Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1215/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MEB 1.23.0 (landing page) Jiadi Zhu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MEB package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEB.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: MEB |
Version: 1.23.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MEB.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MEB_1.23.0.tar.gz |
StartedAt: 2025-10-11 01:34:46 -0400 (Sat, 11 Oct 2025) |
EndedAt: 2025-10-11 01:38:16 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 210.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MEB.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MEB.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MEB_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MEB.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘MEB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MEB’ version ‘1.23.0’ * 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 ‘MEB’ 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 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘NIMEB.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from NIMEB.Rmd:240-243 [unnamed-chunk-14] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.requirePackage()`: ! unable to load required package 'GenomeInfoDb' --- Backtrace: ▆ 1. ├─tools::buildVignettes(...) 2. │ ├─base::tryCatch(...) 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 6. │ └─engine$weave(file, quiet = quiet, encoding = enc) 7. │ └─knitr:::vweave_rmarkdown(...) 8. │ └─rmarkdown::render(...) 9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10. │ └─knitr:::process_file(text, output) 11. │ ├─xfun:::handle_error(...) 12. │ ├─base::withCallingHandlers(...) 13. │ └─knitr:::process_group(group) 14. │ └─knitr:::call_block(x) 15. │ └─knitr:::block_exec(params) 16. │ └─knitr:::eng_r(options) 17. │ ├─knitr:::in_input_dir(...) 18. │ │ └─knitr:::in_dir(input_dir(), expr) 19. │ └─knitr (local) evaluate(...) 20. │ └─evaluate::evaluate(...) 21. │ ├─base::withRestarts(...) 22. │ │ └─base (local) withRestartList(expr, restarts) 23. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 24. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 25. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 26. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 27. │ │ └─base (local) doWithOneRestart(return(expr), restart) 28. │ ├─evaluate:::with_handlers(...) 29. │ │ ├─base::eval(call) 30. │ │ │ └─base::eval(call) 31. │ │ └─base::withCallingHandlers(...) 32. │ └─watcher$print_value(ev$value, ev$visible, envir) 33. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 34. │ └─evaluate:::handle_value(handler, value, visible, envir) 35. │ └─handler$value(value, visible) 36. │ └─knitr (local) fun(x, options = options) 37. │ ├─base::withVisible(knit_print(x, ...)) 38. │ ├─knitr::knit_print(x, ...) 39. │ └─knitr:::knit_print.default(x, ...) 40. │ └─knitr::normal_print(x) 41. │ ├─methods::show(x) 42. │ └─methods::show(x) 43. │ ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object)) 44. │ │ └─base::ifelse(nzchar(vals), vals, "''") 45. │ ├─SingleCellExperiment::reducedDimNames(object) 46. │ └─SingleCellExperiment::reducedDimNames(object) 47. │ └─SingleCellExperiment:::.get_internal_names(...) 48. │ ├─BiocGenerics::updateObject(x) 49. │ └─SingleCellExperiment::updateObject(x) 50. │ ├─methods::callNextMethod() 51. │ └─SummarizedExperiment (local) .nextMethod(object = object) 52. │ ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose) 53. │ └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose) 54. │ ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose) 55. │ └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose) 56. │ └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose) 57. └─methods:::.extendsForS3(`<chr>`) 58. └─methods::extends(Class, maybe = FALSE) 59. └─methods::getClassDef(class1) 60. └─methods:::.requirePackage(package) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'NIMEB.Rmd' failed with diagnostics: unable to load required package 'GenomeInfoDb' --- failed re-building ‘NIMEB.Rmd’ SUMMARY: processing the following file failed: ‘NIMEB.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.22-bioc/meat/MEB.Rcheck/00check.log’ for details.
MEB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MEB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘MEB’ ... ** this is package ‘MEB’ version ‘1.23.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (MEB)
MEB.Rcheck/MEB-Ex.timings
name | user | system | elapsed | |
NIMEB | 2.138 | 0.016 | 2.154 | |
scMEB | 3.382 | 0.040 | 3.423 | |