Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:40:02 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 2051/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
structToolbox 1.15.1 (landing page) Gavin Rhys Lloyd
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.15.1 |
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_1.15.1.tar.gz |
StartedAt: 2024-03-02 11:25:34 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 11:45:46 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1211.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: structToolbox.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘structToolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘structToolbox’ version ‘1.15.1’ * 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 ... ERROR Running examples in ‘structToolbox-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: glog_opt_plot > ### Title: Glog optimisation > ### Aliases: glog_opt_plot > > ### ** Examples > > M = glog_opt_plot( + plot_grid = numeric(0)) > > D = iris_DatasetExperiment() > M = glog_transform(qc_label='versicolor',factor_name='Species') > M = model_apply(M,D) Error!Lambda tending to infinity! Using standard Error!Lambda tending to infinity! Using standard > C = glog_opt_plot() > chart_plot(C,M,D) Error in `geom_line()`: ! Problem while computing aesthetics. ℹ Error occurred in the 2nd layer. Caused by error in `data[["lambda"]]`: ! object of type 'closure' is not subsettable Backtrace: ▆ 1. ├─base (local) `<fn>`(x) 2. ├─ggplot2:::print.ggplot(x) 3. │ ├─ggplot2::ggplot_build(x) 4. │ └─ggplot2:::ggplot_build.ggplot(x) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$compute_aesthetics(d, plot) 14. │ └─ggplot2 (local) compute_aesthetics(..., self = self) 15. │ └─base::lapply(aesthetics, eval_tidy, data = data, env = env) 16. │ └─rlang (local) FUN(X[[i]], ...) 17. └─rlang (local) `<fn>`(`<ntSbsttE>`) 18. └─handlers[[1L]](cnd) 19. └─cli::cli_abort(...) 20. └─rlang::abort(...) Execution halted * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.19-bioc/meat/structToolbox.Rcheck/00check.log’ for details.
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-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 156 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 156 ] > > proc.time() user system elapsed 427.918 5.497 501.777
structToolbox.Rcheck/structToolbox-Ex.timings
name | user | system | elapsed | |
ANOVA | 0.479 | 0.014 | 0.590 | |
AUC | 4.799 | 0.279 | 6.111 | |
DFA | 0.473 | 0.005 | 0.582 | |
DatasetExperiment_boxplot | 1.582 | 0.058 | 1.991 | |
DatasetExperiment_dist | 2.479 | 0.118 | 3.188 | |
DatasetExperiment_factor_boxplot | 0.489 | 0.007 | 0.605 | |
DatasetExperiment_heatmap | 0.942 | 0.039 | 1.266 | |
HCA | 0.160 | 0.010 | 0.234 | |
HSD | 0.694 | 0.040 | 0.952 | |
HSDEM | 0.880 | 0.041 | 1.101 | |
MTBLS79_DatasetExperiment | 0.002 | 0.001 | 0.003 | |
OPLSDA | 0.027 | 0.000 | 0.031 | |
OPLSR | 0.038 | 0.001 | 0.046 | |
PCA | 0.011 | 0.000 | 0.013 | |
PLSDA | 0.063 | 0.002 | 0.088 | |
PLSR | 0.025 | 0.001 | 0.033 | |
SVM | 0.072 | 0.001 | 0.088 | |
as_data_frame | 0.300 | 0.006 | 0.375 | |
autoscale | 0.179 | 0.003 | 0.218 | |
balanced_accuracy | 4.144 | 0.043 | 5.039 | |
blank_filter | 0.769 | 0.029 | 0.968 | |
blank_filter_hist | 0.001 | 0.000 | 0.002 | |
bootstrap | 0.043 | 0.001 | 0.053 | |
calculate | 0.011 | 0.001 | 0.015 | |
chart_plot | 0.063 | 0.003 | 0.077 | |
classical_lsq | 0.734 | 0.007 | 0.884 | |
compare_dist | 6.974 | 0.257 | 8.643 | |
confounders_clsq | 6.994 | 0.061 | 8.433 | |
confounders_lsq_barchart | 7.264 | 0.062 | 8.731 | |
confounders_lsq_boxplot | 7.143 | 0.065 | 8.849 | |
constant_sum_norm | 0.032 | 0.001 | 0.040 | |
corr_coef | 0.631 | 0.010 | 0.779 | |
dfa_scores_plot | 1.668 | 0.020 | 1.988 | |
dratio_filter | 0.729 | 0.016 | 0.826 | |
equal_split | 0.294 | 0.004 | 0.359 | |
feature_boxplot | 0.078 | 0.002 | 0.100 | |
feature_profile | 0.922 | 0.020 | 1.264 | |
feature_profile_array | 1.061 | 0.016 | 1.213 | |
filter_by_name | 0.073 | 0.001 | 0.092 | |
filter_na_count | 3.470 | 0.112 | 4.152 | |
filter_smeta | 0.154 | 0.002 | 0.171 | |
fisher_exact | 22.796 | 0.200 | 26.151 | |
fold_change | 27.765 | 0.283 | 33.796 | |
fold_change_int | 45.554 | 0.443 | 53.808 | |
fold_change_plot | 0.028 | 0.001 | 0.035 | |
forward_selection_by_rank | 14.781 | 0.257 | 17.662 | |
fs_line | 14.381 | 0.177 | 16.721 | |