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This page was generated on 2024-11-20 12:03 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 2079/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.18.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_20
git_last_commit: 6758b3b
git_last_commit_date: 2024-10-29 10:43:03 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for structToolbox on teran2

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.

raw results


Summary

Package: structToolbox
Version: 1.18.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings structToolbox_1.18.0.tar.gz
StartedAt: 2024-11-20 10:24:31 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:37:40 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 789.1 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings structToolbox_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.18.0’
* 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 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 11.246  0.007  11.254
fold_change      7.978  0.011   7.990
fisher_exact     6.730  0.006   6.736
* 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


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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)

Tests output

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: 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 
125.790   0.959 126.783 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.1470.0030.150
AUC1.3830.1461.539
DFA0.1350.0010.138
DatasetExperiment_boxplot1.2920.0181.310
DatasetExperiment_dist1.0380.0401.078
DatasetExperiment_factor_boxplot0.1430.0000.143
DatasetExperiment_heatmap0.2730.0030.276
HCA0.0450.0010.046
HSD0.2040.0030.229
HSDEM0.2170.0020.220
MTBLS79_DatasetExperiment0.0010.0000.001
OPLSDA0.0050.0020.008
OPLSR0.010.000.01
PCA0.0030.0000.003
PLSDA0.0170.0000.017
PLSR0.0070.0000.007
SVM0.0190.0000.018
as_data_frame0.0840.0000.083
autoscale0.050.000.05
balanced_accuracy1.1520.0031.155
blank_filter0.2270.0080.240
blank_filter_hist0.0000.0000.001
bootstrap0.0110.0000.012
calculate0.0030.0000.004
chart_plot0.0170.0010.019
classical_lsq0.2120.0010.213
compare_dist3.3180.0743.394
confounders_clsq1.9700.0041.975
confounders_lsq_barchart2.0410.0092.051
confounders_lsq_boxplot1.9850.0051.990
constant_sum_norm0.010.000.01
corr_coef0.1830.0010.184
dfa_scores_plot0.4850.0000.485
dratio_filter0.1880.0000.188
equal_split0.0860.0000.086
feature_boxplot0.0200.0010.021
feature_profile0.2610.0010.262
feature_profile_array0.3080.0000.308
filter_by_name0.0320.0000.032
filter_na_count0.7340.0010.735
filter_smeta0.0550.0000.055
fisher_exact6.7300.0066.736
fold_change7.9780.0117.990
fold_change_int11.246 0.00711.254
fold_change_plot0.0080.0000.009
forward_selection_by_rank4.2610.0394.300
fs_line4.8710.0194.890
glog_opt_plot0.3210.0000.321
glog_transform0.1870.0020.189
grid_search_1d2.2670.0192.286
gs_line000
hca_dendrogram000
kfold_xval2.2550.0082.262
kfoldxcv_grid2.4550.0062.467
kfoldxcv_metric0.0010.0000.001
knn_impute0.0080.0000.009
kw_p_hist000
kw_rank_sum0.0550.0000.055
linear_model0.0180.0000.019
log_transform0.0090.0000.009
mean_centre0.0020.0000.002
mean_of_medians0.0920.0000.092
mixed_effect0.1070.0000.106
model_apply0.0150.0000.015
model_predict0.0360.0000.036
model_reverse0.0270.0000.028
model_train0.0320.0010.033
mv_boxplot0.1860.0000.187
mv_feature_filter0.0880.0000.089
mv_feature_filter_hist0.0010.0000.000
mv_histogram0.170.000.17
mv_sample_filter0.0100.0010.011
mv_sample_filter_hist0.0000.0000.001
nroot_transform0.0080.0000.009
ontology_cache000
pairs_filter0.0100.0010.010
pareto_scale0.0370.0010.037
pca_biplot0.0130.0000.013
pca_correlation_plot0.0080.0000.007
pca_dstat_plot0.0080.0000.010
pca_loadings_plot0.0100.0000.009
pca_scores_plot0.3520.0010.354
pca_scree_plot0.0070.0000.008
permutation_test0.0120.0000.011
permutation_test_plot0.0010.0000.002
permute_sample_order0.0100.0000.009
pls_regcoeff_plot0.2330.0010.234
pls_scores_plot0.4620.0020.464
pls_vip_plot0.2700.0030.273
plsda_feature_importance_plot0.4110.0010.412
plsda_predicted_plot0.3010.0010.301
plsda_roc_plot0.7970.0030.802
plsr_cook_dist0.0080.0000.009
plsr_prediction_plot0.0070.0000.008
plsr_qq_plot0.0080.0000.007
plsr_residual_hist0.0070.0000.007
pqn_norm0.2280.0000.228
pqn_norm_hist0.0010.0000.001
prop_na0.0120.0000.012
r_squared0.0010.0000.000
resample0.0150.0010.015
resample_chart0.0020.0000.001
rsd_filter0.0130.0010.014
rsd_filter_hist0.0010.0000.000
run0.0190.0010.020
sb_corr0.0220.0000.023
scatter_chart0.2400.0000.239
split_data0.010.000.01
stratified_split0.0800.0010.080
svm_plot_2d0.4400.0000.444
tSNE0.0210.0000.021
tSNE_scatter0.0070.0000.008
tic_chart0.1400.0000.141
ttest0.0140.0000.015
vec_norm0.0000.0000.001
wilcox_p_hist0.0000.0000.001
wilcox_test0.0160.0000.017