Re: [R-SIG-Mac] Permanently fix R to open Help page in html

[Christofer Bogaso]

Performed steps according to Marc's suggestions :

But not help page is not openning in Browser.

On Tue, Jul 11, 2017 at 7:28 AM, Marc Schwartz  wrote:
>
>> On Jul 10, 2017, at 5:19 PM, Duncan Murdoch  wrote:
>>
>> On 10/07/2017 5:02 PM, Christofer Bogaso wrote:
>>> Hi,
>>>
>>> I wanted R to open any Help page in html permanently.
>>>
>>> So 1st I created .Rprofile file with below code in terminal:
>>>
>>> touch ~/.Rprofile
>>>
>>> open -a Textedit ~/.Rprofile
>>>
>>>
>>> And then in the .Rprofile file, I wrote below code :
>>>
>>> options(help_type = ‘html’)
>>>
>>> However after that when I start R (from Terminal) I get below error on 
>>> loading R
>>>
>>> Error: 1:20: unexpected input
>>>
>>> 1: options(help_type = ?
>>>
>>>   ^
>>
>> Those don't look like ASCII quotes.  Use the R.app editor, not Textedit, and 
>> it won't put in funny "smart quotes".
>
>
> Alternatively, you can set TextEdit to not use "Smart quotes"  by disabling 
> them in:
>
>   Preferences -> New Document
>
> There is a checkbox under Options for Smart quotes. Uncheck it.
>
> Regards,
>
> Marc Schwartz
>
>
>>
>> Duncan Murdoch
>>
>>>
>>> [Previously saved workspace restored]
>>>
>>>

>>>
>>> Can someone please point me on where I made mistake.
>>>
>>> Thanks for your time.
>

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Re: [R-SIG-Mac] Permanently fix R to open Help page in html

[Marc Schwartz]

> On Jul 10, 2017, at 5:19 PM, Duncan Murdoch  wrote:
> 
> On 10/07/2017 5:02 PM, Christofer Bogaso wrote:
>> Hi,
>> 
>> I wanted R to open any Help page in html permanently.
>> 
>> So 1st I created .Rprofile file with below code in terminal:
>> 
>> touch ~/.Rprofile
>> 
>> open -a Textedit ~/.Rprofile
>> 
>> 
>> And then in the .Rprofile file, I wrote below code :
>> 
>> options(help_type = ‘html’)
>> 
>> However after that when I start R (from Terminal) I get below error on 
>> loading R
>> 
>> Error: 1:20: unexpected input
>> 
>> 1: options(help_type = ?
>> 
>>   ^
> 
> Those don't look like ASCII quotes.  Use the R.app editor, not Textedit, and 
> it won't put in funny "smart quotes".


Alternatively, you can set TextEdit to not use "Smart quotes"  by disabling 
them in:

  Preferences -> New Document

There is a checkbox under Options for Smart quotes. Uncheck it.

Regards,

Marc Schwartz


> 
> Duncan Murdoch
> 
>> 
>> [Previously saved workspace restored]
>> 
>> 
>>> 
>> 
>> Can someone please point me on where I made mistake.
>> 
>> Thanks for your time.

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Re: [R-SIG-Mac] Permanently fix R to open Help page in html

[Duncan Murdoch]

On 10/07/2017 5:02 PM, Christofer Bogaso wrote:

Hi,

I wanted R to open any Help page in html permanently.

So 1st I created .Rprofile file with below code in terminal:

touch ~/.Rprofile

open -a Textedit ~/.Rprofile


And then in the .Rprofile file, I wrote below code :

options(help_type = ‘html’)

However after that when I start R (from Terminal) I get below error on loading R

Error: 1:20: unexpected input

1: options(help_type = ?

   ^


Those don't look like ASCII quotes.  Use the R.app editor, not Textedit, 
and it won't put in funny "smart quotes".


Duncan Murdoch



[Previously saved workspace restored]






Can someone please point me on where I made mistake.

Thanks for your time.

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Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[peter dalgaard]

Thanks Don,

Can you perhaps make that a little closer to being reproducible for people who 
might want to try it on newer hardware? (packages, location of input file).

(And by the way, xterm? What did Terminal.app do to you?)

This, along with a thread from 2014 that Google dug up, strongly suggests that 
quartz() is the culprit. It might not be our fault though, as it seems that 
"matplotlib" (Python) has had similar problems. In the latter case, it seems to 
have worked to "switch to the agg backend", whatever that means. (AGG is 
AntiGrain Geometry, which is apparently so stable that it hasn't changed since 
2006. Its author died suddenly in 2013, it seems.)

-pd


> On 10 Jul 2017, at 19:59 , MacQueen, Don  wrote:
> 
> For what it's worth, here is my experience on a late 2013 Mac Pro.
> (I normally run R from an xterm shell within an X Windows context)
> 
> The best performance for displaying the image on-screen uses cairographics 
> and Polypath. It's the only one fast enough to be satisfactory for 
> interactive use, in my opinion [though x11(type='Xlib') could be tolerated]. 
> pdf() is even faster.
> 
> -Don
> 
>> nsw <- readOGR('data','SA3_2016_AUST', stringsAsFactors=FALSE)
> OGR data source with driver: ESRI Shapefile 
> Source: "data", layer: "SA3_2016_AUST"
> with 358 features
> It has 9 fields
> Warning message:
> In readOGR("data", "SA3_2016_AUST", stringsAsFactors = FALSE) :
>  Dropping null geometries: 93, 94, 161, 162, 245, 246, 275, 276, 311, 312, 
> 328, 329, 339, 340, 351, 352, 357, 358
> 
> ## The "original" X windows device (does not support Polypath)
>> x11(type='Xlib')
>> system.time( plot(nsw, usePolypath=FALSE) )
>   user  system elapsed 
>  0.882   0.512  99.618 
> 
> ## a more "modern" version of the X windows device
>> x11(type='cairo')
>> system.time( plot(nsw, usePolypath=FALSE) )
>   user  system elapsed 
>  2.233   5.007  68.410 
> 
> 
> ## Polypath gives large improvement
>> x11(type='cairo')
>> system.time( plot(nsw, usePolypath=TRUE) )
>   user  system elapsed 
>  1.772   0.461   5.785 
> 
> ## Same R session as above, but using the quartz device
>> quartz()
>> system.time( plot(nsw) )
>user   system  elapsed 
> 1135.6061.556 1137.445 
> 
>> pdf('test.pdf')
>> system.time( plot(nsw) )
>   user  system elapsed 
>  2.029   0.200   2.248 
>> dev.off()
> 
> 
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> other attached packages:
> [1] rgdal_1.2-8 sp_1.2-5   
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.1  tools_3.4.1 grid_3.4.1  lattice_0.20-35
> 
> 
> -- 
> Don MacQueen
> 
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> 
> 
> On 7/10/17, 4:40 AM, "R-SIG-Mac on behalf of Ashley Betts" 
>  ashley.be...@saltbushsoftware.com> wrote:
> 
>Hi Peter, outputting to PDF made a huge difference! It ran for only 15 
> seconds and there was no trailing unresponsive prompt. The PDF ended up being 
> around 2Mb and opened and displayed almost immediately in Preview.
> 
>I did watch the system when I was outputting to the quartz device last 
> time and the process was steadily consuming a single core. When I watched it 
> on the Windows machines I saw it use most of the cores but not to capacity. 
> After seeing this I read up on multithreading libraries on Mac and finally 
> setup R to use the Accelerate library. I’ve verified this library is being 
> loaded by sampling the process. It make zero difference however and the 
> print(plt) still only consumes a single core.
> 
>Regards,
> 
>Ashley
> 
>> On 10 Jul 2017, at 6:21 PM, peter dalgaard  wrote:
>> 
>> Pretty clear that the process is getting stuck in Apple-graphics land, then. 
>> This could be inefficiency of the device driver, but also just ... Apple. 
>> Could you try running the same thing to a PDF (AFAIR, just open the device 
>> with pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would be 
>> good to know if this is fast, and also whether viewing the resulting PDF in 
>> Preview is slow (in which case it is Not Our Problem).
>> 
>> Also, does running the Activity Monitor give any clues? Like, perhaps you 
>> are running out of memory. 
>> 
>> -pd
>> 
>>> On 10 Jul 2017, at 00:05 , Ashley Betts  
>>> wrote:
>>> 
>>> Oh yes, sorry about that. I originally had screen shots attached showing 
>>> the timings but the email ended up being too large. All of the time is in 

[R-SIG-Mac] Permanently fix R to open Help page in html

[Christofer Bogaso]

Hi,

I wanted R to open any Help page in html permanently.

So 1st I created .Rprofile file with below code in terminal:

touch ~/.Rprofile

open -a Textedit ~/.Rprofile


And then in the .Rprofile file, I wrote below code :

options(help_type = ‘html’)

However after that when I start R (from Terminal) I get below error on loading R

Error: 1:20: unexpected input

1: options(help_type = ?

   ^

[Previously saved workspace restored]


>

Can someone please point me on where I made mistake.

Thanks for your time.

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Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[MacQueen, Don]

For what it's worth, here is my experience on a late 2013 Mac Pro.
(I normally run R from an xterm shell within an X Windows context)

The best performance for displaying the image on-screen uses cairographics and 
Polypath. It's the only one fast enough to be satisfactory for interactive use, 
in my opinion [though x11(type='Xlib') could be tolerated]. pdf() is even 
faster.

-Don

> nsw <- readOGR('data','SA3_2016_AUST', stringsAsFactors=FALSE)
OGR data source with driver: ESRI Shapefile 
Source: "data", layer: "SA3_2016_AUST"
with 358 features
It has 9 fields
Warning message:
In readOGR("data", "SA3_2016_AUST", stringsAsFactors = FALSE) :
  Dropping null geometries: 93, 94, 161, 162, 245, 246, 275, 276, 311, 312, 
328, 329, 339, 340, 351, 352, 357, 358

## The "original" X windows device (does not support Polypath)
> x11(type='Xlib')
> system.time( plot(nsw, usePolypath=FALSE) )
   user  system elapsed 
  0.882   0.512  99.618 

## a more "modern" version of the X windows device
> x11(type='cairo')
> system.time( plot(nsw, usePolypath=FALSE) )
   user  system elapsed 
  2.233   5.007  68.410 


## Polypath gives large improvement
> x11(type='cairo')
> system.time( plot(nsw, usePolypath=TRUE) )
   user  system elapsed 
  1.772   0.461   5.785 

## Same R session as above, but using the quartz device
> quartz()
> system.time( plot(nsw) )
user   system  elapsed 
1135.6061.556 1137.445 

> pdf('test.pdf')
> system.time( plot(nsw) )
   user  system elapsed 
  2.029   0.200   2.248 
> dev.off()


> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] rgdal_1.2-8 sp_1.2-5   

loaded via a namespace (and not attached):
[1] compiler_3.4.1  tools_3.4.1 grid_3.4.1  lattice_0.20-35


-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062


On 7/10/17, 4:40 AM, "R-SIG-Mac on behalf of Ashley Betts" 
 wrote:

Hi Peter, outputting to PDF made a huge difference! It ran for only 15 
seconds and there was no trailing unresponsive prompt. The PDF ended up being 
around 2Mb and opened and displayed almost immediately in Preview.

I did watch the system when I was outputting to the quartz device last time 
and the process was steadily consuming a single core. When I watched it on the 
Windows machines I saw it use most of the cores but not to capacity. After 
seeing this I read up on multithreading libraries on Mac and finally setup R to 
use the Accelerate library. I’ve verified this library is being loaded by 
sampling the process. It make zero difference however and the print(plt) still 
only consumes a single core.

Regards,

Ashley

> On 10 Jul 2017, at 6:21 PM, peter dalgaard  wrote:
> 
> Pretty clear that the process is getting stuck in Apple-graphics land, 
then. This could be inefficiency of the device driver, but also just ... Apple. 
Could you try running the same thing to a PDF (AFAIR, just open the device with 
pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would be good to 
know if this is fast, and also whether viewing the resulting PDF in Preview is 
slow (in which case it is Not Our Problem).
> 
> Also, does running the Activity Monitor give any clues? Like, perhaps you 
are running out of memory. 
> 
> -pd
> 
>> On 10 Jul 2017, at 00:05 , Ashley Betts 
 wrote:
>> 
>> Oh yes, sorry about that. I originally had screen shots attached showing 
the timings but the email ended up being too large. All of the time is in the 
print. Nearly all other commands run within seconds. Oddly, after approximately 
half hour the prompt returns which I get one Sys.time() to execute but then the 
prompt hangs when I enter the second Sys.time() for the best part of an hour 
and half.
>> 
>> I tried to profile but that failed. I tried sampling the process a 
number of times and every time I sampled execution was buried in 
CGContextDrawPath
>> GEPolygon  (in libR.dylib) + 127  [0x101cb54df]  engine.c:0
>>+ 

  2502 clipPolygon  (in libR.dylib) + 571  
[0x101cb574b]  engine.c:1080
>>+ 

  

Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[Ashley Betts]

Hi Peter, outputting to PDF made a huge difference! It ran for only 15 seconds 
and there was no trailing unresponsive prompt. The PDF ended up being around 
2Mb and opened and displayed almost immediately in Preview.

I did watch the system when I was outputting to the quartz device last time and 
the process was steadily consuming a single core. When I watched it on the 
Windows machines I saw it use most of the cores but not to capacity. After 
seeing this I read up on multithreading libraries on Mac and finally setup R to 
use the Accelerate library. I’ve verified this library is being loaded by 
sampling the process. It make zero difference however and the print(plt) still 
only consumes a single core.

Regards,

Ashley

> On 10 Jul 2017, at 6:21 PM, peter dalgaard  wrote:
> 
> Pretty clear that the process is getting stuck in Apple-graphics land, then. 
> This could be inefficiency of the device driver, but also just ... Apple. 
> Could you try running the same thing to a PDF (AFAIR, just open the device 
> with pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would be 
> good to know if this is fast, and also whether viewing the resulting PDF in 
> Preview is slow (in which case it is Not Our Problem).
> 
> Also, does running the Activity Monitor give any clues? Like, perhaps you are 
> running out of memory. 
> 
> -pd
> 
>> On 10 Jul 2017, at 00:05 , Ashley Betts  
>> wrote:
>> 
>> Oh yes, sorry about that. I originally had screen shots attached showing the 
>> timings but the email ended up being too large. All of the time is in the 
>> print. Nearly all other commands run within seconds. Oddly, after 
>> approximately half hour the prompt returns which I get one Sys.time() to 
>> execute but then the prompt hangs when I enter the second Sys.time() for the 
>> best part of an hour and half.
>> 
>> I tried to profile but that failed. I tried sampling the process a number of 
>> times and every time I sampled execution was buried in CGContextDrawPath
>> GEPolygon  (in libR.dylib) + 127  [0x101cb54df]  engine.c:0
>>+ 
>>  
>>  2502 clipPolygon  (in libR.dylib) + 571  
>> [0x101cb574b]  engine.c:1080
>>+ 
>>  
>>2502 CGContextDrawPath  (in CoreGraphics) + 181  
>> [0x7fff8d433e59]
>>+ 
>>  
>>  2502 ripc_DrawPath  (in libRIP.A.dylib) + 417  
>> [0x7fff8ec631a3]
>>+ 
>>  
>>2502 ripc_Render  (in libRIP.A.dylib) + 380  
>> [0x7fff8ec4f750]
>>+ 
>>  
>>  2502 RIPRenderCoverage  (in libRIP.A.dylib) 
>> + 1844  [0x7fff8ec4ff84]
>> 
>> 
>> Regards,
>> 
>> Ashley
>> 
>> 
>> 
>> 
>>> On 9 Jul 2017, at 9:35 PM, peter dalgaard  wrote:
>>> 
>>> Hmm, you're not telling us much about where the time is being spent. Some 
>>> more detailed timing using system.time() could be useful.
>>> 
>>> If it is a graphics device issue, I would expect almost everything in the 
>>> final print(plt). You could try switching graphics device, e.g. to pdf() 
>>> which should be pretty much the same on all platforms. You might also try 
>>> creating PDF files on one machine and displaying on the other. 
>>> 
>>> -pd 
>>> 
 On 9 Jul 2017, at 12:45 , Ashley Betts  
 wrote:
 
 Hi All,
 I'm quite new to R and recently started investigating the geospatial 
 plotting capabilities of R via ggplot2. I started by using some of the 
 publicly available datasets from the Australian Bureau of Statistics. 
 Plotting the Level 3 Statistical Area boundaries took over 2 hours on my 
 2012 Mac Book Pro. As there were over 3M rows in the fortify’ed data frame 
 I initially thought this was just how long it must take. I then ran the 
 exact same script on my work laptop which is similarly spec’ed and it ran 
 in approximately 30 seconds. This now has me extremely disappointed in the 
 performance on the Mac which is where I use R the most. I changed my BLAS 
 library to the Accelerate library in a whim that this might make a 
 difference. It did not. Whilst I primarily use RStudio I also 

Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[peter dalgaard]

Pretty clear that the process is getting stuck in Apple-graphics land, then. 
This could be inefficiency of the device driver, but also just ... Apple. Could 
you try running the same thing to a PDF (AFAIR, just open the device with 
pdf(file="myplot.pdf"), then print(plt), then dev.off()). It would be good to 
know if this is fast, and also whether viewing the resulting PDF in Preview is 
slow (in which case it is Not Our Problem).

Also, does running the Activity Monitor give any clues? Like, perhaps you are 
running out of memory. 

-pd

> On 10 Jul 2017, at 00:05 , Ashley Betts  
> wrote:
> 
> Oh yes, sorry about that. I originally had screen shots attached showing the 
> timings but the email ended up being too large. All of the time is in the 
> print. Nearly all other commands run within seconds. Oddly, after 
> approximately half hour the prompt returns which I get one Sys.time() to 
> execute but then the prompt hangs when I enter the second Sys.time() for the 
> best part of an hour and half.
> 
> I tried to profile but that failed. I tried sampling the process a number of 
> times and every time I sampled execution was buried in CGContextDrawPath
> GEPolygon  (in libR.dylib) + 127  [0x101cb54df]  engine.c:0
> + 
>   
> 2502 clipPolygon  (in libR.dylib) + 571  
> [0x101cb574b]  engine.c:1080
> + 
>   
>   2502 CGContextDrawPath  (in CoreGraphics) + 181  
> [0x7fff8d433e59]
> + 
>   
> 2502 ripc_DrawPath  (in libRIP.A.dylib) + 417  
> [0x7fff8ec631a3]
> + 
>   
>   2502 ripc_Render  (in libRIP.A.dylib) + 380  
> [0x7fff8ec4f750]
> + 
>   
> 2502 RIPRenderCoverage  (in libRIP.A.dylib) + 
> 1844  [0x7fff8ec4ff84]
> 
> 
> Regards,
> 
> Ashley
> 
> 
> 
> 
>> On 9 Jul 2017, at 9:35 PM, peter dalgaard  wrote:
>> 
>> Hmm, you're not telling us much about where the time is being spent. Some 
>> more detailed timing using system.time() could be useful.
>> 
>> If it is a graphics device issue, I would expect almost everything in the 
>> final print(plt). You could try switching graphics device, e.g. to pdf() 
>> which should be pretty much the same on all platforms. You might also try 
>> creating PDF files on one machine and displaying on the other. 
>> 
>> -pd 
>> 
>>> On 9 Jul 2017, at 12:45 , Ashley Betts  
>>> wrote:
>>> 
>>> Hi All,
>>>  I'm quite new to R and recently started investigating the geospatial 
>>> plotting capabilities of R via ggplot2. I started by using some of the 
>>> publicly available datasets from the Australian Bureau of Statistics. 
>>> Plotting the Level 3 Statistical Area boundaries took over 2 hours on my 
>>> 2012 Mac Book Pro. As there were over 3M rows in the fortify’ed data frame 
>>> I initially thought this was just how long it must take. I then ran the 
>>> exact same script on my work laptop which is similarly spec’ed and it ran 
>>> in approximately 30 seconds. This now has me extremely disappointed in the 
>>> performance on the Mac which is where I use R the most. I changed my BLAS 
>>> library to the Accelerate library in a whim that this might make a 
>>> difference. It did not. Whilst I primarily use RStudio I also ran the same 
>>> script in R.app and if there was any improvement it was not noticeable. I 
>>> did notice in the Windows run that it seemed to use multiple cores (which 
>>> is what made me investigate the BLAS change) whilst the Mac seems to stay 
>>> bound to a single core. My initial thoughts were that it must be something 
>>> to do with ggplot but after sampling the rsession process a number of times 
>>> (see attached Sample of rsession.txt) it appears to be spending most of 
>>> it’s time in CGContextDrawPath in Apples CoreGraphics so I assume it is a 
>>> Graphics related issue. I’m running R 3.4 on my Mac and 3.3.2 on the 
>>> Windows machine. I’ve attached the script and have screen dumps of the 
>>> process sample text and a number of others which I can supply if helpful in 
>>> analysing the issue. Could someone possibly let me know if this is PEBCAK 
>>> issue or an