[R-SIG-Mac] Blank help window

Duncan Murdoch murdoch@dunc@n @ending from gm@il@com
Thu Oct 18 02:30:42 CEST 2018 

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         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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