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 11:39:19 -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 922/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GWENA 1.13.0 (landing page) Gwenaëlle Lemoine
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the GWENA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWENA.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: GWENA |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.13.0.tar.gz |
StartedAt: 2024-03-02 05:06:08 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 05:30:37 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1469.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GWENA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GWENA.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 ‘GWENA/DESCRIPTION’ ... OK * this is package ‘GWENA’ version ‘1.13.0’ * 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 ‘GWENA’ can be installed ... WARNING Found the following significant warnings: Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 See ‘/Users/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck/00install.out’ for details. * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 ... WARNING prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69 * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed z_summary 15.122 0.168 19.634 compare_conditions 10.356 0.140 13.935 plot_enrichment 2.847 0.209 8.730 bio_enrich 0.519 0.035 11.104 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 8. │ └─base::lapply(...) 9. │ └─testthat (local) FUN(X[[i]], ...) 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) 11. │ ├─base::withCallingHandlers(...) 12. │ └─base::eval(exprs, env) 13. │ └─base::eval(exprs, env) 14. │ └─GWENA::bio_enrich(res_detection$modules) at tests/testthat/setup-GWENA.R:37:27 15. │ └─gprofiler2::gost(query = module, ...) 16. │ └─gprofiler2:::gprofiler_request(url, body) 17. │ └─base::stop(error_message) 18. └─base::.handleSimpleError(...) 19. └─testthat (local) h(simpleError(msg, call)) 20. └─rlang::abort(...) Execution halted * 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, 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck/00check.log’ for details.
GWENA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWENA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GWENA’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 *** 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 (GWENA)
GWENA.Rcheck/tests/testthat.Rout.fail
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(GWENA) > > test_check("GWENA") Error in `FUN()`: ! In path: "/Users/biocbuild/bbs-3.19-bioc/meat/GWENA.Rcheck/tests/testthat/setup-GWENA.R" Caused by error in `gprofiler_request()`: ! There's an issue with your request to g:Profiler. Error code: 504. Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee Backtrace: ▆ 1. ├─testthat::test_check("GWENA") 2. │ └─testthat::test_dir(...) 3. │ └─testthat:::test_files(...) 4. │ └─testthat:::test_files_serial(...) 5. │ └─testthat:::test_files_setup_state(...) 6. │ └─testthat::source_test_setup(".", env) 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 8. │ └─base::lapply(...) 9. │ └─testthat (local) FUN(X[[i]], ...) 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) 11. │ ├─base::withCallingHandlers(...) 12. │ └─base::eval(exprs, env) 13. │ └─base::eval(exprs, env) 14. │ └─GWENA::bio_enrich(res_detection$modules) at tests/testthat/setup-GWENA.R:37:27 15. │ └─gprofiler2::gost(query = module, ...) 16. │ └─gprofiler2:::gprofiler_request(url, body) 17. │ └─base::stop(error_message) 18. └─base::.handleSimpleError(...) 19. └─testthat (local) h(simpleError(msg, call)) 20. └─rlang::abort(...) Execution halted
GWENA.Rcheck/GWENA-Ex.timings
name | user | system | elapsed | |
associate_phenotype | 0.045 | 0.009 | 0.064 | |
bio_enrich | 0.519 | 0.035 | 11.104 | |
build_graph_from_sq_mat | 0.271 | 0.006 | 0.284 | |
build_net | 3.795 | 0.059 | 4.734 | |
compare_conditions | 10.356 | 0.140 | 13.935 | |
detect_modules | 2.103 | 0.045 | 2.634 | |
filter_RNA_seq | 0.002 | 0.001 | 0.002 | |
filter_low_var | 0.019 | 0.001 | 0.021 | |
get_fit.cor | 1.016 | 0.013 | 1.279 | |
get_fit.expr | 1.022 | 0.015 | 1.295 | |
get_hub_degree | 0.231 | 0.002 | 0.285 | |
get_hub_genes | 0.002 | 0.001 | 0.002 | |
get_hub_high_co | 0.001 | 0.001 | 0.002 | |
get_hub_kleinberg | 0.459 | 0.005 | 0.573 | |
get_sub_clusters | 2.075 | 0.030 | 2.548 | |
is_data_expr | 0.000 | 0.001 | 0.001 | |
is_gost | 0.044 | 0.004 | 2.280 | |
is_module | 0.001 | 0.001 | 0.002 | |
is_network | 0.000 | 0.001 | 0.001 | |
join_gost | 0.041 | 0.005 | 1.501 | |
plot_comparison_stats | 0.479 | 0.014 | 0.516 | |
plot_enrichment | 2.847 | 0.209 | 8.730 | |
plot_expression_profiles | 3.930 | 0.071 | 4.626 | |
plot_module | 0.381 | 0.010 | 0.453 | |
plot_modules_merge | 2.230 | 0.027 | 2.577 | |
plot_modules_phenotype | 0.994 | 0.010 | 1.162 | |
z_summary | 15.122 | 0.168 | 19.634 | |