java folder missing?

[tapj]

Hi,

I tried to run you example code:

library(omixerRpm)
# read a functional profile matrix into R or create it inside R
dat <- read.table("test/matrix.tsv", header=T, sep="\t")
# Run the module mapping on the loaded table.
mods <- rpm(dat, minimum.coverage=0.3, annotation = 1)

but I have this error

> mods <- rpm(dat, minimum.coverage=0.3, annotation = 1)
Error: Unable to access jarfile 0.3

when I l look into your code, it seems that you need to call a jar file from a java folder

 system.file("java", "omixer-rpm.jar", package = "omixerRpm")

which is not provided from this repo. Where could I find "omixer-rpm.jar"?

Thank you,

Julien

[omixer]

Hi Julien,

The omixer-rpm.jar is provided in the inst/java folder of the distribution package!
However I just realized it only works for Linux!

If you are not on Linux, the new source package contains all the dependencies and should work now (I need to double check on a windows machine though, but on macOS Sierra it works)

[tapj]

Hi,

that's why on windows I tried to install it directly from the repository instead of the distribution package using

devtools::install_github

but cloning the repo and copy/paste the jar file on the right place (java folder) and recompile it solved my issue