I am creating an R package to plot some data from VCF files. I need to include Biostrings package.
The problem is that if I specify Biostrings in my DESCRIPTION file:
#...
Imports:
BiocManager (>= 1.30.19),
tidyverse (>= 1.3.2),
GenomicFeatures (>= 1.48.4),
Biostrings (>= 2.64.1),
ggbio (>= 1.44.1)
#...
It tells me it does not find it:
> devtools::install_github("cccnrc/plot-VCF")
Using github PAT from envvar GITHUB_TOKEN
Downloading GitHub repo cccnrc/plot-VCF@HEAD
Skipping 3 packages not available: ggbio, Biostrings, GenomicFeatures
✔ checking for file ‘/tmp/RtmpZkWQ8w/remotes2ee5f54e7e2a6/cccnrc-plot-VCF-d0a0d12/DESCRIPTION’ ...
─ preparing ‘plotVCF’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘plotVCF_0.0.0.9000.tar.gz’
Installing package into ‘/home/enrico/app/packrat-prove/plot-VCF-install/packrat/lib/x86_64-pc-linux-gnu/4.2.1’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘GenomicFeatures’, ‘Biostrings’, ‘ggbio’ are not available for package ‘plotVCF’
On the other han, if I remove them from DESCRIPTION, the package does not work as it does not find the function:
#...
Error in loadNamespace(x) : there is no package called ‘Biostrings’
#...
How can I work this out? I tried to google and search here but no luck!
Use BiocManager to install your github package:
BiocManager::install("cccnrc/plot-VCF")
Or use BiocManager::repositories() to tell github_install() about additional repositories. devtools delegates to the remotes package, so use remotes directly
remotes::install_github(
"cccnrc/plot-VCF",
repos = BiocManager::repositories()
)
Ask questions about Bioconductor on the Bioconductor support site.