[R-SIG-Mac] installation of affy under Mac OS X 10.5.6 (Leopard)
paboyoun at fhcrc.org
Tue Apr 21 20:53:40 CEST 2009
I'll break down these issues in two and go through them in turn:
1) stale binaries for R 2.8 at bioconductor.org
You had found that the Mac OS X binary packages at bioconductor.org that
used fortran, like preprocessCore, had a bad gfortran link in them. I
updated those packages last week and they are now properly redirected to
the gfortran library that is provided with the pre-built version of R
2.8. To fix this issue, please download the troublesome libraries again
for a fix.
2) Determining which binary packages are appropriate for your Mac
I think you were downloading the Mac OS X 10.4 binary packages from
bioconductor.org rather than the Mac OS X 10.5 binary packages because
your pkgType == "mac.binary" instead of "mac.binary.leopard". You and
either perform a global setting of the pkgType to "mac.binary.leopard"
using options("pkgType" = "mac.binary.leopard") or specify type =
"mac.binary.leopard" when using the biocLite / install.packages functions.
I have also modified the underpinnings of biocLite to produce a warning
message when you specify type = "mac.binary" when you are running on Mac
OS X 10.5 machine with some suggestions on what you can do to avoid this
type of problem in the future.
Simon Urbanek wrote:
> On Apr 21, 2009, at 9:10 AM, Massimo Pinto wrote:
>> Greetings all
>> last week I attempted to install the genefilter package using
>> BiocLite(genefilter) from the R prompt. Despite having a Mac OS X
>> (Tiger), for some reason which I don't understand in full, BioC 2.3
>> I am running on Mac OS X 10.4 (Leopard)
>> R version 2.8.1 (2008-12-22)
> This shows you what kind of R you are running (i.e. where was the R
> compiled), not what your OS is. You are running the Tiger release of
> R, which is ok since it is designed for Mac OS X 10.4 (Tiger) and
> later which includes your 10.5.
>> therefore, when I run biocLite, general Mac binaries are installed
>> and this results in execution errors.
> The "therefore" is wrong here ;).
>> Much thanks to the help found on this list, I have downloaded the
>> tarball for OSX 10.5 binaries and installed manually. It worked just
>> Today I have encountered a similar problem with the package affy.
>> Accordingly, I have downloaded the OS X 10.5 binaries and installed
>>> repos=NULL, dependencies=TRUE)
>> however, when I load the library:
>> Loading required package: Biobase
>> Loading required package: tools
>> Welcome to Bioconductor
>> Vignettes contain introductory material. To view, type
>> 'openVignette()'. To cite Bioconductor, see
>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library
>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
>> Referenced from:
>> Reason: image not found
>> Error: package/namespace load failed for 'affy'
> The problem above doesn't come from affy, but from the preprocessCore
> package (see the error). The binary for preprocessCore you use is not
> quite correct. It uses local Fortran libraries on the machine that
> built it where it should be using the Fortran library inside R. If
> this is a binary from the BioC repository, please notify the
> maintainers, otherwise re-install the binary of preprocessCore from
> BioC. Note the the correct mailing list for such questions is BioC.
> A work-around (that fixes the symptom, not the problem) is to install
> the full R (you seem to have only the mini version installed) which
> includes a local Fortran compiler - or you can install the Fortran
> manually from
>> ===the package does not get loaded as a library cannot be found.
>> I run into problems if I install as follows:
>>> install.packages("affy", repos="
>> trying URL '
>> Content type 'application/x-gzip' length 1452708 bytes (1.4 Mb)
>> Could it be that the binaries at
>> in fact compiled for Tiger?
>> Massimo Pinto
>> Post Doctoral Research Fellow
>> Enrico Fermi Centre and Italian Public Health Research Institute
>> (ISS), Rome
>> [[alternative HTML version deleted]]
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
More information about the R-SIG-Mac