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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1597/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phyloseq 1.53.0 (landing page) Paul J. McMurdie
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
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To the developers/maintainers of the phyloseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phyloseq.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: phyloseq |
| Version: 1.53.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phyloseq |
| StartedAt: 2025-10-26 17:32:34 -0400 (Sun, 26 Oct 2025) |
| EndedAt: 2025-10-26 17:33:42 -0400 (Sun, 26 Oct 2025) |
| EllapsedTime: 67.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phyloseq
###
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* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* preparing ‘phyloseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘phyloseq-FAQ.Rmd’ using rmarkdown
2025-10-26 17:32:47.335 R[4542:550862961] XType: Using static font registry.
[WARNING] Could not fetch resource http://i.imgur.com/j9NYXiQ.png: HttpExceptionRequest Request {
host = "i.imgur.com"
port = 80
secure = False
requestHeaders = []
path = "/j9NYXiQ.png"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
ConnectionTimeout
--- finished re-building ‘phyloseq-FAQ.Rmd’
--- re-building ‘phyloseq-analysis.Rmd’ using rmarkdown
--- finished re-building ‘phyloseq-analysis.Rmd’
--- re-building ‘phyloseq-basics.Rmd’ using rmarkdown
YAML parse exception at line 2, column 6,
while scanning a block scalar:
did not find expected comment or line break
Error: processing vignette 'phyloseq-basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 64
--- failed re-building ‘phyloseq-basics.Rmd’
--- re-building ‘phyloseq-mixture-models.Rmd’ using rmarkdown
--- finished re-building ‘phyloseq-mixture-models.Rmd’
SUMMARY: processing the following file failed:
‘phyloseq-basics.Rmd’
Error: Vignette re-building failed.
Execution halted