Closed pauline-ng closed 1 year ago
Yes (e.g. devtools::install_github("PapenfussLab/StructuralVariantAnnotation", ref="pre_bioconductor")
) but you'll need to appropriate version of BioConductor for R 3.6 because of the dependencies on other bioconductor package.
I finally got a working dockerfile. This took me a while, so I'm putting it here in case others find it helpful.
FROM rocker/r-ver:4.0.2
RUN apt-get update && \
apt-get -y install zlib1g-dev \
libxml2 \
libbz2-dev \
liblzma-dev \
libcurl4-openssl-dev vim \
python3.7 python3-pip python3-setuptools
RUN R -e "install.packages('stringr')"
RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/BiocManager/BiocManager_1.30.10.tar.gz",repos = NULL,type = "source")' && \
R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_0.60.0.tar.gz", repos=NULL, type="source")' && \
R -e 'BiocManager::install("VariantAnnotation", version="3.12")' && \
R -e 'BiocManager::install("StructuralVariantAnnotation", version="3.12")'
Hi,
I'm getting the following error:
ERROR: this R is version 3.6.3, package 'StructuralVariantAnnotation' requires R >= 4.1.0
Is there a version of StructuralVariantAnnotation that works with R v3.6?
Thanks