I'm struggling to install the rtracklayer package. This is my Dockerfile
FROM rocker/tidyverse:latest RUN apt-get update && apt-get install -y \ sudo \ libbz2-dev \ zlib1g-dev \ libncurses5-dev \ libncursesw5-dev \ liblzma-dev RUN R -e "install.packages('BiocManager')" RUN R -e "BiocManager::install('Rhtslib')" RUN R -e "BiocManager::install('rtracklayer')" RUN R -e "devtools::install_github('mrcieu/gwasdataimport')"
I get the following compilation error
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/local/lib/R/site-library/S4Vectors/include' -I'/usr/local/lib/R/site-library/IRanges/include' -I'/usr/local/lib/R/site-library/XVector/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chain_io.c -o chain_io.o chain_io.c:1:10: fatal error: S.h: No such file or directory 1 | #include <S.h> | ^~~~~ compilation terminated. make: *** [/usr/local/lib/R/etc/Makeconf:168: chain_io.o] Error 1 ERROR: compilation failed for package ‘rtracklayer’ * removing ‘/usr/local/lib/R/site-library/rtracklayer’
Any idea what I'm doing wrong? Perhaps relatedly - is there a more appropriate docker image to build from?