Re: [R-SIG-Mac] Blank help window

Not born that way. I've migrated several laptops. This is the first time I lost /etc/hosts. > On 2018-10-19, at 05:01, Peter Dalgaard wrote: > > What? Are they born that way, or does Migration Assistent bungle things up? > Or maybe OpenVPN does? > > Anyways, try adding a line saying > > 12

Re: [R-SIG-Mac] Blank help window

What? Are they born that way, or does Migration Assistent bungle things up? Or maybe OpenVPN does? Anyways, try adding a line saying 127.0.0.1 localhost -pd > On 19 Oct 2018, at 00:34 , Ben Tupper wrote: > > Hi, > > > ben@gale ~ $ ping localhost > ping: cannot resolve localhost: Unkn

Re: [R-SIG-Mac] Blank help window

> Many, many thanks for all your timely efforts and considerable help, Hear! Hear! Thanks so much for sticking with us! I now have populated help pages in R.app! Yeha! Cheers, Ben > On Oct 18, 2018, at 8:32 PM, zListserv wrote: > > Ha! My /etc/hosts was empty (perhaps an error by

Re: [R-SIG-Mac] Blank help window

Ha! My /etc/hosts was empty (perhaps an error by Migration Assistant?). Populating it with the /etc/hosts from the host computer (particularly defining localhost) solves the problem. Many, many thanks for all your timely efforts and considerable help, > On 2018-10 -18, at 19:52, Marc Schwartz

Re: [R-SIG-Mac] Blank help window

Hi, Ok, that confirms the issue, as surmised. The default hosts file on macOS typically contains the following entries: ## ## # Host Database # # localhost is used to configure the loopback interface # when the system is booting. Do not change this entry. ## 127.0.0.1 localhost 255.255.255.255 b

Re: [R-SIG-Mac] Blank help window

Ok, I think that Peter and Duncan are on to the key issue here. I have been trying to figure out what the difference is between displaying HTML help in R.app versus in the terminal and we now know. If running R in R.app, where .Platform$GUI == "AQUA", the key line in the HTML browser display pr

Re: [R-SIG-Mac] Blank help window

Hi, ben@gale ~ $ ping localhost ping: cannot resolve localhost: Unknown host Here's /etc/hosts in its entirety. ben@gale ~ $ more /etc/hosts # BEGIN section for OpenVPN Client SSL sites 127.94.0.1 client.openvpn.net 127.94.0.2 openvpn-client.vpn.bigelow.org # END section for OpenVPN C

Re: [R-SIG-Mac] Blank help window

Ugggh I was fully expecting it to fail, given my presumptive new found wisdom... Had it failed, then it would support the notion that R,app was irrelevant to the underlying issue with help and there was something going on with the server itself. However, this now suggests (back to my origi

Re: [R-SIG-Mac] Blank help window

On 18/10/2018 5:09 PM, Ben Tupper 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.

Re: [R-SIG-Mac] Blank help window

Oops. I did not try it but now have. ben@gale ~ $ defaults write org.R-project.R use.external.help YES Using a fresh session of R.app ?plot open the external browser with... "Hmm. We’re having trouble finding that site. We can’t connect to the server at localhost. If that address is corre

Re: [R-SIG-Mac] Blank help window

Cannot _find_ localhost?? Can you do this (in a Terminal window) ? Peter-Dalgaards-MacBook-Air:STAT pd$ ping localhost PING localhost (127.0.0.1): 56 data bytes Request timeout for icmp_seq 0 Request timeout for icmp_seq 1 ^C --- localhost ping statistics --- 3 packets transmitted, 0 packets recei

Re: [R-SIG-Mac] Blank help window

Hi, ben@gale ~ $ R R version 3.5.1 (2018-07-02) -- "Feather Spray" > options(help_type = "html") > ?plot starting httpd help server ... done That brings up visible help in the default browser (Safari or Firefox depending upon which is set to be the default browser). > On Oct 18, 2018, at 6

Re: [R-SIG-Mac] Blank help window

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, 20

Re: [R-SIG-Mac] Blank help window

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 > On Oct 18,

Re: [R-SIG-Mac] Blank help window

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 > On Oct 18,

Re: [R-SIG-Mac] Blank help window

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 a

Re: [R-SIG-Mac] Blank help window

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)

Re: [R-SIG-Mac] Blank help window

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 foll

Re: [R-SIG-Mac] Blank help window

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

Re: [R-SIG-Mac] Blank help window

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@gale ~ $ diff R-vanilla-options R-app-options 81c81 < --- > 107a108,110 > $help_type > [1

Re: [R-SIG-Mac] Blank help window

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 a

Re: [R-SIG-Mac] Blank help window

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... > debu

Re: [R-SIG-Mac] Blank help window

> On 2018-10-17, at 22:29, Marc Schwartz 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.a

Re: [R-SIG-Mac] Blank help window

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.

Re: [R-SIG-Mac] Blank help window

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 w

Re: [R-SIG-Mac] Blank help window

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

Re: [R-SIG-Mac] Blank help window

> On 2018-10 -17, at 17:42, Peter Dalgaard wrote: > > Hmm, when trying from R.app, do you see the following? > >> ?data.frame > starting httpd help server ... done >> (tools::startDynamicHelp(NA)) > [1] 26163 R> ?mean starting httpd help server ... done R> (tools::startDynamicHelp(NA)) [1]

Re: [R-SIG-Mac] Blank help window

Ahoy! > ?data.frame starting httpd help server ... done > (tools::startDynamicHelp(NA)) [1] 31048 Connecting to 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 t

Re: [R-SIG-Mac] Blank help window

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 f

Re: [R-SIG-Mac] Blank help window

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 > 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

Re: [R-SIG-Mac] Blank help window

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

Re: [R-SIG-Mac] Blank help window

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 configura

Re: [R-SIG-Mac] Blank help window

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, Chri

Re: [R-SIG-Mac] Blank help window

Hum, it's not like it cannot work (on iMac running High Sierra): > help("help") # works fine You might want to check if anything is non-TRUE here: > capabilities() jpeg pngtiff tcltk X11aqua http/ftp sockets TRUETRUETRU

Re: [R-SIG-Mac] Blank help window

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/op

Re: [R-SIG-Mac] Blank help window

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 I have been using RStudio in lieu of R.app. I like RStudio, but I miss R.app. Ben >

[R-SIG-Mac] Blank help window

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 wi