Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:42 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 1720/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
recount 1.30.0 (landing page) Leonardo Collado-Torres
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
To the developers/maintainers of the recount 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: recount |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount |
StartedAt: 2024-05-06 18:37:27 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 18:53:15 -0400 (Mon, 06 May 2024) |
EllapsedTime: 947.8 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount ### ############################################################################## ############################################################################## * checking for file ‘recount/DESCRIPTION’ ... OK * preparing ‘recount’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘recount-quickstart.Rmd’ using rmarkdown trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB) ================================================== downloaded 3.0 MB 2024-05-06 18:38:17.324 R[68497:36669272] XType: Using static font registry. [WARNING] This document format requires a nonempty <title> element. Defaulting to 'SRP009615-results.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". Quitting from lines at lines 524-532 [define_ers] (recount-quickstart.Rmd) Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics: UCSC library operation failed --- failed re-building ‘recount-quickstart.Rmd’ "/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "library(rmarkdown); render('recount-quickstart.Rmd')" Attaching package: ‘BiocStyle’ The following objects are masked from ‘package:rmarkdown’: html_document, md_document, pdf_document processing file: recount-quickstart.Rmd 1/100 2/100 [vignetteSetup] 3/100 4/100 [installDer] 5/100 6/100 [citation] 7/100 8/100 [ultraQuick] 9/100 10/100 [er_analysis] 11/100 12/100 [install] 13/100 14/100 [start] 15/100 16/100 [search_abstract] 17/100 18/100 [download] trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB) ================================================== downloaded 3.0 MB 19/100 20/100 [explore_rse] 21/100 22/100 [browse] 23/100 24/100 [sample_info] 25/100 26/100 [scale_counts] 27/100 28/100 [add_sample_info] 29/100 30/100 [de_analysis] 31/100 32/100 [maplot] 2024-05-06 18:45:53.500 R[42337:36807345] XType: Using static font registry. 33/100 34/100 [make_report] 35/100 36/100 [make_report_real] [WARNING] This document format requires a nonempty <title> element. Defaulting to 'SRP009615-results.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". 37/100 38/100 [geneSymbols] 39/100 40/100 [define_ers] Quitting from lines at lines 524-532 [define_ers] (recount-quickstart.Rmd) Error in `FUN()`: ! UCSC library operation failed Backtrace: 1. recount::expressed_regions(...) 2. derfinder::loadCoverage(files = meanFile, chr = chr, chrlen = chrlen) 4. S4Vectors::lapply(...) 6. base::lapply(as.list(X), match.fun(FUN), ...) 7. derfinder (local) FUN(X[[i]], ...) Execution halted make: *** [recount-quickstart.html] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted