Simon,
I just tested the scenario of using standard R-2.x.x.dmg from CRAN is
installed on a Mac OS X 10.5 machine and download the standard set of
BioC packages and it worked as you predicted using the default type =
"mac.binary". My bad. The OS version was a red herring.
Patrick
Simon Urbanek wrote:
Patrick,
On Apr 21, 2009, at 14:53 , Patrick Aboyoun wrote:
Massimo,
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?
Cheers,
Simon
Simon Urbanek wrote:
Massimo,
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
10.5.6.
(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)
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
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:
install.packages("/Users/massimopinto/Desktop/affy_1.20.2.tgz",
repos=NULL, dependencies=TRUE)
however, when I load the library:
library(affy)
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
'/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so,
6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/preprocessCore/libs/i386/preprocessCore.so
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
http://cran.r-project.org/bin/macosx/tools/
Cheers,
Simon
===the package does not get loaded as a library cannot be found.
Similarly,
I run into problems if I install as follows:
install.packages("affy", repos="
http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/";,
contriburl="
http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/";,
dependencies=TRUE)
trying URL '
http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8//affy_1.20.2.tgz
'
Content type 'application/x-gzip' length 1452708 bytes (1.4 Mb)
[...]
Could it be that the binaries at
http://www.bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/are
in fact compiled for Tiger?
Massimo
--
Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute
(ISS), Rome
http://claimid.com/massimopinto
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