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This page was generated on 2024-05-04 11:41:11 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2095/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
structToolbox 1.16.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/structToolbox
git_branch: RELEASE_3_19
git_last_commit: daf3d2f
git_last_commit_date: 2024-04-30 11:20:29 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for structToolbox on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: structToolbox
Version: 1.16.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings structToolbox_1.16.0.tar.gz
StartedAt: 2024-05-04 12:31:37 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:42:41 -0000 (Sat, 04 May 2024)
EllapsedTime: 663.3 seconds
RetCode: 0
Status:   OK  
CheckDir: structToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:structToolbox.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings structToolbox_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘structToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘structToolbox’ version ‘1.16.0’
* 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           26.961  0.140  27.158
fold_change               17.284  0.076  17.395
fisher_exact              14.050  0.024  14.101
fs_line                   10.282  0.115  10.419
forward_selection_by_rank  8.867  0.060   8.945
compare_dist               5.488  0.391   5.893
grid_search_1d             5.737  0.007   5.758
kfoldxcv_grid              5.154  0.008   5.172
* 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


Installation output

structToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL structToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 156 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
269.844   1.781 272.127 

Example timings

structToolbox.Rcheck/structToolbox-Ex.timings

nameusersystemelapsed
ANOVA0.2970.0000.299
AUC2.8540.2793.141
DFA0.2940.0000.294
DatasetExperiment_boxplot1.0360.0281.066
DatasetExperiment_dist3.4930.0883.588
DatasetExperiment_factor_boxplot0.3050.0000.306
DatasetExperiment_heatmap0.5230.0280.553
HCA0.0920.0240.116
HSD0.4130.0880.509
HSDEM0.4740.1180.595
MTBLS79_DatasetExperiment0.0010.0000.002
OPLSDA0.0160.0080.024
OPLSR0.0190.0080.027
PCA0.0060.0000.007
PLSDA0.0380.0000.038
PLSR0.0140.0000.014
SVM0.0410.0000.041
as_data_frame0.1800.0040.184
autoscale0.1050.0120.117
balanced_accuracy2.4630.1482.618
blank_filter0.4940.0320.527
blank_filter_hist0.0020.0000.001
bootstrap0.0270.0000.027
calculate0.0070.0000.007
chart_plot0.0380.0040.041
classical_lsq0.4780.0160.495
compare_dist5.4880.3915.893
confounders_clsq4.2750.0684.352
confounders_lsq_barchart4.4970.0324.539
confounders_lsq_boxplot4.3090.0444.362
constant_sum_norm0.020.000.02
corr_coef0.3910.0070.400
dfa_scores_plot0.9860.0121.001
dratio_filter0.4840.0000.485
equal_split0.1870.0000.187
feature_boxplot0.0440.0000.044
feature_profile0.5280.0000.528
feature_profile_array0.6570.0030.662
filter_by_name0.0430.0000.043
filter_na_count1.5210.0191.543
filter_smeta0.0870.0000.086
fisher_exact14.050 0.02414.101
fold_change17.284 0.07617.395
fold_change_int26.961 0.14027.158
fold_change_plot0.0160.0000.016
forward_selection_by_rank8.8670.0608.945
fs_line10.282 0.11510.419
glog_opt_plot0.6960.0000.698
glog_transform0.4130.0010.415
grid_search_1d5.7370.0075.758
gs_line0.0010.0000.001
hca_dendrogram0.0010.0000.001
kfold_xval4.7040.0044.717
kfoldxcv_grid5.1540.0085.172
kfoldxcv_metric0.0010.0000.001
knn_impute0.0170.0000.017
kw_p_hist0.0010.0000.001
kw_rank_sum0.1110.0000.110
linear_model0.0400.0000.039
log_transform0.0190.0000.019
mean_centre0.0040.0000.004
mean_of_medians0.1740.0000.174
mixed_effect0.2210.0000.221
model_apply0.0320.0000.031
model_predict0.0750.0000.075
model_reverse0.0590.0000.059
model_train0.0700.0000.071
mv_boxplot0.3980.0000.399
mv_feature_filter0.1810.0000.182
mv_feature_filter_hist0.0010.0000.001
mv_histogram0.3490.0040.353
mv_sample_filter0.0210.0000.021
mv_sample_filter_hist0.0010.0000.000
nroot_transform0.0190.0000.019
ontology_cache0.0010.0000.000
pairs_filter0.0230.0000.024
pareto_scale0.0770.0000.077
pca_biplot0.0280.0000.028
pca_correlation_plot0.0150.0000.016
pca_dstat_plot0.0190.0000.019
pca_loadings_plot0.020.000.02
pca_scores_plot0.7560.0000.758
pca_scree_plot0.0160.0000.016
permutation_test0.0250.0000.025
permutation_test_plot0.0040.0000.004
permute_sample_order0.0210.0000.021
pls_regcoeff_plot0.4850.0000.486
pls_scores_plot0.9630.0280.993
pls_vip_plot0.5200.0080.529
plsda_feature_importance_plot0.8700.0040.877
plsda_predicted_plot0.6270.0000.629
plsda_roc_plot1.6680.0001.671
plsr_cook_dist0.0160.0000.016
plsr_prediction_plot0.0160.0000.015
plsr_qq_plot0.0160.0000.016
plsr_residual_hist0.0160.0000.016
pqn_norm0.5080.0000.509
pqn_norm_hist0.0010.0000.001
prop_na0.0230.0000.023
r_squared0.0010.0000.001
resample0.0320.0000.033
resample_chart0.0030.0000.003
rsd_filter0.0280.0000.028
rsd_filter_hist0.0010.0000.001
run0.0410.0000.041
sb_corr0.0470.0000.047
scatter_chart0.4730.0000.473
split_data0.0200.0000.019
stratified_split0.1680.0000.169
svm_plot_2d0.8800.0000.883
tSNE0.0420.0000.043
tSNE_scatter0.0160.0000.016
tic_chart0.2840.0000.285
ttest0.0270.0000.028
vec_norm0.0010.0000.001
wilcox_p_hist0.0010.0000.001
wilcox_test0.0310.0040.036