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?
Yes, that sounds like a problem with the BioC builds (libintl.3.dylib
is really strange - we use libintl.8.dylib as a part of optional Gtk
on CRAN, but never libintl3.dylib..). I didn't test BioC builds ever
since we stopped building it on CRAN, but I have heard complains about
their binaries linking various stuff from /usr/local, so I'd suggest
to file a bug report with them (BTW: Xcode should not be required from
binary installs).
Cheers,
S
Vince Carey reports that a student of his had a similar problem.
Kasper
On Jun 16, 2008, at 6:53 AM, jason smith wrote:
Thanks Steve,
Here is what I get from otool:
jason-smiths-macbook:~ sjorges2002$ otool -L /Users/sjorges2002/
Library/R/2.7/library/affy/libs/i386/affy.so
/Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so:
affy.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
1.2.3)
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/
libR.dylib (compatibility version 2.7.0, current version 2.7.0)
/usr/local/lib/libintl.3.dylib (compatibility version 8.0.0,
current version 8.3.0)
/usr/lib/libiconv.2.dylib (compatibility version 5.0.0, current
version 5.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 88.3.10)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/
CoreFoundation (compatibility version 150.0.0, current version
368.35.0)
/usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
Best
Jason
--- On Mon, 6/16/08, Steve Lianoglou
<[EMAIL PROTECTED]> wrote:
You're not doing it right :-)
otool -L
/Users/sjorges2002/Library/R/2.7/library/affy/libs/i386/affy.so
Let's see what you get from that.
-steve
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