[R-SIG-Mac] Blank help window
Ben Tupper
btupper @ending from bigelow@org
Thu Oct 18 02:06:12 CEST 2018
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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