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 way to do this. I’ve been look to Rsamtools <https://github.com/Bioconductor/Rsamtools> for some sources of inspiration, since it relies on multiple CLI tools (rsamtools, tabix). I’m unfamiliar with getting bash scripts to run while installing R packages, but looking into this now. Best, Brian > On 13 Dec 2021, at 13:59, Kasper Daniel Hansen <kasperdanielhan...@gmail.com> > wrote: > > 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 should > anything else but R be here? > $HOME > working directory > > In my opinion, if you want to do something like this, you need to do it at > installation time and you should install MAGMA in the package location. > > > > On Thu, Dec 9, 2021 at 8:30 AM Vincent Carey <st...@channing.harvard.edu > <mailto:st...@channing.harvard.edu>> wrote: > 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 > > On Thu, Dec 9, 2021 at 7:37 AM Brian Schilder < > brian_schil...@alumni.brown.edu <mailto:brian_schil...@alumni.brown.edu>> > wrote: > > > Hi everyone, > > > > I’m a developer for the R package MAGMA.Celltyping < > > https://github.com/neurogenomics/MAGMA_Celltyping/tree/bschilder_dev > > <https://github.com/neurogenomics/MAGMA_Celltyping/tree/bschilder_dev>> (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 <https://ctg.cncr.nl/software/magma > > <https://ctg.cncr.nl/software/magma>>, which is only available as a > > CLI program. > > > > I have everything passing CRAN/Bioc checks on my local machine, but the > > final hurdle is installing MAGMA <https://ctg.cncr.nl/software/magma > > <https://ctg.cncr.nl/software/magma>> on > > other machines (e.g. via GitHub Actions checks) such that it can be called > > from within R. > > > > Here’s the steps I’ve taken: > > Upon .onLoad < > > https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/zzz.R > > > > <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/zzz.R>> > > of MAGMA.Celltyping, magma_installed_version() < > > https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_installed_version.R > > > > <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_installed_version.R>> > > will check whether MAGMA is installed. If not, it proceeds to try and > > install it via magma_install() < > > https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_install.R > > > > <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/magma_install.R>> > > . > > magma_install() finds the latest version of MAGMA in their archives < > > https://ctg.cncr.nl/software/MAGMA/prog/ > > <https://ctg.cncr.nl/software/MAGMA/prog/>>, installs it wherever the user > > has permissions (from a list of possible installation locations < > > https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/find_install_dir.R > > > > <https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/R/find_install_dir.R>>), > > and sets up the symlink. > > Checks that MAGMA is indeed installed and callable from within R using > > functions like system(“magma ….”). > > This all seems to work fine locally, but when I launch to GitHub actions, > > MAGMA.Celltyping can’t seems to install/find MAGMA. it doesn’t seem to be > > able to find it. > > > > Does anyone know of any solutions to this that are Bioc (or at least CRAN) > > -compatible? > > > > Many thanks in advance, > > Brian > > ___________ > > Brian Schilder > > PhD Candidate > > UK Dementia Research Institute at Imperial College London > > Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab > > Profile | bit.ly/imperial_profile <http://bit.ly/imperial_profile> > > <https://bit.ly/imperial_profile <https://bit.ly/imperial_profile>> > > LinkedIn | linkedin.com/in/brian-schilder > > <http://linkedin.com/in/brian-schilder> < > > https://www.linkedin.com/in/brian-schilder/ > > <https://www.linkedin.com/in/brian-schilder/>> > > Twitter | twitter.com/BMSchilder <http://twitter.com/BMSchilder> > > <http://www.twitter.com/BMSchilder <http://www.twitter.com/BMSchilder>> > > Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/> > > <http://neurogenomics.co.uk/ <http://neurogenomics.co.uk/>> > > UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/> <http://www.ukdri.ac.uk/ > > <http://www.ukdri.ac.uk/>> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > -- > The information in this e-mail is intended only for th...{{dropped:16}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
