[Bioc-devel] installing devel pre-compiled binary for MacOSX

[Steve Lianoglou]

Hi Stefano,

On Mon, Mar 19, 2012 at 8:50 AM, Stefano Berri <S.Berri at leeds.ac.uk> wrote:
> Hi.
>
> I am not sure this is the right place to ask, but could not find anywhere
> better.
>
> I am author of CNAnorm. I have a problem when MACOSX users want to install
> packages.
>
> it works fine if they do
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("CNAnorm")
>
> but this install the "stable" version 1.0.0
>
> It is also fine if they download CNAnorm_1.1.8.tar.gz and then
>
> R CMD INSTALL CNAnorm_1.1.8.tar.gz
>
> but this requires XCode and a fortran compiler which is not so straight
> forward for some users
>
> If they download MacOS 10.5 (Leopard) binary  CNAnorm_1.1.8.tgz
> and then
>
> R CMD INSTALL CNAnorm_1.1.8.tgz
>
> they get
>
> * installing to library
> Œ/Library/Frameworks/R.framework/Versions/2.14/Resources/library¹
> * installing *binary* package ŒCNAnorm¹ ...
>
> * DONE (CNAnorm)
>
> but then when starting CNAnorm
>
> library(CNAnorm)
> Loading required package: DNAcopy
>
> **************************************************************************
>   The plan to change the data format for CNA object has been postponed
>  in order to ensure backward compatibility with older versions of DNAcopy
> **************************************************************************
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
> '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/CNAnorm/lib
> s/x86_64/CNAnorm.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/CNAno
> rm/libs/x86_64/CNAnorm.so, 6): Library not loaded:
> /Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dy
> lib
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/CNAnorm/libs
> /x86_64/CNAnorm.so
>  Reason: image not found
> In addition: Warning message:
> package ŒCNAnorm¹ was built under R version 2.15.0
> Error: package/namespace load failed for ŒCNAnorm¹
>
>
> The user has R 2.14.1
>
> What am I doing wrong? Is there a way to install the development version of
> CNAnorm using biocLite?

You aren't doing anything wrong ... this is the intended behavior.

The package versions that biocLite installs are tied to the version of
R that is being used. Someone who is running R-2.14.x is "tied" to the
bioconductor 2.9 "release train." If you want the development version
of packages, you need to be running R-devel.

When R-2.15.0 comes out, it will be "tied" to bioconductor 2.10 packages.

For the time being, if the mac users want to install the devel version
of CNAnorm, they can either:

(1) just download and install the source manually -- which usually
isn't recommended and you might be opening the door to dependency
hell, but ... it can be done. As you point out, the users will also
need XCode and a gfortran compiler, which they can get from here:

http://r.research.att.com/gfortran-4.2.3.dmg

(2) they can grab the R-2.15-beta installer from the link below and
install the devel versions of *all* bioconductor packages using
biocLite:

http://r.research.att.com/R-2.15-branch-leopard.pkg

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact