[R-SIG-Mac] Error: package 'affyio' is not installed for 'arch=x86_64'

[Patrick Aboyoun]

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 <engrav at u.washington.edu>:

> 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 <dwinsemius at comcast.net>
>> Date: Sun, 1 Mar 2009 12:39:07 -0500
>> To: Loren Engrav <engrav at u.washington.edu>
>> Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
>> 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
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
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