Re: [R-SIG-Mac] R is taking too long to load

2017-05-18 Thread Ben Tupper 
Check out this exchange

https://stat.ethz.ch/pipermail/r-sig-mac/2013-February/009979.html


On Friday, May 19, 2017, peter dalgaard  wrote:

> Most easily by typing "R --vanilla" the command line of Terminal.app.
> Dunno if you can do it with R.app.
>
> -pd
>
>
> > On 19 May 2017, at 00:58 , Christofer Bogaso <
> bogaso.christo...@gmail.com > wrote:
> >
> > Thanks,
> >
> > How can I start R with --vanilla in Mac? Sorry if this question is very
> trivial.
> >
> > On Fri, May 19, 2017 at 3:11 AM, Hervé Pagès  > wrote:
> >> Hi,
> >>
> >> First thing I would do is make sure you don't have any startup file
> >> or .Rhistory in the way. If starting R with --vanilla is fast, then
> >> that's probably the case.
> >>
> >> H.
> >>
> >>
> >> On 05/18/2017 12:44 PM, Christofer Bogaso wrote:
> >>>
> >>> Hi,
> >>>
> >>> It just started happening recently that R is taking too long to load
> >>> and entire system freezes during its loading.
> >>>
> >>> Have anyone experienced something similar? Previously my R was
> >>> completely okay, however it just started recently.
> >>>
> >>> Any solution for this? I have reinstalled R and now it is the latest
> >>> version 3.4.0. I am using Sierra iOS.
> >>>
> >>> Appreciate for any pointer.
> >>>
> >>> Thanks,
> >>>
> >>> ___
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac@r-project.org 
> >>>
> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwICAg=
> eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=
> m7VSPPECqAsFryKwwUO-q8QiizXtbiWc-kj9qtPO2h0=cSQVI4BrFUKhUyo5ZPrQMQOwu-
> ZSCMWpxh5IJ8y9L6s=
> >>>
> >>
> >> --
> >> Hervé Pagès
> >>
> >> Program in Computational Biology
> >> Division of Public Health Sciences
> >> Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N, M1-B514
> >> P.O. Box 19024
> >> Seattle, WA 98109-1024
> >>
> >> E-mail: hpa...@fredhutch.org 
> >> Phone:  (206) 667-5791
> >> Fax:(206) 667-1319
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org 
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk   Priv: pda...@gmail.com 
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org 
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] R is taking too long to load

2017-05-18 Thread peter dalgaard 
Most easily by typing "R --vanilla" the command line of Terminal.app. Dunno if 
you can do it with R.app. 

-pd


> On 19 May 2017, at 00:58 , Christofer Bogaso  
> wrote:
> 
> Thanks,
> 
> How can I start R with --vanilla in Mac? Sorry if this question is very 
> trivial.
> 
> On Fri, May 19, 2017 at 3:11 AM, Hervé Pagès  wrote:
>> Hi,
>> 
>> First thing I would do is make sure you don't have any startup file
>> or .Rhistory in the way. If starting R with --vanilla is fast, then
>> that's probably the case.
>> 
>> H.
>> 
>> 
>> On 05/18/2017 12:44 PM, Christofer Bogaso wrote:
>>> 
>>> Hi,
>>> 
>>> It just started happening recently that R is taking too long to load
>>> and entire system freezes during its loading.
>>> 
>>> Have anyone experienced something similar? Previously my R was
>>> completely okay, however it just started recently.
>>> 
>>> Any solution for this? I have reinstalled R and now it is the latest
>>> version 3.4.0. I am using Sierra iOS.
>>> 
>>> Appreciate for any pointer.
>>> 
>>> Thanks,
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=m7VSPPECqAsFryKwwUO-q8QiizXtbiWc-kj9qtPO2h0=cSQVI4BrFUKhUyo5ZPrQMQOwu-ZSCMWpxh5IJ8y9L6s=
>>> 
>> 
>> --
>> Hervé Pagès
>> 
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>> 
>> E-mail: hpa...@fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:(206) 667-1319
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] R is taking too long to load

2017-05-18 Thread Christofer Bogaso 
Thanks,

How can I start R with --vanilla in Mac? Sorry if this question is very trivial.

On Fri, May 19, 2017 at 3:11 AM, Hervé Pagès  wrote:
> Hi,
>
> First thing I would do is make sure you don't have any startup file
> or .Rhistory in the way. If starting R with --vanilla is fast, then
> that's probably the case.
>
> H.
>
>
> On 05/18/2017 12:44 PM, Christofer Bogaso wrote:
>>
>> Hi,
>>
>> It just started happening recently that R is taking too long to load
>> and entire system freezes during its loading.
>>
>> Have anyone experienced something similar? Previously my R was
>> completely okay, however it just started recently.
>>
>> Any solution for this? I have reinstalled R and now it is the latest
>> version 3.4.0. I am using Sierra iOS.
>>
>> Appreciate for any pointer.
>>
>> Thanks,
>>
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=m7VSPPECqAsFryKwwUO-q8QiizXtbiWc-kj9qtPO2h0=cSQVI4BrFUKhUyo5ZPrQMQOwu-ZSCMWpxh5IJ8y9L6s=
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

2017-05-18 Thread peter dalgaard 
The culprit seems to have been in Xcode 8.3.1, see this Ticket 

http://core.tcl.tk/tk/tktview/3f323bf2b42b668a5678

This was found and fixed little more than a month ago, so I was being unfair to 
ActiveState in a previous note (which may or may not make its way through 
moderation).

The Ticket also contains a two-line patch for the Tk sources, so I suppose this 
provides a way for us to build at least the framework format, with Xft support. 

-pd

> On 17 May 2017, at 21:21 , Peter Dalgaard  wrote:
> 
> And a bit more. The Rcmdr crash happens here:
> 
> debugging in: .Tcl.objv(.Tcl.args.objv(...))
> debug: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
> Browse[2]> objv
> [[1]]
>  wm 
> 
> [[2]]
>  protocol 
> 
> [[3]]
>  .1 
> 
> [[4]]
>  WM_DELETE_WINDOW 
> 
> [[5]]
>  R_call 0x7fedc1987ff8 
> 
> Browse[2]> 
> Abort trap: 6
> 
> and I can make the same thing happen in wish, so it is Not Our Fault:
> 
> Peter-Dalgaards-iMac:BUILD pd$ /usr/local/bin/wish
> % toplevel .1
> .1
> % wm protocol .1 WM_DELETE_WINDOW {puts hi}   
> /usr/local/bin/wish: line 2: 32765 Abort trap: 6   "$(dirname 
> $0)/../../../Library/Frameworks/Tk.framework/Versions/8.6/Resources/Wish.app/Contents/MacOS/Wish"
>  "$@"
> 
> 
> -pd
> 
>> On 17 May 2017, at 20:51 , Peter Dalgaard  wrote:
>> 
>> A few more data points:
>> 
>> I tried building Tcl/Tk 8.6.6 from the sources from sourceforge. Contrary to 
>> what it says on the package, it insists on building Tcl and Tk as 
>> frameworks, which in turn requires that R's configure needs special 
>> instructions. This works reasonably well for simple tcltk stuff (demos, the 
>> CRAN selection menu), but unfortunately, library(Rcmdr) causes an "Abort 
>> trap: 6" almost immediately. (I get a sense of deja vu about this... Did 
>> Brian try something similar years ago?)
>> 
>> It does actually seem to work to build R against the system-supplied v.8.5 
>> frameworks. However, this is Aqua-based, and the fonts are a bit weird 
>> (smooth, but way too small) and the Rcmdr menus get moved to the top bar.
>> 
>> I am pretty sure by now that all this stuff is a generic tcltk build problem 
>> and way out of John's domain. (Thanks for posting the font code, John. I 
>> hope I can get around to having a closer look at it at some point. Those 
>> .Tcl(paste()) constructs make me cringe a bit, but not all are easily 
>> eliminated.)
>> 
>> -pd
>> 
>>> On 16 May 2017, at 23:52 , peter dalgaard  wrote:
>>> 
>>> 
 On 16 May 2017, at 21:03 , peter dalgaard  wrote:
 
 I don't think the config flags for R matter in this regard. The behaviour 
 is completely paralleled by wish8.6: 
>>> 
>>> Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I 
>>> tried some of the ActiveState installs and a source build. This stuff is 
>>> making my head spin!
>>> 
>>> However, I discovered that it is possible to install R-3.4.0.pkg as usual, 
>>> and then a customized install of (say) R-3.3-branch-mavericks.pkg, omitting 
>>> everything except the Tcl/Tk stuff. That gives you R 3.4.0 and Rcmdr with 
>>> antialiased fonts.
>>> 
>>> -- 
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Office: A 4.23
>>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] R is taking too long to load

2017-05-18 Thread Hervé Pagès 

Hi,

First thing I would do is make sure you don't have any startup file
or .Rhistory in the way. If starting R with --vanilla is fast, then
that's probably the case.

H.

On 05/18/2017 12:44 PM, Christofer Bogaso wrote:

Hi,

It just started happening recently that R is taking too long to load
and entire system freezes during its loading.

Have anyone experienced something similar? Previously my R was
completely okay, however it just started recently.

Any solution for this? I have reinstalled R and now it is the latest
version 3.4.0. I am using Sierra iOS.

Appreciate for any pointer.

Thanks,

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=m7VSPPECqAsFryKwwUO-q8QiizXtbiWc-kj9qtPO2h0=cSQVI4BrFUKhUyo5ZPrQMQOwu-ZSCMWpxh5IJ8y9L6s=



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[R-SIG-Mac] R is taking too long to load

2017-05-18 Thread Christofer Bogaso 
Hi,

It just started happening recently that R is taking too long to load
and entire system freezes during its loading.

Have anyone experienced something similar? Previously my R was
completely okay, however it just started recently.

Any solution for this? I have reinstalled R and now it is the latest
version 3.4.0. I am using Sierra iOS.

Appreciate for any pointer.

Thanks,

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac