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ccagc / QDNAseq

QDNAseq package for Bioconductor
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getBinAnnotations: Error in download.file #81

Closed ilarischeinin closed 3 years ago

ilarischeinin commented 5 years ago

If you get an error message like the following from getBinAnnotations(), this is because bin annotations are no longer hosted on S3 like they used to.

getBinAnnotations(15)
## Annotation package QDNAseq.hg19 not found.
## Downloading bin annotations for genome hg19, bin size 15kbp, and experiment type SR50 from URL http://qdnaseq.s3.amazonaws.com ...
## Error in download.file(url, destfile = pathnameT, mode = mode, quiet = !isVisible(verbose),  : 
##   cannot open URL 'http://qdnaseq-ireland.s3.amazonaws.com/QDNAseq.hg19.15kbp.SR50.rds'

The solution is to install an annotation package (like QDNAseq.hg19) from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QDNAseq.hg19")