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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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Missing system libraries on Ubuntu 20.04 for EBImage #52

Closed jwindhager closed 3 years ago

jwindhager commented 3 years ago

I know that this does not directly affect cytomapper, but probably good to document it somewhere.

On Ubuntu 20.04, the following system libraries are required for EBImage:

sudo apt-get install libfftw3-3 libfftw3-dev libtiff5-dev
jwindhager commented 3 years ago

Furthermore, for building the development version of cytomapper with vignettes, I needed to install:

sudo apt-get install libfontconfig1-dev

as well as the following R packages from CRAN:

install.packages(c("rmarkdown", "cowplot"))

and the following Bioconductor package:

BiocManager::install("BiocStyle")
nilseling commented 3 years ago

Hmm, for the R packages they should be installed by default since they are listed under Suggests. How did you install the cytomapper devel?

jwindhager commented 3 years ago

Maybe those are ignored by devtools::install_github?

Did the following, as indicated in the README:

devtools::install_github("BodenmillerGroup/cytomapper", build_vignettes = TRUE)
nilseling commented 3 years ago

Ok, I'll have a look. The build_vignettes parameter should trigger exactly this.

nilseling commented 3 years ago

Alright, thanks for checking this. I have now updated the installation instructions in the README and started a cytomapper wiki with more detailed installation instructions.