Entering edit mode
There are several cross-platform issues with seq2pathway.
This package calls a Python script in a Windows-specific manner (see here: https://github.com/Bioconductor-mirror/seq2pathway/blob/master/R/seq2pathway-internal.r#L750) and the way paths are built is also not platform-independent.
It is easy to fix this to run on Linux but I don't know how to do it in a way that is compatible with all platforms.
Perhaps the best option would be to call the revelant Python functions using a library which allows this interface in R instead of running the python script from the command line.
The package maintainer has been notified about this problem; they have not yet updated their package and in the interim it has been marked as 'deprecated' in the devel branch. Superficially it seems that it would be straight-forward to implement the python code using GenomicRanges; calling python in a system independent way is also straight-forward.