Back to Books build report for BioC 3.20 |
This page was generated on 2024-07-19 14:00 -0400 (Fri, 19 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4683 |
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 6/10 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
OSCA.basic 1.13.3 (landing page) Peter Hickey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
To the developers/maintainers of the OSCA.basic package: - 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: OSCA.basic |
Version: 1.13.3 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.basic |
StartedAt: 2024-07-19 07:02:06 -0400 (Fri, 19 Jul 2024) |
EndedAt: 2024-07-19 07:20:48 -0400 (Fri, 19 Jul 2024) |
EllapsedTime: 1122.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.basic ### ############################################################################## ############################################################################## * checking for file ‘OSCA.basic/DESCRIPTION’ ... OK * preparing ‘OSCA.basic’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘stub.Rmd’ using rmarkdown [WARNING] This document format requires a nonempty <title> element. Please specify either 'title' or 'pagetitle' in the metadata, e.g. by using --metadata pagetitle="..." on the command line. Falling back to 'stub.knit' --- finished re-building ‘stub.Rmd’ "/home/biocbuild/bbs-3.20-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)" R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. Natural language support but running in an English locale 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. > work.dir <- rebook::bookCache('OSCA.basic'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle) # # # processing file: cell-annotation.Rmd # 1/76 # 2/76 [setup] # 3/76 # 4/76 [unnamed-chunk-1] # 5/76 # 6/76 [unnamed-chunk-2] # 7/76 # 8/76 [unnamed-chunk-3] # 9/76 # 10/76 [unnamed-chunk-4] # 11/76 # 12/76 [singler-heat-pbmc] # 13/76 # 14/76 [singler-cluster] # 15/76 # 16/76 [unnamed-chunk-5] # 17/76 # 18/76 [unnamed-chunk-6] # 19/76 # 20/76 [unnamed-chunk-7] # Error in `sce.muraro$label`: # ! $ operator is invalid for atomic vectors # # Quitting from lines 126-132 [unnamed-chunk-7] (cell-annotation.Rmd) # Execution halted Error in compileChapter(path) : failed to compile '~/.cache/rebook/OSCA.basic/1.13.3/cell-annotation.Rmd' Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter Execution halted make: *** [Makefile:4: compiled] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted