Re: [R-SIG-Mac] istate CRAN mirror not working - unable to use .Rprofile to change

2017-06-08 Thread Michael Hall 

> On Jun 8, 2017, at 5:22 PM, Duncan Murdoch  wrote:
> 
> 
> The documentation about .Rprofile is documentation about R.  R.app is a 
> separate project that acts as a front end to R.  Front ends can change things 
> that R does.  R.app uses its own Mac OS ways of storing persistent 
> configuration information.

OK, seems a reasonable split in support. I’m not sure how far you can get away 
from what R does though.
 
> 
>> 
>> But again, for my purposes yes, the preference is fine to change the default 
>> mirror and get me working normally. Thanks again.
>> 
>> I am still a little curious if there are any thoughts on why the iastate 
>> mirror stopped working?
> 
> You would likely have to figure out who was running it, and ask them. Mirrors 
> are coordinated by CRAN, but are run by the local people who run them.

I think for one mirror I did notice a contact person name, but I’m not sure I 
saw any contact information. Iowa is close but not close enough to go and try 
to track a responsible individual down.

Thanks again

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Re: [R-SIG-Mac] istate CRAN mirror not working - unable to use .Rprofile to change

2017-06-08 Thread Duncan Murdoch 

On 08/06/2017 5:50 PM, Michael Hall wrote:



On Jun 8, 2017, at 5:53 AM, Duncan Murdoch  wrote:

If you are using R.app, you can also set the mirror in the Preferences menu.  
Perhaps this setting overrides the .Rprofile setting.



I was using the app and wasn’t aware of the preference, so thanks.

There was no .Rprofile before I added one.

I wasn’t sure what the app was basing this on. I didn’t see a Rprofile. 
site anywhere in the framework either. Just a csv file 
that seemed to include all the mirrors turned up in a search.

Whether or not being unable to do this with .Rprofile is a concern I don’t 
know. Looking again at help(Startup) it shows doing this as an example for 
Rprofile.site and not .Rprofile. I haven’t tried with .Rprofile.site.
But I can’t exactly say it is documented that this should work. Although you 
might assume that you should be able to do in .Rprofile whatever might be done 
in Rprofile.site.


The documentation about .Rprofile is documentation about R.  R.app is a 
separate project that acts as a front end to R.  Front ends can change 
things that R does.  R.app uses its own Mac OS ways of storing 
persistent configuration information.




But again, for my purposes yes, the preference is fine to change the default 
mirror and get me working normally. Thanks again.

I am still a little curious if there are any thoughts on why the iastate mirror 
stopped working?


You would likely have to figure out who was running it, and ask them. 
Mirrors are coordinated by CRAN, but are run by the local people who run 
them.


Duncan Murdoch

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Re: [R-SIG-Mac] istate CRAN mirror not working - unable to use .Rprofile to change

2017-06-08 Thread Michael Hall 

> On Jun 8, 2017, at 5:53 AM, Duncan Murdoch  wrote:
> 
> If you are using R.app, you can also set the mirror in the Preferences menu.  
> Perhaps this setting overrides the .Rprofile setting.
> 

I was using the app and wasn’t aware of the preference, so thanks.

There was no .Rprofile before I added one. 

I wasn’t sure what the app was basing this on. I didn’t see a Rprofile. 
site anywhere in the framework either. Just a csv file 
that seemed to include all the mirrors turned up in a search.

Whether or not being unable to do this with .Rprofile is a concern I don’t 
know. Looking again at help(Startup) it shows doing this as an example for 
Rprofile.site and not .Rprofile. I haven’t tried with .Rprofile.site.
But I can’t exactly say it is documented that this should work. Although you 
might assume that you should be able to do in .Rprofile whatever might be done 
in Rprofile.site.

But again, for my purposes yes, the preference is fine to change the default 
mirror and get me working normally. Thanks again. 

I am still a little curious if there are any thoughts on why the iastate mirror 
stopped working? 


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Re: [R-SIG-Mac] istate CRAN mirror not working - unable to use .Rprofile to change

2017-06-08 Thread Duncan Murdoch 
If you are using R.app, you can also set the mirror in the Preferences 
menu.  Perhaps this setting overrides the .Rprofile setting.


Duncan Murdoch

On 08/06/2017 5:05 AM, Michael Hall wrote:

I started getting errors installing packages using my default repository 
instate…

Warning: unable to access index for repository 
http://streaming.stat.iastate.edu/CRAN/src/contrib:
  cannot open URL 'http://streaming.stat.iastate.edu/CRAN/src/contrib/PACKAGES'
Warning: unable to access index for repository 
http://streaming.stat.iastate.edu/CRAN/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 
'http://streaming.stat.iastate.edu/CRAN/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning message:
package ‘RWeka’ is not available (for R version 3.4.0)

Googling, I was able to do this using a different mirror selected with 
chooseCRANmirror(), I chose Kansas.

I googled how to make this the new default and was pointed to .Rprofile.
This doesn’t seem able to do this, with…

message(".Rprofile")
local({r <- getOption("repos")
  r["CRAN"] <- "https://rweb.crmda.ku.edu/cran;
  options(repos=r)})

I get…

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

.Rprofile
[R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]

[History restored from /Users/mjh/.Rapp.history]

Which shows the “.Rprofile” message indicating it has run.
However…


r <- getOption("repos")
r

CRAN
"http://streaming.stat.iastate.edu/CRAN;

Still shows iastate.
Then doing…


source(".Rprofile")

.Rprofile

r <- getOption("repos")
r

CRAN
"https://rweb.crmda.ku.edu/cran”

so the .Rprofile does work. R must be changing it to iastate after the profile 
is run?
I had googled a mailing list thread where it was said .Rprofile wasn’t working 
on OS X. It was suggested in there that this be posted to this list. I checked 
the archives for the last couple months but didn’t see any mention.

Is this a problem that needs addressing? Or has a workaround besides sourcing 
.Rprofile whenever I want to install packages?




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[R-SIG-Mac] istate CRAN mirror not working - unable to use .Rprofile to change

2017-06-08 Thread Michael Hall 
I started getting errors installing packages using my default repository 
instate…

Warning: unable to access index for repository 
http://streaming.stat.iastate.edu/CRAN/src/contrib:
  cannot open URL 'http://streaming.stat.iastate.edu/CRAN/src/contrib/PACKAGES'
Warning: unable to access index for repository 
http://streaming.stat.iastate.edu/CRAN/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 
'http://streaming.stat.iastate.edu/CRAN/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning message:
package ‘RWeka’ is not available (for R version 3.4.0) 

Googling, I was able to do this using a different mirror selected with 
chooseCRANmirror(), I chose Kansas.

I googled how to make this the new default and was pointed to .Rprofile.
This doesn’t seem able to do this, with…

message(".Rprofile")
local({r <- getOption("repos")
  r["CRAN"] <- "https://rweb.crmda.ku.edu/cran;
  options(repos=r)})

I get…

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

.Rprofile
[R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]

[History restored from /Users/mjh/.Rapp.history]

Which shows the “.Rprofile” message indicating it has run.
However…

> r <- getOption("repos")
> r
CRAN 
"http://streaming.stat.iastate.edu/CRAN; 

Still shows iastate.
Then doing…

> source(".Rprofile")
.Rprofile
> r <- getOption("repos")
> r
CRAN 
"https://rweb.crmda.ku.edu/cran” 

so the .Rprofile does work. R must be changing it to iastate after the profile 
is run?
I had googled a mailing list thread where it was said .Rprofile wasn’t working 
on OS X. It was suggested in there that this be posted to this list. I checked 
the archives for the last couple months but didn’t see any mention.

Is this a problem that needs addressing? Or has a workaround besides sourcing 
.Rprofile whenever I want to install packages?

 


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