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.
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.
Cheers,
Patrick
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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