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This page was generated on 2024-05-04 11:37:03 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1720/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.30.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/recount
git_branch: RELEASE_3_19
git_last_commit: d1f152b
git_last_commit_date: 2024-04-30 10:52:46 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    TIMEOUT  skipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

BUILD results for recount on nebbiolo1


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.

raw results


Summary

Package: recount
Version: 1.30.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recount
StartedAt: 2024-05-03 18:54:12 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 19:12:18 -0400 (Fri, 03 May 2024)
EllapsedTime: 1086.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/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

[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  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’

"/home/biocbuild/bbs-3.19-bioc/R/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]          
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  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: *** [Makefile:12: recount-quickstart.html] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted