On Tue, Mar 15, 2011 at 3:00 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> Hi Gabriel,
>
>
>
> On Tue, Mar 15, 2011 at 2:41 PM, Gabriel Nathan Kaufman, Mr <
> gabriel.kaufman@mail.mcgill.ca> wrote:
>
> > I tried reinstalling the graph package from binary, in both the 32- and
> > 64-bit R GUI, and still can't manage to load iFlow properly. I keep
> getting
> > a flowCore installation error that doesn't seem to go away when I
> reinstall
> > flowCore in the GUI.
> >
> > When I run R in Terminal (in both 32- and 64-bit) it loads up fine. Any
> > other ideas?
> >
> >
> > The console from my last try in the R.app 64-bit GUI is copied below.
> >
> >
> > Gabriel Kaufman
> > McGill University Complex Traits Group
> >
> >
> > ----------------------------------
> >
> > > library(iFlow)
> > Loading required package: flowCore
> > Loading required package: Biobase
> >
> > Welcome to Bioconductor
> >
> >  Vignettes contain introductory material. To view, type
> >  'browseVignettes()'. To cite Bioconductor, see
> >  'citation("Biobase")' and for packages 'citation(pkgname)'.
> >
> > Loading required package: rrcov
> > Loading required package: robustbase
> > Loading required package: pcaPP
> > Loading required package: mvtnorm
> > Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
> > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> >   unable to load shared object
> >
> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/flowCore/libs/x86_64/flowCore.so':
> >
>  dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/flowCore/libs/x86_64/flowCore.so,
> > 6): Library not loaded:
> > /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
> >  Referenced from:
> >
> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/flowCore/libs/x86_64/flowCore.so
> >   Reason: image not found
> >
>
>
> Whenever you see this type of error it means that a library for a
> particular
> package (in this case flowCore) and architecture (in this case x86_64) is
> missing.
>

This looks to me like he installed a binary package built for 2.12 but is
using R 2.13. But your solution of reinstalling from Bioc should work
anyway.


> This can happen when you build packages from source. There are ways to
> build
> packages for all architectures (see
>
> http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Building-universal-package
> ),
> however, it's much simpler to download the binary version of the package
> that bioconductor supplies. You can do this by always supplying the
> type="mac.binary.leopard" argument to biocLite.
>
> So, reinstall flowCore as follows:
>
> biocLite("flowCore", type="mac.binary.leopard")
>
> Then try again to run iFlow and if you get a similar error but referring to
> a different package, install that package with the
> type="mac.binary.leopard"
> argument.
>
> You probably want to do binary installs by default, so you can put this
> line:
>
> options("pkgType" = "mac.binary.leopard")
>
> in your ~/.Rprofile file and it will be the default, so you won't have to
> supply the "type" argument to biocLite() any more.
>
> Hope this helps
> Dan
>
>
>
>
>
> > Error: package 'flowCore' could not be loaded
> >
> >
> > ________________________________________
> > From: Dan Tenenbaum [dtenenba@fhcrc.org]
> > Sent: March 14, 2011 3:30 PM
> > To: Gabriel Nathan Kaufman, Mr;
> bioconductor@stat.math.ethz.chbioconductor
> > Subject: Re: [BioC] iFlow/flowCore installation problem
> >
> > Thanks! Let me know and keep it on the list as well so we can all
> > benefit from what you find out.
> > Dan
> >
>
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>
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