Thanks to all for bringing this issue of the BioC 2.2 Max OS X binary
packages to light, and I apologize for any inconvenience these
non-standard binary packages have caused the BioC user community. If all
goes well with the build system tomorrow morning, the Mac OS X binary
packages will be produced under the standard Mac OS X R framework. I
will send out an e-mail tomorrow morning notifying you on its status.
I don't want to get too much into the gory details of the build system,
but I will provide you with a high level synopsis on what caused the
breakdown. Back when the Bioconductor core team released BioC 2.2 in
May, we had a last minute scramble for the Mac OS X binary packages
builds. Up until release time, we were building the packages on Mac OS
X Leopard (10.5.2). It was brought to our attention the week of the
release that those builds were not working on Mac OS X Tiger. When we
switched to a Tiger build machine, we experienced problems with the png
device (type = "quartz", the default, failed to work in our build
environment). In order to be expedient we used a custom build of R 2.7.0
to get around this issue. This had the unintended consequence that you
discovered. We have since reverted back to using the standard R 2.7.1
build for the Mac and are using a configuration file to set
options(bitmapType = "cairo") to get around the png device issue. These
new Mac binary package builds will be linking into the dynamic libraries
located in the standard R directory
/Library/Frameworks/R.framework/Resources/lib.
Cheers,
Patrick
Simon Urbanek wrote:
On Jun 19, 2008, at 2:03 PM, Kasper Daniel Hansen wrote:
Another way Jason can get up and run quickly is to do something like
R> options(pkgType = "source")
and then do biocLite. That is probably a better solution than trying
to install gettext
Definitely, and especially since it doesn't help (see my comments to
Steve below).
I wouldn't recommend installing gettext (unless you know what you're
doing) simply because it will modify your system such that all future
configurations will detect it and behave differently. As long as you
don't plan to copy anything to another machine it is not a big deal,
but if you do, you'll learn very quickly why that's a bad idea ;).
Nonetheless, there are valid cases.
However, as Jan pointed out correctly, this is not the only problem
that BioC builds have, unfortunately. I can only repeat my plea that I
sent while ago to the BioC team to fix their Mac builds.
Kasper
On Jun 19, 2008, at 10:18 AM, Steve Lianoglou wrote:
Hi,
On Jun 19, 2008, at 12:58 PM, Kasper Daniel Hansen wrote:
Ok, I will take this over to the R-SIG-Mac list and cc Herve who is
the build manager of Bioconductor. I suspect that something is
wrong with the Bioconductor builds.
Synopsis: Jason is running R-2.7.0 from CRAN on an Intel macbook
running 10.5.3. He says he has Xcode 3.0 installed. He tries to
install the binary version of aff from Bioconductor using the normal
biocLite("affy")
However, even though the tarball downloads and gets installed, the
package won't load. It complains that it needs the library
/usr/local/lib/libintl.3.dylib (and an otool -L really confirms
this), but apparently this files does not exists. I am a bit
surprised that the binary version links to something in /usr/local.
I have this file on my PPC G4 running 10.5.3. As I see it, this
should work out of the box with the system Jason is running. Does
anyone have any good ideas? My hunch is that something might be up
with the binary builds?
Just so Jason can get up and running quickly (and not have to wait
for this to get sorted out in the builds or whatever), I would
recommend as a band-aid procedure to just install gettext for now,
as I am fairly certain that this will provide the
/usr/local/lib/libintl.3.dylib that he is missing.
Are you? Did you actually test it? I'm pretty sure that you're wrong,
because the commands below compile libintl.8.dylib(!) and thus won't
help (that one is fine and part of your Gtk binary). I'm still puzzled
at where the BioC team gets libintl.3 ...
Cheers,
Simon
I gather that he might not be very comfortable from the command
line, so following these steps in a terminal session should do the
trick:
cd /tmp
curl http://mirrors.usc.edu/pub/gnu/gettext/gettext-0.17.tar.gz |
tar xz
cd gettext-0.17
./configure
make
sudo make install
HTH,
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics, and Systems Biology
Weill Medical College, Cornell University
http://cbio.mskcc.org/~lianos
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