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
Error: package 'affyio' is not installed for 'arch=x86_64'
4 messages · Loren Engrav, David Winsemius, Patrick Aboyoun
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
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
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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac