CanardAbsurd: Durable #RStats workflows with DuckDB state and Quack remote SQL (Slop)
Sloppy attempt to solve some recurring issues around durability (and resumption) especially for (frontend or api) exposed (costly) workflow coordination.
repo: github.com/RGenomicsETL...
![Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'
Bundles the 'duckhts' 'DuckDB' extension for reading 'HTS' file formats (VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, tabix) from 'R' via 'DuckDB'. The extension and its 'htslib' dependency are compiled from vendored sources during package installation.
Authors:Sounkou Mahamane Toure [aut, cre], htslib authors [ctb], DuckDB C Extension API authors [ctb]
Rduckhts_0.1.1-0.0.1.tar.gz
Rduckhts_0.1.1-0.0.1.zip(r-4.6)Rduckhts_0.1.1-0.0.1.zip(r-4.5)Rduckhts_0.1.1-0.0.1.zip(r-4.4)
Rduckhts_0.1.1-0.0.1.tgz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tgz(r-4.5-any)
Rduckhts_0.1.1-0.0.1.tar.gz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tar.gz(r-4.5-any)
Rduckhts.pdf |Rduckhts.html✨
Rduckhts/json (API)
NEWS
# Install 'Rduckhts' in R:
install.packages('Rduckhts', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))
Bug tracker:https://github.com/rgenomicsetl/duckhts/issues0 issues
On CRAN: no
3.75 score 12 exports 2 dependencies
Last updated0 hours ago from:e99a28a305. Checks:7 OK, 1 NOTE, 1 FAIL. Indexed: yes.
Citation
To cite package ‘Rduckhts’ in publications use:
Toure S (2026). Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'. R package version 0.1.1-0.0.1, https://github.com/rgenomicsetl/duckhts.
Corresponding BibTeX entry:
@Manual{,
title = {Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'},
author = {Sounkou Mahamane Toure},
year = {2026},
note = {R package version 0.1.1-0.0.1},
url = {https://github.com/rgenomicsetl/duckhts},
}](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:hmk4f5yf3ohtsvw32sbtwvk3/bafkreibky4c2dqxxb264xvbzd3a5voj6dbizhq5zhleqvjhurwezyga6li)
![Quick Start
The extension is loaded with rduckhts_load(con, extension_path = NULL). We can create tables with rduckhts_bcf, rduckhts_bam, rduckhts_fasta, rduckhts_fastq, rduckhts_gff, rduckhts_gtf, and rduckhts_tabix using the parameters documented in their help pages
library(DBI)
library(duckdb)
library(Rduckhts)
ext_path <- system.file("extdata", "duckhts.duckdb_extension", package = "Rduckhts")
fasta_path <- system.file("extdata", "ce.fa", package = "Rduckhts")
fastq_r1 <- system.file("extdata", "r1.fq", package = "Rduckhts")
fastq_r2 <- system.file("extdata", "r2.fq", package = "Rduckhts")
con <- dbConnect(duckdb::duckdb(config = list(allow_unsigned_extensions = "true")))
rduckhts_load(con, extension_path = ext_path)
#> [1] TRUE
rduckhts_fasta(con, "sequences", fasta_path, overwrite = TRUE)
rduckhts_fastq(con, "reads", fastq_r1, mate_path = fastq_r2, overwrite = TRUE)
dbGetQuery(con, "SELECT COUNT(*) AS n FROM sequences")
#> n
#> 1 7
dbGetQuery(con, "SELECT COUNT(*) AS n FROM reads")
#> n
#> 1 10](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:hmk4f5yf3ohtsvw32sbtwvk3/bafkreigg3cxmwg3qfafvyvalkkeqpskndn3vwbnvbxpcpq6ttlrzdywi4y)
