Spade in FlowJo v10.0

Question

I have an issue with installing the spade package in R:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite("spade")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘spade’
Old packages: 'foreign', 'survival'
Update all/some/none? [a/s/n]: 
n
Warning message:
package ‘spade’ is not available (for R version 3.5.1) 
> 

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Answer 1

The problem is likely related to the fact that spade appears in the list of packages removed at BioConductor version 3.4. See: https://bioconductor.org/about/removed-packages/

Trying to install the latest version of spade_1.8.0 into R 3.5.1 fails because it depends on another abandoned package igraph0. igraph0 has bee replaced by igraph. Since igraph has substantial differences from igraph0, you would probably need to identify all the use of that package and rewrite the package code and then install locally.

The other puzzle is that you chose not to update the packages the installer script identified as missing. That didn't make a difference in this case (and it was a misleading message anyway), but it's not a practice I would recommend in the future.