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Blank help window

37 messages · Simon Urbanek, Peter Dalgaard, cstrato +4 more

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zListserv
# 
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
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 <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
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/
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
Peter Dalgaard
# 
Hum, it's not like it cannot work (on iMac running High Sierra):
You might want to check if anything is non-TRUE here:
jpeg         png        tiff       tcltk         X11        aqua    http/ftp     sockets 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
     libxml        fifo      cledit       iconv         NLS     profmem       cairo         ICU 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
long.double     libcurl 
       TRUE        TRUE 

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

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      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

  
  


  


      

    

    

      
      

        


  

        

      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:

            

      
      
      
    

        
Nothing noticeable in the error console, though I?m inexpert at reading it.

            

      
      
      
    

        
No effect

            

      
      
      
    

        
Help works when running R from console

            

      
      
      
    

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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
      #
    

  


  

      
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 <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

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      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

            

      
      
      
    

        
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]

            

      
      
      
    

        
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

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
      #
    

  


  

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

            

      
      
      
    

        
starting httpd help server ... done

            

      
      
      
    

        
[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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
      #
    

  


  

      
Ahoy!

            

      
      
      
    

        
starting httpd help server ... done

            

      
      
      
    

        
[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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      zListserv
    

    

      
      #
    

  


  

          

      
      
      
    

        
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.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      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]

            

      
      
      
    

        
starting httpd help server ... done

            

      
      
      
    

        
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

            

      
      
      
    

        
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 at 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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
      #
    

  


  

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

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
      #
    

  


  

      
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      zListserv
    

    

      
      #
    

  


  

          

      
      
      
    

        
No firewall; no anti-virus or other malware software

            

      
      
      
    

        
Nope.  Blank is blank.  No invisible text detected.

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
      #
    

  


  

      
I also have no firewall running on the platform.  I do have anti-virus/malware and have turned it off.  The help window still renders with a blank page and there is no text captured with a copy-paste.

I tried debug() as Duncan suggested and get the following in a fresh R.app session...

            

      
      
      
    

        
debugging in: print.help_files_with_topic(x)
debug: {
    browser <- getOption("browser")
    topic <- attr(x, "topic")
    type <- attr(x, "type")
    if (.Platform$GUI == "AQUA" && type == "html") 
        browser <- get("aqua.browser", envir = as.environment("tools:RGUI"))
    paths <- as.character(x)
    if (!length(paths)) {
        writeLines(c(gettextf("No documentation for %s in specified packages and libraries:", 
            sQuote(topic)), gettextf("you could try %s", sQuote(paste0("??", 
            topic)))))
        return(invisible(x))
    }
    port <- if (type == "html") 
        tools::startDynamicHelp(NA)
    else NULL
    if (attr(x, "tried_all_packages")) {
        paths <- unique(dirname(dirname(paths)))
        msg <- gettextf("Help for topic %s is not in any loaded package but can be found in the following packages:", 
            sQuote(topic))
        if (type == "html" && port > 0L) {
            path <- file.path(tempdir(), ".R/doc/html")
            dir.create(path, recursive = TRUE, showWarnings = FALSE)
            out <- paste0("<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">\n", 
                "<html><head><title>R: help</title>\n", "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=\"UTF-8\">\n", 
                "<link rel=\"stylesheet\" type=\"text/css\" href=\"/doc/html/R.css\">\n", 
                "</head><body>\n\n<hr>\n")
            out <- c(out, "<p>", msg, "</p><br>")
            out <- c(out, "<table width=\"100%\" summary=\"R Package list\">\n", 
                "<tr align=\"left\" valign=\"top\">\n", "<td width=\"25%\">Package</td><td>Library</td></tr>\n")
            pkgs <- basename(paths)
            links <- paste0("<a href=\"http://127.0.0.1:", port, 
                "/library/", pkgs, "/help/", topic, "\">", pkgs, 
                "</a>")
            out <- c(out, paste0("<tr align=\"left\" valign=\"top\">\n", 
                "<td>", links, "</td><td>", dirname(paths), "</td></tr>\n"))
            out <- c(out, "</table>\n</p>\n<hr>\n</body></html>")
            writeLines(out, file.path(path, "all.available.html"))
            browseURL(paste0("http://127.0.0.1:", port, "/doc/html/all.available.html"), 
                browser)
        }
        else {
            writeLines(c(strwrap(msg), "", paste0("  ", formatDL(c(gettext("Package"), 
                basename(paths)), c(gettext("Library"), dirname(paths)), 
                indent = 22))))
        }
    }
    else {
        if (length(paths) > 1L) {
            if (type == "html" && port > 0L) {
                browseURL(paste0("http://127.0.0.1:", port, "/library/NULL/help/", 
                  URLencode(topic, reserved = TRUE)), browser)
                return(invisible(x))
            }
            file <- paths[1L]
            p <- paths
            msg <- gettextf("Help on topic %s was found in the following packages:", 
                sQuote(topic))
            paths <- dirname(dirname(paths))
            txt <- formatDL(c("Package", basename(paths)), c("Library", 
                dirname(paths)), indent = 22L)
            writeLines(c(strwrap(msg), "", paste0("  ", txt), 
                ""))
            if (interactive()) {
                fp <- file.path(paths, "Meta", "Rd.rds")
                tp <- basename(p)
                titles <- tp
                if (type == "html" || type == "latex") 
                  tp <- tools::file_path_sans_ext(tp)
                for (i in seq_along(fp)) {
                  tmp <- try(readRDS(fp[i]))
                  titles[i] <- if (inherits(tmp, "try-error")) 
                    "unknown title"
                  else tmp[tools::file_path_sans_ext(tmp$File) == 
                    tp[i], "Title"]
                }
                txt <- paste0(titles, " {", basename(paths), 
                  "}")
                res <- menu(txt, title = gettext("Choose one"), 
                  graphics = getOption("menu.graphics"))
                if (res > 0) 
                  file <- p[res]
            }
            else {
                writeLines(gettext("\nUsing the first match ..."))
            }
        }
        else file <- paths
        if (type == "html") {
            if (port > 0L) {
                path <- dirname(file)
                dirpath <- dirname(path)
                pkgname <- basename(dirpath)
                browseURL(paste0("http://127.0.0.1:", port, "/library/", 
                  pkgname, "/html/", basename(file), ".html"), 
                  browser)
            }
            else {
                warning("HTML help is unavailable", call. = FALSE)
                att <- attributes(x)
                xx <- sub("/html/([^/]*)\\.html$", "/help/\\1", 
                  x)
                attributes(xx) <- att
                attr(xx, "type") <- "text"
                print(xx)
            }
        }
        else if (type == "text") {
            pkgname <- basename(dirname(dirname(file)))
            temp <- tools::Rd2txt(.getHelpFile(file), out = tempfile("Rtxt"), 
                package = pkgname)
            file.show(temp, title = gettextf("R Help on %s", 
                sQuote(topic)), delete.file = TRUE)
        }
        else if (type %in% "pdf") {
            path <- dirname(file)
            dirpath <- dirname(path)
            texinputs <- file.path(dirpath, "help", "figures")
            tf2 <- tempfile("Rlatex")
            tools::Rd2latex(.getHelpFile(file), out = tf2)
            .show_help_on_topic_offline(tf2, topic, type, texinputs)
            unlink(tf2)
        }
    }
    invisible(x)
}
Browse[2]> c

... at which point the blank help window pops.

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
      #
    

  


  

      
Hi,

Two things:

1. Can one or both of you guys check locally on your own computers, to see if there is any difference between the output of options() in R.app, versus the output when R is run from a Terminal session. Many elements will not be germane to this issue, but others might, if there are differences.

Just wondering if some option() is altered from the default and/or causing a conflict unique to R.app.



2. Exit from R.app so that it is not running.

Then look for the file:

  ~/Library/Preferences/org.R-project.R.plist

            

      
      
      
    

        
With R.app NOT running, delete that file, or drag it to the desktop, if preferred.

Then start R.app and see what happens with help. The above .plist file, will be created new, with the new R.app session, so will return to default settings. Perhaps there is something in there screwing things up.


Marc

<snip>

  
  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
      #
    

  


  

      
Hi,

Thanks for your persistence and kind help.

(1)  Comparing output of options()

R.app options() includes 

$help_type
[1] "html"

that terminal R options() does not.  Here's the diff of the two...

ben at gale ~ $ diff R-vanilla-options R-app-options 
81c81
< <bytecode: 0x7fd3f638b858>
---

            

      
      
      
    

        
107a108,110

            

      
      
      
    

        
181,182c184,185
<     CRAN 
< "@CRAN@" 
---

            

      
      
      
    

        
244c247
< [1] 80
---

            

      
      
      
    

        
(2) Removing ~/Library/Preferences/org.R-project.R.plist

Starting R.app after removing the plist does not resolve the blank help window (but did restore R.app's factory-default appearance and settings.)

            

      
      
      
    

        
starting httpd help server ... done

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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Hi Ben,

Ok, if I read correctly, it looks like you must have started R in the terminal using 'R --vanilla', based upon the file name below.

In that case, R should bring up help pages in the terminal using the internal text pager, as opposed to externally in a browser with HTML.

Start R in the Terminal just using 'R' and see what, if any, differences there are in the output of options() in that case.


Grasping at another straw, let's change the default browser in R.app to see if using an external browser, instead of the built-in browser, behaves differently.

As it turns out, from discussions some years ago, it is a bit more complex with R.app, as it does not honor the usual options() settings.

So, with R.app NOT running, in a terminal, use:

  defaults write org.R-project.R use.external.help YES

and hit enter.

Then, start R.app and try to use help again and see what happens.


To restore the default use of the internal R.app browser, exit R.app and in a terminal, use:

  defaults delete org.R-project.R use.external.help 

and hit enter.


See if that does anything.

Marc

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
      #
    

  


  

      
On 18/10/2018 8:50 AM, Ben Tupper wrote:

            

      
      
      
    

        
Okay, that wasn't as informative as I had hoped.  Could you try the 
following:

debug(get("aqua.browser", envir = as.environment("tools:RGUI")))

then ask for help on something.  You should stop in the debugger seeing 
something like

debugging in: browser(if (encodeIfNeeded) URLencode(url) else url)
debug: {
     x <- gsub("http://127.0.0.1", "http://localhost", x, fixed = TRUE)
     .Call("aqua.custom.print", "help-files", x)
     invisible(x)
}

At the prompt, type "n" (without the quotes, followed by return) twice, 
until you are at the .Call line.  Then type

browseURL(x)

This should open your external browser.  It will either show a blank 
page, or the help page:  that will indicate whether the problem is in 
the internal browser or in the server.

Then go back to R.app, and type "c".  This should open the same help 
page in the internal browser.  It might show a blank page, or the 
regular help page:  either one would tell us something.

Duncan Murdoch

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
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Hi,

In a fresh R.app session

            

      
      
      
    

        
starting httpd help server ... done
debugging in: browser(if (encodeIfNeeded) URLencode(url) else url)
debug: {
    x <- gsub("http://127.0.0.1", "http://localhost", x, fixed = TRUE)
    .Call("aqua.custom.print", "help-files", x)
    invisible(x)
}
Browse[2]> n
debug: x <- gsub("http://127.0.0.1", "http://localhost", x, fixed = TRUE)
Browse[2]> n
debug: .Call("aqua.custom.print", "help-files", x)
Browse[2]> browseURL(x)


opens the external browser http://localhost:28450/library/utils/html/help.html <http://localhost:28450/library/utils/html/help.html>

but the browser says...

"Hmm. We?re having trouble finding that site.
We can?t connect to the server at localhost.
If that address is correct, here are three other things you can try:

    Try again later.
    Check your network connection.
    If you are connected but behind a firewall, check that Firefox has permission to access the Web."


And...

Browse[2]> c
exiting from: browser(if (encodeIfNeeded) URLencode(url) else url)

... opens the blank help window.


Finally, following up on Marc's suggestion that I invoke R without --vanilla...

ben at gale ~ $ diff R-app-options R-options 
81c81
< <bytecode: 0x7fd0b1fcbbc0>
---

            

      
      
      
    

        
108,110d107
< $help_type
< [1] "html"
< 
184,185c181,182
<                             CRAN 
< "http://cran.utstat.utoronto.ca" 
---

            

      
      
      
    

        
247c244
< [1] 168
---

            

      
      
      
    

        

      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
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Hi Ben,

A question, because as I go back and re-read both this thread and the prior one you posted on this issue, I have been presuming that when you run R from the terminal, you can successfully get help to open in an external browser.

However, given my re-read and what you now post below, I am wondering if, in fact, when running R in the terminal, you simply get the help displaying in the text pager.

I don't use RStudio, so not sure if help comes up in their own internal browser, or if it comes up in an external browser. Albeit, looking at their website, it appears to be an internal browser that stays within the IDE, in contrast to R.app opening the internal browser in an external window.

Can you confirm that when you run R from the terminal, does help appear within the terminal window in the pager, or does it come up in whatever external browser you are using, which I am guessing is Firefox based upon the output below.

Thanks,

Marc

            

      
      
      
    

        
<snip>

  
  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
      #
    

  


  

      
You are correct that it only comes up in the text pager when I invoke R from the terminal (with or without --vanilla).

RStudio help works as expected in the sense that help content is rendered within the RStudio panes on the "Help" tab - just as you surmised.

Cheers (really!),
Ben

            

      
      
      
    

        
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/

  
  


  


      

    

    

      
      

        


  

        

      Marc Schwartz
    

    

      
      #
    

  


  

      
Hi Ben,

Ok, thanks for that clarification. That fundamentally alters my view of the issue.

For verification, can you start R in a terminal and then type:

  options(help_type = "html")

after which, then try help for some function (e.g. ?plot) and see what happens.

Thanks,

Marc

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ben Tupper
    

    

      
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Just a little followup.  Switching the default browser from Firefox to Safari yields a similar message in the browser after...

Browse[2]> browseURL(x)

'Safari can't open the page "localhost:29682/library/utils/html/help.html"
because Safari can't find the server "localhost".'

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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/