[Bioc-devel] MAGMA executable

[Kasper Daniel Hansen]

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 <stvjc using 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_schilder using 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>
> (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>, 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> 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
> >
> > of MAGMA.Celltyping, magma_installed_version() <
> >
> 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
> >
> > .
> > magma_install() finds the latest version of MAGMA in their archives <
> > 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
> >),
> > 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 <https://bit.ly/imperial_profile>
> > LinkedIn | linkedin.com/in/brian-schilder <
> > https://www.linkedin.com/in/brian-schilder/>
> > Twitter | twitter.com/BMSchilder <http://www.twitter.com/BMSchilder>
> > Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/>
> > UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/>
> >         [[alternative HTML version deleted]]
> >
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> >
>
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