Leonardo Collado-Torres
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/recount |
| git_branch: devel |
| git_last_commit: c61b672 |
| git_last_commit_date: 2024-03-27 09:07:20 -0400 (Wed, 27 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:39:53 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1698/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.29.1 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
To the developers/maintainers of the recount package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recount.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: recount |
| Version: 1.29.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount |
| StartedAt: 2024-03-27 18:00:27 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 18:20:06 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 1179.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### 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
2024-03-27 18:02:39.413 R[20959:1358896887] XType: com.apple.fonts is not accessible.
2024-03-27 18:02:39.415 R[20959:1358896887] XType: XTFontStaticRegistry is enabled.
[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 'SRP009615-results.knit'
Quitting from 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]
2024-03-27 18:11:51.329 R[93976:1359034354] XType: com.apple.fonts is not accessible.
2024-03-27 18:11:51.329 R[93976:1359034354] XType: XTFontStaticRegistry is enabled.
33/100
34/100 [make_report]
35/100
36/100 [make_report_real]
[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 'SRP009615-results.knit'
37/100
38/100 [geneSymbols]
39/100
40/100 [define_ers]
Quitting from 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