[R-SIG-Mac] Blank help window

Marc Schwartz m@rc_@chw@rtz @ending from me@com
Thu Oct 18 04:29:00 CEST 2018 

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 <btupper using bigelow.org> 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         png        tiff       tcltk         X11        aqua    http/ftp     sockets      libxml        fifo 
>       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
>     cledit       iconv         NLS     profmem       cairo         ICU long.double     libcurl 
>       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
> 
> 
> 
> And from shell...
> 
> ben using 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 <btupper using bigelow.org> wrote:
>> 
>> Ahoy!
>> 
>>> ?data.frame
>> starting httpd help server ... done
>>> (tools::startDynamicHelp(NA))
>> [1] 31048
>> 
>> Connecting to http://127.0.0.1:31048/NEWS <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 <pdalgd using gmail.com <mailto:pdalgd using 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 <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 <btupper using bigelow.org <mailto:btupper using 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
>>>> 
>>>>> ?<something>
>>>> 
>>>> 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         png        tiff       tcltk         X11        aqua    http/ftp     sockets      libxml        fifo 
>>>>      TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
>>>>    cledit       iconv         NLS     profmem       cairo         ICU long.double     libcurl 
>>>>      TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On Oct 17, 2018, at 1:48 PM, zListserv <zlistserv using gmail.com <mailto:zlistserv using gmail.com>> 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 <simon.urbanek using r-project.org <mailto:simon.urbanek using r-project.org>> 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 <zlistserv using gmail.com <mailto:zlistserv using gmail.com>> 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_0.12.17    lattice_0.20-35 digest_0.6.15   MASS_7.3-50    
>>>>>>> [5] chron_2.3-52    grid_3.5.1      plyr_1.8.4      xtable_1.8-2   
>>>>>>> [9] DBI_1.0.0       RSQLite_2.1.1   sqldf_0.4-11    blob_1.1.1     
>>>>>>> [13] sp_1.3-1        gsubfn_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 using r-project.org <mailto:R-SIG-Mac using 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 <http://www.bigelow.org/>
>>>> 
>>>> Ecological Forecasting: https://eco.bigelow.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> -- 
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Office: A 4.23
>>> Email: pd.mes using cbs.dk <mailto:pd.mes using cbs.dk>  Priv: PDalgd using gmail.com <mailto:PDalgd using gmail.com>
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org <http://www.bigelow.org/>
>> 
>> Ecological Forecasting: https://eco.bigelow.org/ <https://eco.bigelow.org/>
>> 
>> 
>> 
>> 
> 
> 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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