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Snapshot Date:

URL: https://git.bioconductor.org/packages/ontoProc2

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: ontoProc2

Version: 0.99.9

RVersion: 4.6

BiocVersion: 3.23

BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc2

BuildTime: 2 minutes 19.89 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: ontoProc2_20260331122912

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ontoProc2. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ontoProc2/DESCRIPTION ... OK
* preparing ontoProc2:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building celltoprotein.Rmd using rmarkdown
trying URL 'https://s3.amazonaws.com/bbop-sqlite/pr.db.gz'
Content type 'binary/octet-stream' length 795519481 bytes (758.7 MB)
==================================
downloaded 523.4 MB


Quitting from celltoprotein.Rmd:53-57 [lkct2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! download from 'https://s3.amazonaws.com/bbop-sqlite/pr.db.gz' failed
---
Backtrace:
    
 1. ontoProc2::get_present_pmp(names(cd8reg))
 2.   ontoProc2::semsql_connect(ontology = "pr")
 3.     ontoProc2::retrieve_semsql_conn(ontology, cache = cache, ...)
 4.       utils::download.file(addr, file.path(td, zdbname), ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'celltoprotein.Rmd' failed with diagnostics:
download from 'https://s3.amazonaws.com/bbop-sqlite/pr.db.gz' failed
--- failed re-building celltoprotein.Rmd

--- re-building ontoProc2.Rmd using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ontoProc2.Rmd

--- re-building uberonpeek.Rmd using rmarkdown
--- finished re-building uberonpeek.Rmd

SUMMARY: processing the following file failed:
  celltoprotein.Rmd

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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