Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo2 Summary

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Package: CleanUpRNAseq

Version: 0.99.1

RVersion: 4.4

BiocVersion: 3.20

BuildCommand: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CleanUpRNAseq

BuildTime: 5 minutes 42.31 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: CleanUpRNAseq_20240617145551

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CleanUpRNAseq. 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.

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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* checking for file ‘CleanUpRNAseq/DESCRIPTION’ ... OK
* preparing ‘CleanUpRNAseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CleanUpRNAseq.Rmd’ using rmarkdown
trying URL 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz'
Content type 'application/x-gzip' length 54325732 bytes (51.8 MB)
==================================================
downloaded 51.8 MB

Warning: call dbDisconnect() when finished working with a connection
trying URL 'https://zenodo.org/records/11458839/files/read_count_summary.RData?download=1'
Content type 'application/octet-stream' length 29895801 bytes (28.5 MB)
==================================================
downloaded 28.5 MB

trying URL 'https://zenodo.org/records/11458839/files/salmon_quant_summary.RData?download=1'
Content type 'application/octet-stream' length 5784846 bytes (5.5 MB)
==================================================
downloaded 5.5 MB

Unknown option --citeproc.
Try pandoc --help for more information.
Error: processing vignette 'CleanUpRNAseq.Rmd' failed with diagnostics:
pandoc document conversion failed with error 2
--- failed re-building ‘CleanUpRNAseq.Rmd’

SUMMARY: processing the following file failed:
  ‘CleanUpRNAseq.Rmd’

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output

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