[Bioc-devel] installing devel pre-compiled binary for MacOSX
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
?/Library/Frameworks/R.framework/Versions/2.14/Resources/library?
* installing *binary* package ?CNAnorm? ...
* 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 ?CNAnorm? was built under R version 2.15.0
Error: package/namespace load failed for ?CNAnorm?
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