Bioconductor Single Package Builder - Build History

Snapshot Date:

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

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: phylobar

Version: 0.99.0

RVersion: 4.6

BiocVersion: 3.23

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

BuildTime: 1 minutes 10.69 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: phylobar_20260323134845

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: phylobar. 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 phylobar/DESCRIPTION ... OK
* preparing phylobar:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building atlas.Rmd using rmarkdown
--- finished re-building atlas.Rmd

--- re-building covid_immunology.Rmd using rmarkdown
trying URL 'https://zenodo.org/records/17477876/files/su-2020.rds?download=1'
Content type 'application/octet-stream' length 13463047 bytes (12.8 MB)
==================================================
downloaded 12.8 MB

--- finished re-building covid_immunology.Rmd

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

--- re-building diet_analysis.Rmd using rmarkdown

Quitting from diet_analysis.Rmd:62-66 [preprocess]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mStat_convert_phyloseq_to_data_obj()`:
! could not find function "mStat_convert_phyloseq_to_data_obj"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'diet_analysis.Rmd' failed with diagnostics:
could not find function "mStat_convert_phyloseq_to_data_obj"
--- failed re-building diet_analysis.Rmd

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

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

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

--- re-building hfhs.Rmd using rmarkdown
trying URL 'https://zenodo.org/records/18791960/files/HFHS-data.rds?download=1'
Content type 'application/octet-stream' length 78041 bytes (76 KB)
==================================================
downloaded 76 KB

--- finished re-building hfhs.Rmd

--- re-building taxonomies.Rmd using rmarkdown

Quitting from taxonomies.Rmd:90-95 [hfhs-invalid]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `find.package()`:
! there is no package called 'LUPINE'
---
Backtrace:
    
 1. utils::data(HFHSdata, package = "LUPINE")
 2.   base::find.package(package, lib.loc, verbose = verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'taxonomies.Rmd' failed with diagnostics:
there is no package called 'LUPINE'
--- failed re-building taxonomies.Rmd

SUMMARY: processing the following files failed:
  diet_analysis.Rmd taxonomies.Rmd

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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