Loren,
Following David's comment, it is hard to determine where/when the
change occurred. The MacOS X leopard binary for the BioC 2.3 release
of affyio does contain the x86_64 binary lib:
Patricks-MacBook-Pro-2:~ patrick$ curl -O
http://bioconductor.org/packages/2.3/bioc/bin/macosx/leopard/contrib/2.8/affyio_1.10.1.tgz
% Total % Received % Xferd Average Speed Time Time
Time Current
Dload Upload Total Spent Left Speed
100 191k 100 191k 0 0 344k 0 --:--:-- --:--:-- --:--:-- 439k
Patricks-MacBook-Pro-2:~ patrick$ tar xfz affyio_1.10.1.tgz
Patricks-MacBook-Pro-2:~ patrick$ ls affyio/libs/x86_64/
affyio.so
One theory is that you installed the package from source while
operating on the 32-bit architecture. If you do find a reproduce,
please post your message to the Bioconductor mailing list since this
is a packaging/distribution issue, rather than a R Mac OS X one.
Patrick
Quoting Loren Engrav <[email protected]>:
Thank you
I went down the R.app Package Manager list and clicked all the boxes and 6
of them gave the error message so on these I did the biocLite (c("xxx",
"yyy", "zzz"), type="source") drill
And all is Ok again
You might be right, I might have hit the binary buttons
From: David Winsemius <[email protected]>
Date: Sun, 1 Mar 2009 12:39:07 -0500
To: Loren Engrav <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [R-SIG-Mac] Error: package 'affyio' is not installed for
'arch=x86_64'
It's a bit difficult to comment about what sort of quasirandom event
may have affected the integrity of your device, but here is a theory
based on my experience: If you updated from binaries (32 bit) that
were on the Bioconductor server, then you may have overwritten your
compiled source 64 bit versions. It is rather easy to do that without
noticing if you are using the GUI Installer. (The fix is also very
easy.)
--
David Winsemius
On Mar 1, 2009, at 12:11 PM, Loren Engrav wrote:
Greetings
SessionInfo()
R version 2.8.0 Patched (2008-11-06 r46845)
i386-apple-darwin9.5.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] affy_1.20.0 affyio_1.10.1 Biobase_2.2.2 maanova_1.12.0
loaded via a namespace (and not attached):
[1] preprocessCore_1.4.0
And MacOS X 10.5.6
Last Nov I ran some 64bit stuff, no problem, and have not installed
removed
any R or BioC stuff since then
Now I need to rerun and for several packages I get
package 'xxx' is not installed for 'arch=x86_64'
So I do
source ("http://www.bioconductor.org/biocLite.R";)
biocLite (c("xxx", "yyy", "zzz"), type="source")
And reload them
And then things work
My question: where how why did my 64bit stuff go?
Thank you
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