Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-07 12:04 -0400 (Tue, 07 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" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 1908/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scFeatures 1.9.0 (landing page) Yue Cao
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the scFeatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scFeatures.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: scFeatures |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz |
StartedAt: 2025-10-07 04:02:09 -0400 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 04:11:25 -0400 (Tue, 07 Oct 2025) |
EllapsedTime: 555.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scFeatures.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scFeatures_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.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 ‘scFeatures/DESCRIPTION’ ... OK * this is package ‘scFeatures’ version ‘1.9.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘scFeatures’ 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 ... WARNING Namespaces in Imports field not imported from: 'DT' 'Seurat' All declared Imports should be used. Missing or unexported object: 'SingleCellSignalR::cell_signaling' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE helper_CCI: no visible global function definition for 'data' helper_CCI: no visible binding for global variable 'LRdb' helper_CCI: no visible global function definition for 'capture.output' helper_pathway_gsva: no visible global function definition for 'capture.output' run_pathway_gsva: no visible global function definition for 'capture.output' Undefined global functions or variables: LRdb capture.output data Consider adding importFrom("utils", "capture.output", "data") to your NAMESPACE file. * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘scFeatures-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run_CCI > ### Title: Generate cell cell communication score > ### Aliases: run_CCI > > ### ** Examples > > > utils::data("example_scrnaseq" , package = "scFeatures") > data <- example_scrnaseq[1:1000, 1:100] Loading required namespace: SeuratObject > celltype <- data$celltype > sample <- data$sample > data <- as.matrix(data@assays$RNA@data) > > alldata <- scFeatures:::formatData(data = data, celltype = celltype, sample = sample ) > feature_CCI <- run_CCI(alldata, type = "scrna" , ncores = 1 ) Warning in data(LRdb, package = "SingleCellSignalR") : data set 'LRdb' not found Error: BiocParallel errors 1 remote errors, element index: 1 18 unevaluated and other errors first remote error: Error: 'cell_signaling' is not an exported object from 'namespace:SingleCellSignalR' Execution halted * 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 ‘scFeatures_overview.Rmd’ using rmarkdown Quitting from scFeatures_overview.Rmd:169-178 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'pheatmap' --- Backtrace: ▆ 1. └─scFeatures::run_association_study_report(scfeatures_result, output_folder) 2. ├─rmarkdown::render(...) 3. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 4. │ └─knitr:::process_file(text, output) 5. │ ├─xfun:::handle_error(...) 6. │ ├─base::withCallingHandlers(...) 7. │ └─knitr:::process_group(group) 8. │ └─knitr:::call_block(x) 9. │ └─knitr:::block_exec(params) 10. │ └─knitr:::eng_r(options) 11. │ ├─knitr:::in_input_dir(...) 12. │ │ └─knitr:::in_dir(input_dir(), expr) 13. │ └─knitr (local) evaluate(...) 14. │ └─evaluate::evaluate(...) 15. │ ├─base::withRestarts(...) 16. │ │ └─base (local) withRestartList(expr, restarts) 17. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 18. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 19. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 20. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 21. │ │ └─base (local) doWithOneRestart(return(expr), restart) 22. │ ├─evaluate:::with_handlers(...) 23. │ │ ├─base::eval(call) 24. │ │ │ └─base::eval(call) 25. │ │ └─base::withCallingHandlers(...) 26. │ ├─base::withVisible(eval(expr, envir)) 27. │ └─base::eval(expr, envir) 28. │ └─base::eval(expr, envir) 29. └─base::library(pheatmap) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'scFeatures_overview.Rmd' failed with diagnostics: there is no package called 'pheatmap' --- failed re-building ‘scFeatures_overview.Rmd’ SUMMARY: processing the following file failed: ‘scFeatures_overview.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/scFeatures.Rcheck/00check.log’ for details.
scFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scFeatures’ ... ** this is package ‘scFeatures’ version ‘1.9.0’ ** using staged installation ** R ** data ** 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 (scFeatures)
scFeatures.Rcheck/scFeatures-Ex.timings
name | user | system | elapsed | |
get_num_cell_per_spot | 0.167 | 0.015 | 0.181 | |
remove_mito_ribo | 0.536 | 0.056 | 0.592 | |