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@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 <btup...@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 <pda...@gmail.com
<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 <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 <btup...@bigelow.org
<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
?<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 <zlists...@gmail.com
<mailto:zlists...@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.urba...@r-project.org
<mailto:simon.urba...@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 <zlists...@gmail.com
<mailto:zlists...@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
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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....@cbs.dk <mailto:pd....@cbs.dk> Priv: pda...@gmail.com
<mailto:pda...@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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