[R-SIG-Mac] installation of affy under Mac OS X 10.5.6 (Leopard)
simon.urbanek at r-project.org
Tue Apr 21 21:46:30 CEST 2009
On Apr 21, 2009, at 14:53 , Patrick Aboyoun wrote:
> 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.
Do NOT do that manually! You can only use Tiger binaries in Tiger
build of R even if you are running Leopard system, so the default
setting is there for a reason (at least in CRAN binaries). The OS
version is entirely irrelevant in this matter.
> 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.
That will be very bad for the reason above ... Are you sure you mean
that? Or am I missing something - are you talking about the running OS
or the R build OS?
> 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 believes
>>> 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 fine.
>>> Today I have encountered a similar problem with the package affy.
>>> Accordingly, I have downloaded the OS X 10.5 binaries and
>>> installed manually:
>>>> 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
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