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unable to install bioconductor packages into R #447
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Ok. I think I found a work-around for phyloseq, but not dada2. It looks like phyloseq depends on igraph, and the cran version thereof isn't compatible with this version of R. I fond installing igraph from github first got around this issue.
Less luck with the dada2 installation. It appears to depend on package ShortRead, which I can't seem to install from either biocLite, or from github. biocLite("ShortRead") This site https://ubuntuforums.org/showthread.php?t=692704 says, that I require zlib1g-dev. I tried running I'm kind of new at editing docker containers, mabye there is a proper way to install linux packages within them? I'd appreciate any leads. |
Further progress:
then, since I am in bash
then I can launch jupyter notebook
and install ShortRead
and then phyloseq
at that point
I'm not closing this issue because I think these bioconductor packages ought to install without this much fuss. |
I'm guessing the problems here stem from the use of conda and R packages from conda-forge to setup the base images. It's possible that both phyloseq and dada2 from bioconda will install more easily and be compatible with the underlying libs coming from conda-forge (e.g., zlib). Try If that doesn't work, then I imagine this only gets simpler if and when there are conda-forge packages for bioconductor available. |
I am unable to install the phyloseq, or dada2 package (or possibly any package) from bioconductor into R when using the jupyter/r-notebook docker.
What docker image you are using?
Example:
jupyter/r-notebook
What complete docker command do you run to launch the container (omitting sensitive values)?
Example:
docker run -it --rm -p 8888:8888 jupyter/r-notebook
What steps do you take once the container is running to reproduce the issue?
Example:
source('http://bioconductor/org/biocLite.R')
biocLite('phyloseq')
What do you expect to happen?
I expect phyloseq to successfully install into R, as it does in a normal R installation
What actually happens?
I get the following output which contains error messages message
Similar process for package dada2. I presume this is universal across bioconductor packages.
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