000 | 0.015 | |
PCA | 0.005 | 0.000 | 0.004 | |
PLSDA | 0.025 | 0.001 | 0.026 | |
PLSR | 0.010 | 0.000 | 0.009 | |
SVM | 0.027 | 0.001 | 0.028 | |
as_data_frame | 0.140 | 0.012 | 0.151 | |
autoscale | 0.074 | 0.004 | 0.078 | |
balanced_accuracy | 1.766 | 0.019 | 1.786 | |
blank_filter | 0.367 | 0.008 | 0.376 | |
blank_filter_hist | 0.001 | 0.000 | 0.001 | |
bootstrap | 0.017 | 0.001 | 0.017 | |
calculate | 0.005 | 0.001 | 0.005 | |
chart_plot | 0.029 | 0.000 | 0.029 | |
classical_lsq | 0.297 | 0.001 | 0.298 | |
compare_dist | 4.462 | 0.144 | 4.607 | |
confounders_clsq | 2.846 | 0.001 | 2.847 | |
confounders_lsq_barchart | 3.022 | 0.004 | 3.025 | |
confounders_lsq_boxplot | 2.895 | 0.026 | 2.920 | |
constant_sum_norm | 0.013 | 0.000 | 0.014 | |
corr_coef | 0.247 | 0.001 | 0.249 | |
dfa_scores_plot | 0.698 | 0.009 | 0.708 | |
dratio_filter | 0.286 | 0.000 | 0.287 | |
equal_split | 0.122 | 0.002 | 0.124 | |
feature_boxplot | 0.028 | 0.002 | 0.029 | |
feature_profile | 0.361 | 0.000 | 0.361 | |
feature_profile_array | 0.453 | 0.018 | 0.471 | |
filter_by_name | 0.031 | 0.001 | 0.032 | |
filter_na_count | 0.961 | 0.010 | 0.972 | |
filter_smeta | 0.056 | 0.000 | 0.057 | |
fisher_exact | 10.022 | 0.092 | 10.115 | |
fold_change | 10.826 | 0.028 | 10.854 | |
fold_change_int | 16.043 | 0.204 | 16.247 | |
fold_change_plot | 0.011 | 0.000 | 0.011 | |
forward_selection_by_rank | 5.785 | 0.048 | 5.835 | |
fs_line | 5.829 | 0.031 | 5.861 | |
glog_opt_plot | 0.459 | 0.001 | 0.460 | |
glog_transform | 0.261 | 0.000 | 0.261 | |
grid_search_1d | 3.321 | 0.043 | 3.366 | |
gs_line | 0.000 | 0.001 | 0.001 | |
hca_dendrogram | 0.001 | 0.000 | 0.001 | |
kfold_xval | 3.207 | 0.010 | 3.217 | |
kfoldxcv_grid | 3.564 | 0.007 | 3.570 | |
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 | 0.089 | 0.000 | 0.089 | |
linear_model | 0.026 | 0.000 | 0.027 | |
log_transform | 0.012 | 0.000 | 0.012 | |
mean_centre | 0.002 | 0.001 | 0.003 | |
mean_of_medians | 0.111 | 0.000 | 0.111 | |
mixed_effect | 0.156 | 0.001 | 0.157 | |
model_apply | 0.022 | 0.001 | 0.022 | |
model_predict | 0.049 | 0.001 | 0.050 | |
model_reverse | 0.04 | 0.00 | 0.04 | |
model_train | 0.05 | 0.00 | 0.05 | |
mv_boxplot | 0.301 | 0.001 | 0.302 | |
mv_feature_filter | 0.116 | 0.000 | 0.116 | |
mv_feature_filter_hist | 0.000 | 0.000 | 0.001 | |
mv_histogram | 0.241 | 0.000 | 0.241 | |
mv_sample_filter | 0.016 | 0.000 | 0.016 | |
mv_sample_filter_hist | 0.001 | 0.000 | 0.001 | |
nroot_transform | 0.013 | 0.000 | 0.014 | |
ontology_cache | 0.000 | 0.000 | 0.001 | |
pairs_filter | 0.017 | 0.000 | 0.017 | |
pareto_scale | 0.059 | 0.000 | 0.059 | |
pca_biplot | 0.019 | 0.001 | 0.020 | |
pca_correlation_plot | 0.011 | 0.000 | 0.011 | |
pca_dstat_plot | 0.015 | 0.000 | 0.014 | |
pca_loadings_plot | 0.014 | 0.000 | 0.015 | |
pca_scores_plot | 0.552 | 0.000 | 0.553 | |
pca_scree_plot | 0.012 | 0.000 | 0.012 | |
permutation_test | 0.018 | 0.000 | 0.018 | |
permutation_test_plot | 0.004 | 0.000 | 0.003 | |
permute_sample_order | 0.015 | 0.000 | 0.015 | |
pls_regcoeff_plot | 0.362 | 0.001 | 0.362 | |
pls_scores_plot | 0.688 | 0.000 | 0.688 | |
pls_vip_plot | 0.355 | 0.000 | 0.356 | |
plsda_feature_importance_plot | 0.585 | 0.003 | 0.588 | |
plsda_predicted_plot | 0.454 | 0.002 | 0.456 | |
plsda_roc_plot | 1.066 | 0.001 | 1.067 | |
plsr_cook_dist | 0.011 | 0.000 | 0.012 | |
plsr_prediction_plot | 0.010 | 0.000 | 0.011 | |
plsr_qq_plot | 0.010 | 0.001 | 0.011 | |
plsr_residual_hist | 0.011 | 0.000 | 0.010 | |
pqn_norm | 0.349 | 0.003 | 0.352 | |
pqn_norm_hist | 0.000 | 0.001 | 0.001 | |
prop_na | 0.016 | 0.000 | 0.016 | |
r_squared | 0.000 | 0.001 | 0.001 | |
resample | 0.021 | 0.000 | 0.021 | |
resample_chart | 0.003 | 0.000 | 0.003 | |
rsd_filter | 0.016 | 0.003 | 0.019 | |
rsd_filter_hist | 0.000 | 0.000 | 0.001 | |
run | 0.027 | 0.001 | 0.028 | |
sb_corr | 0.031 | 0.000 | 0.031 | |
scatter_chart | 0.33 | 0.00 | 0.33 | |
split_data | 0.013 | 0.001 | 0.014 | |
stratified_split | 0.132 | 0.000 | 0.132 | |
svm_plot_2d | 0.625 | 0.005 | 0.630 | |
tSNE | 0.029 | 0.001 | 0.030 | |
tSNE_scatter | 0.011 | 0.001 | 0.013 | |
tic_chart | 0.212 | 0.000 | 0.213 | |
ttest | 0.018 | 0.002 | 0.020 | |
vec_norm | 0.001 | 0.000 | 0.001 | |
wilcox_p_hist | 0.000 | 0.000 | 0.001 | |
wilcox_test | 0.022 | 0.001 | 0.023 | |