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".'
> On Oct 18, 2018, at 5:09 PM, Ben Tupper <btup...@bigelow.org> wrote:
>
> Hi,
>
> In a fresh R.app session
>
> > debug(get("aqua.browser", envir = as.environment("tools:RGUI")))
> > help('help')
> starting httpd help server ... done
> debugging in: browser(if (encodeIfNeeded) URLencode(url) else url)
> debug: {
> x <- gsub("http://127.0.0.1 <http://127.0.0.1/>", "http://localhost
> <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://127.0.0.1/>", "http://localhost
> <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@gale ~ $ diff R-app-options R-options
> 81c81
> < <bytecode: 0x7fd0b1fcbbc0>
> ---
> > <bytecode: 0x7fb46a177890>
> 108,110d107
> < $help_type
> < [1] "html"
> <
> 184,185c181,182
> < CRAN
> < "http://cran.utstat.utoronto.ca <http://cran.utstat.utoronto.ca/>"
> ---
> > CRAN
> > "@CRAN@"
> 247c244
> < [1] 168
> ---
> > [1] 80
>
>
>
>
>
>
>
>> On Oct 18, 2018, at 4:49 PM, Duncan Murdoch <murdoch.dun...@gmail.com
>> <mailto:murdoch.dun...@gmail.com>> wrote:
>>
>> On 18/10/2018 8:50 AM, Ben Tupper wrote:
>>> I also have no firewall running on the platform. I do have
>>> anti-virus/malware and have turned it off. The help window still renders
>>> with a blank page and there is no text captured with a copy-paste.
>>> I tried debug() as Duncan suggested and get the following in a fresh R.app
>>> session...
>>
>> Okay, that wasn't as informative as I had hoped. Could you try the
>> following:
>>
>> debug(get("aqua.browser", envir = as.environment("tools:RGUI")))
>>
>> then ask for help on something. You should stop in the debugger seeing
>> something like
>>
>> debugging in: browser(if (encodeIfNeeded) URLencode(url) else url)
>> debug: {
>> x <- gsub("http://127.0.0.1 <http://127.0.0.1/>", "http://localhost
>> <http://localhost/>", x, fixed = TRUE)
>> .Call("aqua.custom.print", "help-files", x)
>> invisible(x)
>> }
>>
>> At the prompt, type "n" (without the quotes, followed by return) twice,
>> until you are at the .Call line. Then type
>>
>> browseURL(x)
>>
>> This should open your external browser. It will either show a blank page,
>> or the help page: that will indicate whether the problem is in the internal
>> browser or in the server.
>>
>> Then go back to R.app, and type "c". This should open the same help page in
>> the internal browser. It might show a blank page, or the regular help page:
>> either one would tell us something.
>>
>> Duncan Murdoch
>>
>>>> debug(utils:::print.help_files_with_topic)
>>>> help("help")
>>> debugging in: print.help_files_with_topic(x)
>>> debug: {
>>> browser <- getOption("browser")
>>> topic <- attr(x, "topic")
>>> type <- attr(x, "type")
>>> if (.Platform$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:
>>> <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: <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: <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$File) ==
>>> tp[i], "Title"]
>>> }
>>> txt <- paste0(titles, " {", basename(paths),
>>> "}")
>>> res <- menu(txt, title = gettext("Choose one"),
>>> graphics = getOption("menu.graphics"))
>>> if (res > 0)
>>> file <- p[res]
>>> }
>>> else {
>>> writeLines(gettext("\nUsing the first match ..."))
>>> }
>>> }
>>> else file <- paths
>>> if (type == "html") {
>>> if (port > 0L) {
>>> path <- dirname(file)
>>> dirpath <- dirname(path)
>>> pkgname <- basename(dirpath)
>>> browseURL(paste0("http://127.0.0.1: <http://127.0.0.1/>",
>>> port, "/library/",
>>> pkgname, "/html/", basename(file), ".html"),
>>> browser)
>>> }
>>> else {
>>> warning("HTML help is unavailable", call. = FALSE)
>>> att <- attributes(x)
>>> xx <- sub("/html/([^/]*)\\.html$", "/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.
>>>
>>>> On Oct 18, 2018, at 6:29 AM, zListserv <zlists...@gmail.com
>>>> <mailto:zlists...@gmail.com>> wrote:
>>>>
>>>>
>>>>> On 2018-10-17, at 22:29, Marc Schwartz <marc_schwa...@me.com
>>>>> <mailto:marc_schwa...@me.com>> wrote:
>>>>>
>>>>> 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.
>>>>
>>>> No firewall; no anti-virus or other malware software
>>>>
>>>>>
>>>>> 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....
>>>>
>>>> Nope. Blank is blank. No invisible text detected.
>>>>
>>>>>
>>>>> Regards,
>>>>>
>>>>> Marc
>>>>> <snip>
>>>>
>>> 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/
>>> [[alternative HTML version deleted]]
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org>
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> <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/ <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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