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...
> 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 <zlists...@gmail.com> wrote:
>
>
>> On 2018-10-17, at 22:29, Marc Schwartz <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
Ecological Forecasting: https://eco.bigelow.org/
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