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This page was generated on 2024-08-15 11:40 -0400 (Thu, 15 Aug 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4703
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4440
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4472
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4420
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4413
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 1683/2255HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.31.2  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-08-14 14:00 -0400 (Wed, 14 Aug 2024)
git_url: https://git.bioconductor.org/packages/recount
git_branch: devel
git_last_commit: f4d2db9
git_last_commit_date: 2024-05-21 13:22:52 -0400 (Tue, 21 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    TIMEOUT  skipped

BUILD results for recount on nebbiolo2

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: 1.31.2
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 recount
StartedAt: 2024-08-14 19:09:29 -0400 (Wed, 14 Aug 2024)
EndedAt: 2024-08-14 19:21:57 -0400 (Wed, 14 Aug 2024)
EllapsedTime: 747.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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'
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB)
==================================================
downloaded 1327.5 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB)
==================================================
downloaded 90.3 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw'
Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB)
==================================================
downloaded 102.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw'
Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB)
==================================================
downloaded 93.1 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw'
Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB)
==================================================
downloaded 91.3 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw'
Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB)
==================================================
downloaded 63.2 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw'
Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB)
==================================================
downloaded 74.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw'
Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB)
==================================================
downloaded 121.9 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw'
Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB)
==================================================
downloaded 83.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw'
Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB)
==================================================
downloaded 75.7 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw'
Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB)
==================================================
downloaded 60.2 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw'
Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB)
==================================================
downloaded 66.5 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw'
Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB)
==================================================
downloaded 63.9 MB


Quitting from lines 533-541 [define_ers] (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes'
--- failed re-building ‘recount-quickstart.Rmd’

"/home/biocbuild/bbs-3.20-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
1/102                   
2/102 [vignetteSetup]   
3/102                   
4/102 [installDer]      
5/102                   
6/102 [citation]        
7/102                   
8/102 [ultraQuick]      
9/102                   
10/102 [er_analysis]     
11/102                   
12/102 [install]         
13/102                   
14/102 [start]           
15/102                   
16/102 [search_abstract] 
17/102                   
18/102 [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

19/102                   
20/102 [explore_rse]     
21/102                   
22/102 [browse]          
23/102                   
24/102 [sample_info]     
25/102                   
26/102 [scale_counts]    
27/102                   
28/102 [add_sample_info] 
29/102                   
30/102 [de_analysis]     
31/102                   
32/102 [maplot]          
33/102                   
34/102 [make_report]     
35/102                   
36/102 [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'
37/102                   
38/102 [geneSymbols]     
39/102                   
40/102 [download_bigwigs]
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB)
==================================================
downloaded 1327.5 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB)
==================================================
downloaded 90.3 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw'
Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB)
==================================================
downloaded 102.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw'
Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB)
==================================================
downloaded 93.1 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw'
Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB)
==================================================
downloaded 91.3 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw'
Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB)
==================================================
downloaded 63.2 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw'
Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB)
==================================================
downloaded 74.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw'
Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB)
==================================================
downloaded 121.9 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw'
Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB)
==================================================
downloaded 83.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw'
Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB)
==================================================
downloaded 75.7 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw'
Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB)
==================================================
downloaded 60.2 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw'
Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB)
==================================================
downloaded 66.5 MB

trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw'
Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB)
==================================================
downloaded 63.9 MB

41/102                   
42/102 [define_ers]      
Error in `file()`:
! cannot open the connection to 'https://raw.githubusercontent.com/nellore/runs/master/gtex/hg38.sizes'
Backtrace:
 1. recount::expressed_regions(...)
 2. utils::read.table(...)
 3. base::file(file, "rt")

Quitting from lines 533-541 [define_ers] (recount-quickstart.Rmd)
Execution halted
make: *** [Makefile:12: recount-quickstart.html] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted