rtracklayer S.h
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gibran • 0
@75f6b08f
Last seen 6 weeks ago
United Kingdom

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?

install • 131 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

You should get the dockerfile from Bioconductor.

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Entering edit mode

Thanks, much appreciated. So I think this approach actually gets binaries and I'm not sure how to isolate the problem I was experiencing as the bioconductor docker container has quite a complex set of dependencies. But I should be able to continue this way

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