Re: [Bioc-devel] MAGMA executable

Hi Kristian, The package installation folder should never been written to once the package has been installed. On many systems this is a read-only folder. I didn't see any mention of Cygwin in your DESCRIPTION or README.md file. Also I noticed some inconsistency between the system requirements

Re: [Bioc-devel] MAGMA executable

Hi Brian, Note that Rsamtools does not relies on any CLI tools. It contains C/C++ code that is _compiled_ and _linked_ against Rhtslib rather than relying on the standalone `samtools` and `tabix` commands. Installing MAGMA at package installation time in the package installation folder of

Re: [Bioc-devel] MAGMA executable

Thank you both for the helpful feedback. I’ll follow up with the developers of MAGMA for clarification on license. Regarding installation, I agree Kasper, this is not an ideal solution. Installing MAGMA at the R package installation time would be ideal, but I’ve been unable to come up with a

Re: [Bioc-devel] MAGMA executable

Ignoring the license issues (which may be significant), I strongly dislike this installation strategy. It (IMO) unreasonable that you potentially write in system locations on package load. You're looking in /usr/local/bin R.home/bin <- this makes not sense, this is the R home location, why

Re: [Bioc-devel] MAGMA executable

I didn't find an obvious licensing statement at the magma site. I did see note that standard copyright applies; the MAGMA binaries and source code may not be distributed or modified) the licensing situation would affect my advice on this process, but others may have other more specific advice

[Bioc-devel] MAGMA executable

Hi everyone, I’m a developer for the R package MAGMA.Celltyping (on the bschilder_dev branch). It’s currently only distributed via GitHub but I’m trying to get it on Bioc if possible. The dilemma is, it relies on MAGMA