Re: [R-SIG-Mac] Blank help window

[Marc Schwartz via R-SIG-Mac]

Ok, strange. I figured that there was some conflict/corruption in place with 
R.app that was not immediately clear.

Peter raised the possibility of a firewall issue, but I am curious as to why 
that would affect the use of help in R.app, but not via other environments, 
like the Mac Terminal app. Theoretically, it should be via similar protocols 
and ports in each setting, unless there is something specific that R.app does 
to the OS environment when running, that would inhibit the dynamic generation 
of the HTML pages. But if so, why just for the two of you?

It seems like the server is starting up ok, but the help pages are not being 
generated by Rd2HTML() in R.app.

However, it sparked a thought in my head, which is always risky, and that is, 
do you guys have any anti-virus/malware software running? I may be grasping at 
straws here, but such applications have been known to cause all kinds of flaky 
behaviors, that are not immediately evident nor associated with them.

One other thought. When you get the blank HTML page, presumably white 
background, drag the cursor around the page to try to highlight text, as if the 
text was also white, thus not showing against the white background. Another 
straw

Regards,

Marc


> On Oct 17, 2018, at 8:06 PM, Ben Tupper  wrote:
> 
> Darn.  No joy from a complete clean-and-reinstall with a reinstall of XQuartz 
> as Marc suggested.  It is still a blank help page.
> 
> Below is everything I can think of from the new session.
> 
> 
> R version 3.5.1 (2018-07-02) -- "Feather Spray"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> 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.
> 
> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
> 
>> ?data.frame
> starting httpd help server ... done
>> sessionInfo()
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.5.1 tools_3.5.1   
> 
>> capabilities()
>   jpeg pngtiff   tcltk X11aqua
> http/ftp sockets  libxmlfifo 
>   TRUETRUETRUETRUETRUETRUE
> TRUETRUETRUETRUE 
> cledit   iconv NLS profmem   cairo ICU 
> long.double libcurl 
>   TRUETRUETRUETRUETRUETRUE
> TRUETRUE 
> 
> 
> 
> And from shell...
> 
> ben@gale ~ $ ll /usr | grep X11
> lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11 -> /opt/X11
> lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11R6 -> /opt/X11
> 
> 
> 
> 
> 
> 
>> On Oct 17, 2018, at 7:20 PM, Ben Tupper  wrote:
>> 
>> Ahoy!
>> 
>>> ?data.frame
>> starting httpd help server ... done
>>> (tools::startDynamicHelp(NA))
>> [1] 31048
>> 
>> Connecting to http://127.0.0.1:31048/NEWS  
>> brings up NEWS as expected.
>> 
>> If I understand the MacOS preferences the firewall is OFF.  
>> 
>> I'll try the clean-then-reinstall that Marc suggests and report back.
>> 
>> Ben
>> 
>>> On Oct 17, 2018, at 5:42 PM, Peter Dalgaard >> > wrote:
>>> 
>>> Hmm, when trying from R.app, do you see the following?
>>> 
 ?data.frame
>>> starting httpd help server ... done
 (tools::startDynamicHelp(NA))
>>> [1] 26163
>>> 
>>> (The last bit is the port number of the HTTP server and will differ between 
>>> invokations. I think you get 0 if the server isn't running and -1 if it 
>>> failed to start.)
>>> 
>>> If the server is there, you could try connecting from your favourite 
>>> browser at (say) http://127.0.0.1:26163/NEWS 
>>> 
>>> If the server is there, but you cannot talk to it, then I suspect that a 
>>> firewall is getting in the way.
>>> 
>>> -pd
>>> 
>>> 
 On 17 Oct 2018, at 20:53 , Ben Tupper >>> > wrote:
 
 Hi,
 
 The behavior I see is identical to what you describe 

Re: [R-SIG-Mac] Blank help window

[Duncan Murdoch]

On 17/10/2018 8:06 PM, Ben Tupper wrote:

Darn.  No joy from a complete clean-and-reinstall with a reinstall of XQuartz 
as Marc suggested.  It is still a blank help page.

Below is everything I can think of from the new session.



You can try

debug(utils:::print.help_files_with_topic)

to see what is going on on your system.  On mine (High Sierra with help 
working), it retrieves as.environment("tools:RGUI")$aqua.browser which 
looks like


function (x, ...)
{
x <- gsub("http://127.0.0.1;, "http://localhost;, x, fixed = TRUE)
.Call("aqua.custom.print", "help-files", x)
invisible(x)
}


If I debug this and try browseURL(x) after x is modified, I see help in 
my usual browser.  If I continue to the .Call(), it appears in the usual 
R.app browser.


Do you see something similar?

Duncan Murdoch



R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

[R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]


?data.frame

starting httpd help server ... done

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1


capabilities()

jpeg pngtiff   tcltk X11aqua
http/ftp sockets  libxmlfifo
TRUETRUETRUETRUETRUETRUE
TRUETRUETRUETRUE
  cledit   iconv NLS profmem   cairo ICU 
long.double libcurl
TRUETRUETRUETRUETRUETRUE
TRUETRUE



And from shell...

ben@gale ~ $ ll /usr | grep X11
lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11 -> /opt/X11
lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11R6 -> /opt/X11







On Oct 17, 2018, at 7:20 PM, Ben Tupper  wrote:

Ahoy!


?data.frame

starting httpd help server ... done

(tools::startDynamicHelp(NA))

[1] 31048

Connecting to http://127.0.0.1:31048/NEWS  brings 
up NEWS as expected.

If I understand the MacOS preferences the firewall is OFF.

I'll try the clean-then-reinstall that Marc suggests and report back.

Ben


On Oct 17, 2018, at 5:42 PM, Peter Dalgaard mailto:pda...@gmail.com>> wrote:

Hmm, when trying from R.app, do you see the following?


?data.frame

starting httpd help server ... done

(tools::startDynamicHelp(NA))

[1] 26163

(The last bit is the port number of the HTTP server and will differ between 
invokations. I think you get 0 if the server isn't running and -1 if it failed 
to start.)

If the server is there, you could try connecting from your favourite browser at (say) 
http://127.0.0.1:26163/NEWS 

If the server is there, but you cannot talk to it, then I suspect that a 
firewall is getting in the way.

-pd



On 17 Oct 2018, at 20:53 , Ben Tupper mailto:btup...@bigelow.org>> wrote:

Hi,

The behavior I see is identical to what you describe regardless of the function 
(I used ?data.frame as an example).  The help commands


?


and


help("something")


both bring up a blank help window.  All of the other steps you have taken yield 
the same result on my system.


R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

[R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]


sessionInfo()

Re: [R-SIG-Mac] Blank help window

[Ben Tupper]

Darn.  No joy from a complete clean-and-reinstall with a reinstall of XQuartz 
as Marc suggested.  It is still a blank help page.

Below is everything I can think of from the new session.


R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

[R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]

> ?data.frame
starting httpd help server ... done
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1   

> capabilities()
   jpeg pngtiff   tcltk X11aqua
http/ftp sockets  libxmlfifo 
   TRUETRUETRUETRUETRUETRUE
TRUETRUETRUETRUE 
 cledit   iconv NLS profmem   cairo ICU 
long.double libcurl 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 



And from shell...

ben@gale ~ $ ll /usr | grep X11
lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11 -> /opt/X11
lrwxr-xr-x 1 root  wheel 8B Oct 17 19:35 X11R6 -> /opt/X11






> On Oct 17, 2018, at 7:20 PM, Ben Tupper  wrote:
> 
> Ahoy!
> 
> > ?data.frame
> starting httpd help server ... done
> > (tools::startDynamicHelp(NA))
> [1] 31048
> 
> Connecting to http://127.0.0.1:31048/NEWS  
> brings up NEWS as expected.
> 
> If I understand the MacOS preferences the firewall is OFF.  
> 
> I'll try the clean-then-reinstall that Marc suggests and report back.
> 
> Ben
> 
>> On Oct 17, 2018, at 5:42 PM, Peter Dalgaard > > wrote:
>> 
>> Hmm, when trying from R.app, do you see the following?
>> 
>>> ?data.frame
>> starting httpd help server ... done
>>> (tools::startDynamicHelp(NA))
>> [1] 26163
>> 
>> (The last bit is the port number of the HTTP server and will differ between 
>> invokations. I think you get 0 if the server isn't running and -1 if it 
>> failed to start.)
>> 
>> If the server is there, you could try connecting from your favourite browser 
>> at (say) http://127.0.0.1:26163/NEWS 
>> 
>> If the server is there, but you cannot talk to it, then I suspect that a 
>> firewall is getting in the way.
>> 
>> -pd
>> 
>> 
>>> On 17 Oct 2018, at 20:53 , Ben Tupper >> > wrote:
>>> 
>>> Hi,
>>> 
>>> The behavior I see is identical to what you describe regardless of the 
>>> function (I used ?data.frame as an example).  The help commands
>>> 
 ?
>>> 
>>> and
>>> 
 help("something")
>>> 
>>> both bring up a blank help window.  All of the other steps you have taken 
>>> yield the same result on my system.
>>> 
>>> 
>>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>>> Copyright (C) 2018 The R Foundation for Statistical Computing
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> 
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>> 
>>>  Natural language support but running in an English locale
>>> 
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>> 
>>> 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.
>>> 
>>> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
>>> 
 sessionInfo()
>>> R version 3.5.1 (2018-07-02)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Sierra 10.12.6
>>> 
>>> Matrix products: default
>>> BLAS: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] 

Re: [R-SIG-Mac] Blank help window

[zListserv]

> On 2018-10 -17, at 17:42, Peter Dalgaard  wrote:
> 
> Hmm, when trying from R.app, do you see the following?
> 
>> ?data.frame
> starting httpd help server ... done
>> (tools::startDynamicHelp(NA))
> [1] 26163


R> ?mean
starting httpd help server ... done
R> (tools::startDynamicHelp(NA))
[1] 10116


http://127.0.0.1:10116/NEWS yields the “R News” page in my browser.

> 
> (The last bit is the port number of the HTTP server and will differ between 
> invokations. I think you get 0 if the server isn't running and -1 if it 
> failed to start.)
> 
> If the server is there, you could try connecting from your favourite browser 
> at (say) http://127.0.0.1:26163/NEWS
> 
> If the server is there, but you cannot talk to it, then I suspect that a 
> firewall is getting in the way.
> 
> -pd
> 
> 
>> On 17 Oct 2018, at 20:53 , Ben Tupper  wrote:
>> 
>> Hi,
>> 
>> The behavior I see is identical to what you describe regardless of the 
>> function (I used ?data.frame as an example).  The help commands
>> 
>>> ?
>> 
>> and
>> 
>>> help("something")
>> 
>> both bring up a blank help window.  All of the other steps you have taken 
>> yield the same result on my system.
>> 
>> 
>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> 
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> 
>>  Natural language support but running in an English locale
>> 
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>> 
>> 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.
>> 
>> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
>> 
>>> sessionInfo()
>> R version 3.5.1 (2018-07-02)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Sierra 10.12.6
>> 
>> Matrix products: default
>> BLAS: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base 
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.5.1
>> 
>> 
>>> capabilities()
>>   jpeg pngtiff   tcltk X11aqua
>> http/ftp sockets  libxmlfifo 
>>   TRUETRUETRUETRUETRUETRUE   
>>  TRUETRUETRUETRUE 
>> cledit   iconv NLS profmem   cairo ICU 
>> long.double libcurl 
>>   TRUETRUETRUETRUETRUETRUE   
>>  TRUETRUE 
>> 
>> 
>> 
>> 
>> 
>>> On Oct 17, 2018, at 1:48 PM, zListserv  wrote:
>>> 
>>> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
>>> as mine.  Ben has problems with ?data.frame.  My issue is a blank help 
>>> window when typing ?mean (or any other function).
>>> 
>>> Peter suggested checking capabilities().  They are all TRUE.
>>> 
>>> You both suggested checking configuration files.  Removing .Rprofile, 
>>> .Rdata, and .Rapp.history made no difference.
>>> 
>>> Simon suggested:
>>> 
 On 2018-10 -17, at 08:57, Simon Urbanek  
 wrote:
 
 Few things to try:
 
 - do you see anything in the error console?
>>> 
>>> Nothing noticeable in the error console, though I’m inexpert at reading it.
 
 - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
 etc.
>>> 
>>> No effect
>>> 
 
 - try running R from the console and starting the html help by hand to see 
 if it works at all:
 tools::startDynamicHelp()
 help.start(browser="/usr/bin/open”)
 
>>> 
>>> Help works when running R from console
>>> 
 - if that works try the same from the R.app gui *before* using help:
 help.start(browser="/usr/bin/open”)
>>> 
>>> No effect in R (except it opens my default browser).
>>> 
 
 Cheers,
 Simon
 
 
> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things 
> that don't transfer such as applications installed by Brew which I 
> installed manually.
> 
> An issue with R arose I can't solve.  The help systen opens with a blank 
> window.
> 
> Help works when I run R from the terminal so I know the files are 
> installed.  Help works fine on the Macintosh I used a the 

Re: [R-SIG-Mac] Blank help window

[Ben Tupper]

Ahoy!

> ?data.frame
starting httpd help server ... done
> (tools::startDynamicHelp(NA))
[1] 31048

Connecting to http://127.0.0.1:31048/NEWS  brings 
up NEWS as expected.

If I understand the MacOS preferences the firewall is OFF.  

I'll try the clean-then-reinstall that Marc suggests and report back.

Ben

> On Oct 17, 2018, at 5:42 PM, Peter Dalgaard  wrote:
> 
> Hmm, when trying from R.app, do you see the following?
> 
>> ?data.frame
> starting httpd help server ... done
>> (tools::startDynamicHelp(NA))
> [1] 26163
> 
> (The last bit is the port number of the HTTP server and will differ between 
> invokations. I think you get 0 if the server isn't running and -1 if it 
> failed to start.)
> 
> If the server is there, you could try connecting from your favourite browser 
> at (say) http://127.0.0.1:26163/NEWS
> 
> If the server is there, but you cannot talk to it, then I suspect that a 
> firewall is getting in the way.
> 
> -pd
> 
> 
>> On 17 Oct 2018, at 20:53 , Ben Tupper  wrote:
>> 
>> Hi,
>> 
>> The behavior I see is identical to what you describe regardless of the 
>> function (I used ?data.frame as an example).  The help commands
>> 
>>> ?
>> 
>> and
>> 
>>> help("something")
>> 
>> both bring up a blank help window.  All of the other steps you have taken 
>> yield the same result on my system.
>> 
>> 
>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> 
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> 
>>  Natural language support but running in an English locale
>> 
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>> 
>> 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.
>> 
>> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
>> 
>>> sessionInfo()
>> R version 3.5.1 (2018-07-02)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Sierra 10.12.6
>> 
>> Matrix products: default
>> BLAS: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base 
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.5.1
>> 
>> 
>>> capabilities()
>>   jpeg pngtiff   tcltk X11aqua
>> http/ftp sockets  libxmlfifo 
>>   TRUETRUETRUETRUETRUETRUE   
>>  TRUETRUETRUETRUE 
>> cledit   iconv NLS profmem   cairo ICU 
>> long.double libcurl 
>>   TRUETRUETRUETRUETRUETRUE   
>>  TRUETRUE 
>> 
>> 
>> 
>> 
>> 
>>> On Oct 17, 2018, at 1:48 PM, zListserv  wrote:
>>> 
>>> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
>>> as mine.  Ben has problems with ?data.frame.  My issue is a blank help 
>>> window when typing ?mean (or any other function).
>>> 
>>> Peter suggested checking capabilities().  They are all TRUE.
>>> 
>>> You both suggested checking configuration files.  Removing .Rprofile, 
>>> .Rdata, and .Rapp.history made no difference.
>>> 
>>> Simon suggested:
>>> 
 On 2018-10 -17, at 08:57, Simon Urbanek  
 wrote:
 
 Few things to try:
 
 - do you see anything in the error console?
>>> 
>>> Nothing noticeable in the error console, though I’m inexpert at reading it.
 
 - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
 etc.
>>> 
>>> No effect
>>> 
 
 - try running R from the console and starting the html help by hand to see 
 if it works at all:
 tools::startDynamicHelp()
 help.start(browser="/usr/bin/open”)
 
>>> 
>>> Help works when running R from console
>>> 
 - if that works try the same from the R.app gui *before* using help:
 help.start(browser="/usr/bin/open”)
>>> 
>>> No effect in R (except it opens my default browser).
>>> 
 
 Cheers,
 Simon
 
 
> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things 
> that don't transfer such as applications installed by Brew which I 
> installed manually.
> 
> An issue with R arose I can't solve.  The help systen 

Re: [R-SIG-Mac] Blank help window

[Peter Dalgaard]

Hmm, when trying from R.app, do you see the following?

> ?data.frame
starting httpd help server ... done
> (tools::startDynamicHelp(NA))
[1] 26163

(The last bit is the port number of the HTTP server and will differ between 
invokations. I think you get 0 if the server isn't running and -1 if it failed 
to start.)

If the server is there, you could try connecting from your favourite browser at 
(say) http://127.0.0.1:26163/NEWS

If the server is there, but you cannot talk to it, then I suspect that a 
firewall is getting in the way.

-pd


> On 17 Oct 2018, at 20:53 , Ben Tupper  wrote:
> 
> Hi,
> 
> The behavior I see is identical to what you describe regardless of the 
> function (I used ?data.frame as an example).  The help commands
> 
> > ?
> 
> and
> 
> > help("something")
> 
> both bring up a blank help window.  All of the other steps you have taken 
> yield the same result on my system.
> 
> 
> R version 3.5.1 (2018-07-02) -- "Feather Spray"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> 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.
> 
> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
> 
> > sessionInfo()
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.5.1
> 
> 
> > capabilities()
>jpeg pngtiff   tcltk X11aqua
> http/ftp sockets  libxmlfifo 
>TRUETRUETRUETRUETRUETRUE   
>  TRUETRUETRUETRUE 
>  cledit   iconv NLS profmem   cairo ICU 
> long.double libcurl 
>TRUETRUETRUETRUETRUETRUE   
>  TRUETRUE 
> 
> 
> 
> 
> 
>> On Oct 17, 2018, at 1:48 PM, zListserv  wrote:
>> 
>> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
>> as mine.  Ben has problems with ?data.frame.  My issue is a blank help 
>> window when typing ?mean (or any other function).
>> 
>> Peter suggested checking capabilities().  They are all TRUE.
>> 
>> You both suggested checking configuration files.  Removing .Rprofile, 
>> .Rdata, and .Rapp.history made no difference.
>> 
>> Simon suggested:
>> 
>>> On 2018-10 -17, at 08:57, Simon Urbanek  wrote:
>>> 
>>> Few things to try:
>>> 
>>> - do you see anything in the error console?
>> 
>> Nothing noticeable in the error console, though I’m inexpert at reading it.
>>> 
>>> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
>>> etc.
>> 
>> No effect
>> 
>>> 
>>> - try running R from the console and starting the html help by hand to see 
>>> if it works at all:
>>> tools::startDynamicHelp()
>>> help.start(browser="/usr/bin/open”)
>>> 
>> 
>> Help works when running R from console
>> 
>>> - if that works try the same from the R.app gui *before* using help:
>>> help.start(browser="/usr/bin/open”)
>> 
>> No effect in R (except it opens my default browser).
>> 
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
 On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
 
 
 I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
 Assistant.  Everything went well, though there are always a few things 
 that don't transfer such as applications installed by Brew which I 
 installed manually.
 
 An issue with R arose I can't solve.  The help systen opens with a blank 
 window.
 
 Help works when I run R from the terminal so I know the files are 
 installed.  Help works fine on the Macintosh I used a the source for the 
 migration so it isn't a problem I inherited.  Re-installing R (see 
 sessionInfo below) didn't solve the problem.
 
 Anyone have any suggestions how I can get help to work?
 
 R version 3.5.1 (2018-07-02)
 Platform: x86_64-apple-darwin15.6.0 (64-bit)
 Running under: macOS High Sierra 10.13.6
 
 Matrix products: default
 

Re: [R-SIG-Mac] Blank help window

[Ben Tupper]

Hi,

The behavior I see is identical to what you describe regardless of the function 
(I used ?data.frame as an example).  The help commands

> ?

and

> help("something")

both bring up a blank help window.  All of the other steps you have taken yield 
the same result on my system.


R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.

[R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1


> capabilities()
   jpeg pngtiff   tcltk X11aqua
http/ftp sockets  libxmlfifo 
   TRUETRUETRUETRUETRUETRUE
TRUETRUETRUETRUE 
 cledit   iconv NLS profmem   cairo ICU 
long.double libcurl 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 





> On Oct 17, 2018, at 1:48 PM, zListserv  wrote:
> 
> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
> as mine.  Ben has problems with ?data.frame.  My issue is a blank help window 
> when typing ?mean (or any other function).
> 
> Peter suggested checking capabilities().  They are all TRUE.
> 
> You both suggested checking configuration files.  Removing .Rprofile, .Rdata, 
> and .Rapp.history made no difference.
> 
> Simon suggested:
> 
>> On 2018-10 -17, at 08:57, Simon Urbanek  wrote:
>> 
>> Few things to try:
>> 
>> - do you see anything in the error console?
> 
> Nothing noticeable in the error console, though I’m inexpert at reading it.
>> 
>> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
>> etc.
> 
> No effect
> 
>> 
>> - try running R from the console and starting the html help by hand to see 
>> if it works at all:
>> tools::startDynamicHelp()
>> help.start(browser="/usr/bin/open”)
>> 
> 
> Help works when running R from console
> 
>> - if that works try the same from the R.app gui *before* using help:
>> help.start(browser="/usr/bin/open”)
> 
> No effect in R (except it opens my default browser).
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
>>> 
>>> 
>>> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
>>> Assistant.  Everything went well, though there are always a few things that 
>>> don't transfer such as applications installed by Brew which I installed 
>>> manually.
>>> 
>>> An issue with R arose I can't solve.  The help systen opens with a blank 
>>> window.
>>> 
>>> Help works when I run R from the terminal so I know the files are 
>>> installed.  Help works fine on the Macintosh I used a the source for the 
>>> migration so it isn't a problem I inherited.  Re-installing R (see 
>>> sessionInfo below) didn't solve the problem.
>>> 
>>> Anyone have any suggestions how I can get help to work?
>>> 
>>> R version 3.5.1 (2018-07-02)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS High Sierra 10.13.6
>>> 
>>> Matrix products: default
>>> BLAS: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods  
>>> [7] base 
>>> 
>>> other attached packages:
>>> [1] HANDLS_0.34 zUtil_0.121
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
>>> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
>>> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
>>> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
>>> [17] 

Re: [R-SIG-Mac] Blank help window

[Marc Schwartz via R-SIG-Mac]

Hi, 

I am on a MBP with Mojave (10.14) and do not observe this issue in R.app, which 
I tested, but don't otherwise use, as I use Emacs/ESS and I don't have any 
issues there either.

It is not clear to me if the use of the Migration Assistant and/or Brew are 
germane or simply red herrings, or if either one are common to what Ben is 
experiencing.

That being said, my recommendation would be to completely remove your R 
installation. If you used the CRAN binary, it should be in:
  
  /Library/Frameworks/R.framework

I would delete the entire R folder tree from R.framework on down.

I would also delete R.app from \Applications, since that seems to be at least 
associated with the issue, if not an actual cause.

Once you have done the above, re-install R using the correct CRAN binary as a 
new, clean install.

After re-installing R, then re-install XQuartz from https://www.xquartz.org 
. In theory, that should be unrelated to this issue, 
I believe, but it should be re-installed after installing/re-installing R in 
either case.

After the above, then try using help in R.app again and see what happens.

Regards,

Marc Schwartz

  

> On Oct 17, 2018, at 1:48 PM, zListserv  wrote:
> 
> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
> as mine.  Ben has problems with ?data.frame.  My issue is a blank help window 
> when typing ?mean (or any other function).
> 
> Peter suggested checking capabilities().  They are all TRUE.
> 
> You both suggested checking configuration files.  Removing .Rprofile, .Rdata, 
> and .Rapp.history made no difference.
> 
> Simon suggested:
> 
>> On 2018-10 -17, at 08:57, Simon Urbanek  wrote:
>> 
>> Few things to try:
>> 
>> - do you see anything in the error console?
> 
> Nothing noticeable in the error console, though I’m inexpert at reading it.
>> 
>> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
>> etc.
> 
> No effect
> 
>> 
>> - try running R from the console and starting the html help by hand to see 
>> if it works at all:
>> tools::startDynamicHelp()
>> help.start(browser="/usr/bin/open”)
>> 
> 
> Help works when running R from console
> 
>> - if that works try the same from the R.app gui *before* using help:
>> help.start(browser="/usr/bin/open”)
> 
> No effect in R (except it opens my default browser).
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
>>> 
>>> 
>>> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
>>> Assistant.  Everything went well, though there are always a few things that 
>>> don't transfer such as applications installed by Brew which I installed 
>>> manually.
>>> 
>>> An issue with R arose I can't solve.  The help systen opens with a blank 
>>> window.
>>> 
>>> Help works when I run R from the terminal so I know the files are 
>>> installed.  Help works fine on the Macintosh I used a the source for the 
>>> migration so it isn't a problem I inherited.  Re-installing R (see 
>>> sessionInfo below) didn't solve the problem.
>>> 
>>> Anyone have any suggestions how I can get help to work?
>>> 
>>> R version 3.5.1 (2018-07-02)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS High Sierra 10.13.6
>>> 
>>> Matrix products: default
>>> BLAS: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods  
>>> [7] base 
>>> 
>>> other attached packages:
>>> [1] HANDLS_0.34 zUtil_0.121
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
>>> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
>>> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
>>> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
>>> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
>>> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 187, Issue 8

[zListserv]

> 
> I am not sure whether the following may cause the problem:
> 
> When I used the Migration Assistant I had some problem with X11,
> and realized that the Migration Assistant did create the symbolic link:
> /usr/X11 -> /opt/X11
> but did not create the symbolic link:
> /usr/X11R6 -> /opt/X11

You are right about Migration Assistant.  I defined both of these symbolic 
links manually while I was trying to solve the problem.  My help window is 
still blank despite their presence.



> 
> Best regards,
> Christian
> 
> 
> 
> 
> --
> 
> Message: 5
> Date: Wed, 17 Oct 2018 13:48:12 -0400
> From: zListserv 
> To: Simon Urbanek , pda...@gmail.com,
>   r-sig-mac@r-project.org, btup...@bigelow.org
> Subject: Re: [R-SIG-Mac] Blank help window
> Message-ID: <963deb05-07e5-44d3-86fd-36bd1a257...@gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Many thanks for your suggestions.  Not sure whether Ben’s issue is the same 
> as mine.  Ben has problems with ?data.frame.  My issue is a blank help window 
> when typing ?mean (or any other function).
> 
> Peter suggested checking capabilities().  They are all TRUE.
> 
> You both suggested checking configuration files.  Removing .Rprofile, .Rdata, 
> and .Rapp.history made no difference.
> 
> Simon suggested:
> 
>> On 2018-10 -17, at 08:57, Simon Urbanek  wrote:
>> 
>> Few things to try:
>> 
>> - do you see anything in the error console?
> 
> Nothing noticeable in the error console, though I’m inexpert at reading it.
>> 
>> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
>> etc.
> 
> No effect
> 
>> 
>> - try running R from the console and starting the html help by hand to see 
>> if it works at all:
>> tools::startDynamicHelp()
>> help.start(browser="/usr/bin/open”)
>> 
> 
> Help works when running R from console
> 
>> - if that works try the same from the R.app gui *before* using help:
>> help.start(browser="/usr/bin/open”)
> 
> No effect in R (except it opens my default browser).
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
>>> 
>>> 
>>> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
>>> Assistant.  Everything went well, though there are always a few things that 
>>> don't transfer such as applications installed by Brew which I installed 
>>> manually.
>>> 
>>> An issue with R arose I can't solve.  The help systen opens with a blank 
>>> window.
>>> 
>>> Help works when I run R from the terminal so I know the files are 
>>> installed.  Help works fine on the Macintosh I used a the source for the 
>>> migration so it isn't a problem I inherited.  Re-installing R (see 
>>> sessionInfo below) didn't solve the problem.
>>> 
>>> Anyone have any suggestions how I can get help to work?
>>> 
>>> R version 3.5.1 (2018-07-02)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS High Sierra 10.13.6
>>> 
>>> Matrix products: default
>>> BLAS: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods  
>>> [7] base 
>>> 
>>> other attached packages:
>>> [1] HANDLS_0.34 zUtil_0.121
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
>>> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
>>> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
>>> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
>>> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
>>> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> 
> 
> 
> --
> 
> Subject: Digest Footer
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
> --
> 
> End of R-SIG-Mac Digest, Vol 187, Issue 8
> *

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Re: [R-SIG-Mac] Blank help window

[zListserv]

Many thanks for your suggestions.  Not sure whether Ben’s issue is the same as 
mine.  Ben has problems with ?data.frame.  My issue is a blank help window when 
typing ?mean (or any other function).

Peter suggested checking capabilities().  They are all TRUE.

You both suggested checking configuration files.  Removing .Rprofile, .Rdata, 
and .Rapp.history made no difference.

Simon suggested:

> On 2018-10 -17, at 08:57, Simon Urbanek  wrote:
> 
> Few things to try:
> 
> - do you see anything in the error console?

Nothing noticeable in the error console, though I’m inexpert at reading it.
> 
> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData 
> etc.

No effect

> 
> - try running R from the console and starting the html help by hand to see if 
> it works at all:
> tools::startDynamicHelp()
> help.start(browser="/usr/bin/open”)
> 

Help works when running R from console

> - if that works try the same from the R.app gui *before* using help:
> help.start(browser="/usr/bin/open”)

No effect in R (except it opens my default browser).

> 
> Cheers,
> Simon
> 
> 
>> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
>> 
>> 
>> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
>> Assistant.  Everything went well, though there are always a few things that 
>> don't transfer such as applications installed by Brew which I installed 
>> manually.
>> 
>> An issue with R arose I can't solve.  The help systen opens with a blank 
>> window.
>> 
>> Help works when I run R from the terminal so I know the files are installed. 
>>  Help works fine on the Macintosh I used a the source for the migration so 
>> it isn't a problem I inherited.  Re-installing R (see sessionInfo below) 
>> didn't solve the problem.
>> 
>> Anyone have any suggestions how I can get help to work?
>> 
>> R version 3.5.1 (2018-07-02)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS High Sierra 10.13.6
>> 
>> Matrix products: default
>> BLAS: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods  
>> [7] base 
>> 
>> other attached packages:
>> [1] HANDLS_0.34 zUtil_0.121
>> 
>> loaded via a namespace (and not attached):
>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
>> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
>> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
>> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
>> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
>> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] Blank help window

[cstrato]

I am not sure whether the following may cause the problem:

When I used the Migration Assistant I had some problem with X11,
and realized that the Migration Assistant did create the symbolic link:
/usr/X11 -> /opt/X11
but did not create the symbolic link:
/usr/X11R6 -> /opt/X11

Best regards,
Christian

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Re: [R-SIG-Mac] Blank help window

[Peter Dalgaard]

Hum, it's not like it cannot work (on iMac running High Sierra):

> help("help") # works fine

You might want to check if anything is non-TRUE here:

> capabilities()
   jpeg pngtiff   tcltk X11aqua
http/ftp sockets 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 
 libxmlfifo  cledit   iconv NLS profmem   
cairo ICU 
   TRUETRUETRUETRUETRUETRUE
TRUETRUE 
long.double libcurl 
   TRUETRUE 

And you seem to have more than the defaults attached, I only have compiler and 
tools. Perhaps check ~/.RData and config files?:

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1   


-pd

> On 17 Oct 2018, at 01:11 , zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things that 
> don't transfer such as applications installed by Brew which I installed 
> manually.
> 
> An issue with R arose I can't solve.  The help systen opens with a blank 
> window.
> 
> Help works when I run R from the terminal so I know the files are installed.  
> Help works fine on the Macintosh I used a the source for the migration so it 
> isn't a problem I inherited.  Re-installing R (see sessionInfo below) didn't 
> solve the problem.
> 
> Anyone have any suggestions how I can get help to work?
> 
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> other attached packages:
> [1] HANDLS_0.34 zUtil_0.121
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
> 
> ___
> 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

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Re: [R-SIG-Mac] Blank help window

[Simon Urbanek]

Few things to try:

- do you see anything in the error console?

- remove (rename) any and all customization files like ~/.Rprofle ~/.RData etc.

- try running R from the console and starting the html help by hand to see if 
it works at all:
tools::startDynamicHelp()
help.start(browser="/usr/bin/open")

- if that works try the same from the R.app gui *before* using help:
help.start(browser="/usr/bin/open")

Cheers,
Simon


> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things that 
> don't transfer such as applications installed by Brew which I installed 
> manually.
> 
> An issue with R arose I can't solve.  The help systen opens with a blank 
> window.
> 
> Help works when I run R from the terminal so I know the files are installed.  
> Help works fine on the Macintosh I used a the source for the migration so it 
> isn't a problem I inherited.  Re-installing R (see sessionInfo below) didn't 
> solve the problem.
> 
> Anyone have any suggestions how I can get help to work?
> 
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> other attached packages:
> [1] HANDLS_0.34 zUtil_0.121
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Blank help window

[Ben Tupper]

Hi,

I have struggled with the same issue, but have found no solution.

https://stat.ethz.ch/pipermail/r-sig-mac/2017-September/012485.html 


I have been using RStudio in lieu of R.app.  I like RStudio, but I miss R.app.

Ben

> On Oct 16, 2018, at 7:11 PM, zListserv  wrote:
> 
> 
> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration 
> Assistant.  Everything went well, though there are always a few things that 
> don't transfer such as applications installed by Brew which I installed 
> manually.
> 
> An issue with R arose I can't solve.  The help systen opens with a blank 
> window.
> 
> Help works when I run R from the terminal so I know the files are installed.  
> Help works fine on the Macintosh I used a the source for the migration so it 
> isn't a problem I inherited.  Re-installing R (see sessionInfo below) didn't 
> solve the problem.
> 
> Anyone have any suggestions how I can get help to work?
> 
> R version 3.5.1 (2018-07-02)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> other attached packages:
> [1] HANDLS_0.34 zUtil_0.121
> 
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15   MASS_7.3-50
> [5] chron_2.3-52grid_3.5.1  plyr_1.8.4  xtable_1.8-2   
> [9] DBI_1.0.0   RSQLite_2.1.1   sqldf_0.4-11blob_1.1.1 
> [13] sp_1.3-1gsubfn_0.7  proto_1.0.0 tools_3.5.1
> [17] Matching_4.9-3  bit64_0.9-7 foreign_0.8-70  bit_1.1-14 
> [21] compiler_3.5.1  maptools_0.9-2  memoise_1.1.0  
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecological Forecasting: https://eco.bigelow.org/






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