[R-SIG-Mac] Blank help window
Ben Tupper
btupper @ending from bigelow@org
Thu Oct 18 23:09:30 CEST 2018
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://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 using gale ~ $ diff R-app-options R-options
81c81
< <bytecode: 0x7fd0b1fcbbc0>
---
> <bytecode: 0x7fb46a177890>
108,110d107
< $help_type
< [1] "html"
<
184,185c181,182
< CRAN
< "http://cran.utstat.utoronto.ca"
---
> CRAN
> "@CRAN@"
247c244
< [1] 168
---
> [1] 80
> On Oct 18, 2018, at 4:49 PM, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 18/10/2018 8:50 AM, Ben Tupper wrote:
>> I also have no firewall running on the platform. I do have anti-virus/malware and have turned it off. The help window still renders with a blank page and there is no text captured with a copy-paste.
>> I tried debug() as Duncan suggested and get the following in a fresh R.app session...
>
> Okay, that wasn't as informative as I had hoped. Could you try the following:
>
> debug(get("aqua.browser", envir = as.environment("tools:RGUI")))
>
> then ask for help on something. You should stop in the debugger seeing something like
>
> debugging in: browser(if (encodeIfNeeded) URLencode(url) else url)
> debug: {
> x <- gsub("http://127.0.0.1 <http://127.0.0.1/>", "http://localhost <http://localhost/>", x, fixed = TRUE)
> .Call("aqua.custom.print", "help-files", x)
> invisible(x)
> }
>
> At the prompt, type "n" (without the quotes, followed by return) twice, until you are at the .Call line. Then type
>
> browseURL(x)
>
> This should open your external browser. It will either show a blank page, or the help page: that will indicate whether the problem is in the internal browser or in the server.
>
> Then go back to R.app, and type "c". This should open the same help page in the internal browser. It might show a blank page, or the regular help page: either one would tell us something.
>
> Duncan Murdoch
>
>>> debug(utils:::print.help_files_with_topic)
>>> help("help")
>> debugging in: print.help_files_with_topic(x)
>> debug: {
>> browser <- getOption("browser")
>> topic <- attr(x, "topic")
>> type <- attr(x, "type")
>> if (.Platform$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:", 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.
>>
>>> On Oct 18, 2018, at 6:29 AM, zListserv <zlistserv using gmail.com> wrote:
>>>
>>>
>>>> On 2018-10-17, at 22:29, Marc Schwartz <marc_schwartz using 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
>> Ecological Forecasting: https://eco.bigelow.org/
>> [[alternative HTML version deleted]]
>> _______________________________________________
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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
Ecological Forecasting: https://eco.bigelow.org/
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