Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 1064/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iSEEfier 1.0.0 (landing page) Najla Abassi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the iSEEfier package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iSEEfier.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: iSEEfier |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEfier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEfier_1.0.0.tar.gz |
StartedAt: 2024-06-09 21:05:02 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 21:09:50 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 288.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: iSEEfier.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEfier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEfier_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/iSEEfier.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘iSEEfier/DESCRIPTION’ ... OK * this is package ‘iSEEfier’ version ‘1.0.0’ * 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 ‘iSEEfier’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed glue_initials 20.671 1.376 23.444 view_initial_tiles 9.665 0.540 10.455 iSEEinit 9.494 0.522 10.247 view_initial_network 9.332 0.542 10.146 iSEEnrich 6.642 0.525 7.407 * 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: 23. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 24. │ └─alabaster.base::altReadObject(path, metadata = metadata, ...) 25. │ └─scRNAseq (local) FUN(...) 26. │ └─alabaster.base::readObject(...) 27. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 28. │ └─alabaster.base::altReadObject(...) 29. │ └─scRNAseq (local) FUN(...) 30. │ └─alabaster.base::readObject(...) 31. │ └─alabaster.matrix (local) meth(path, metadata = metadata, ...) 32. │ └─(function() {... 33. │ └─rhdf5::H5Fopen(fpath) 34. └─base::.handleSimpleError(...) 35. └─testthat (local) h(simpleError(msg, call)) 36. └─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 See ‘/Users/biocbuild/bbs-3.19-bioc/meat/iSEEfier.Rcheck/00check.log’ for details.
iSEEfier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iSEEfier ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘iSEEfier’ ... ** using staged installation ** R ** 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 (iSEEfier)
iSEEfier.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(iSEEfier) > > test_check("iSEEfier") --- Loading packages... - Done! --- Preparing datasets... Error in `FUN()`: ! In path: "/Users/biocbuild/bbs-3.19-bioc/meat/iSEEfier.Rcheck/tests/testthat/setuptests_iSEEfier.R" Caused by error in `H5Fopen()`: ! HDF5. File accessibility. Unable to open file. Backtrace: ▆ 1. ├─testthat::test_check("iSEEfier") 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. │ └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts") at tests/testthat/setuptests_iSEEfier.R:11:1 15. │ └─scRNAseq::fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE) 16. │ └─alabaster.base::altReadObject(...) 17. │ └─scRNAseq (local) FUN(...) 18. │ └─alabaster.base::readObject(...) 19. │ └─alabaster.sce (local) meth(path, metadata = metadata, ...) 20. │ └─alabaster.base::altReadObject(path, metadata, ...) 21. │ └─scRNAseq (local) FUN(...) 22. │ └─alabaster.base::readObject(...) 23. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 24. │ └─alabaster.base::altReadObject(path, metadata = metadata, ...) 25. │ └─scRNAseq (local) FUN(...) 26. │ └─alabaster.base::readObject(...) 27. │ └─alabaster.se (local) meth(path, metadata = metadata, ...) 28. │ └─alabaster.base::altReadObject(...) 29. │ └─scRNAseq (local) FUN(...) 30. │ └─alabaster.base::readObject(...) 31. │ └─alabaster.matrix (local) meth(path, metadata = metadata, ...) 32. │ └─(function() {... 33. │ └─rhdf5::H5Fopen(fpath) 34. └─base::.handleSimpleError(...) 35. └─testthat (local) h(simpleError(msg, call)) 36. └─rlang::abort(...) Execution halted
iSEEfier.Rcheck/iSEEfier-Ex.timings
name | user | system | elapsed | |
glue_initials | 20.671 | 1.376 | 23.444 | |
iSEEinit | 9.494 | 0.522 | 10.247 | |
iSEEnrich | 6.642 | 0.525 | 7.407 | |
view_initial_network | 9.332 | 0.542 | 10.146 | |
view_initial_tiles | 9.665 | 0.540 | 10.455 | |