This question relates to an answer given by Yihui here:
https://groups.google.com/g/shinyapps-users/c/0czcsM4vziM/m/GNuyL3ClCgAJ
In the instruction, it says to:
dir.create('~/.fonts')
Download the fonts, e.g. via download.file(), to ~/.fonts
Run system('fc-cache -f ~/.fonts')
I've put this into my .app code (just after all my library() calls) before trying to deploy the app to shinapps.io.:
dir.create('~/.fonts')
download.file('https://github.com/**MY USERNAME**/fonts', '~/.fonts')
system('fc-cache -f ~/.fonts')
As you can see, I have put all the fonts the app requires into a public repo on my github account. This is the URL that the font .ttf files are from. However, i think i may have misunderstood the directions, as i get this error from shinyapps.io:
Error in value[[3L]](cond) : Error sourcing /srv/connect/apps/font/app.R
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
The fonts I wish to use are derivations of the "Sarabun" and "Garamond" families.
Please can someone provide more detail to Yihui's solution? Any help would be greatly appreciated. If you also have another solution that would be good to hear. However, please note that 'font style packages' tend not to work with shinyapps.io as these look locally for the styles, which defeats the purpose of it! Additionally, I wish to use a specific .ttf file.
Cheers all,
Matt
The URL https://github.com/**MY USERNAME**/fonts points to a repository overview, not the folder itself, so maybe you are downloading just the HTML page on that URL.
You need to download the archive depending on your OS (ZIP on Windows, .TAR.GZ on Unix-alike).
download.file("https://github.com/**USERNAME**/fonts/archive/master.tar.gz", destfile = "fonts.tar.gz")
# or ZIP file on Windows
download.file("https://github.com/**USERNAME**/fonts/archive/master.zip", destfile = "fonts.zip")
Then you have to extract the archive:
untar("fonts.tar.gz", exdir = "~/.fonts/")
# or with ZIP file on Windows
unzip("fonts.zip", exdir = "~/.fonts/")
Then you can use that in your script:
system('fc-cache -f ~/.fonts')
I hope the way is clear as it may vary depending on your OS, fonts and subfolders etc... Something like that should work.
Related
I have been trying for three days now to download a file from an FTP server with R without a result. I have really tried everything and read all questions but still cannot manage.
The url is:
u <- "ftp://user:password#109.2.160.55/AGLO/2020/10/AGLO_00001_03-0_GDBX_1000077_202010032206_860101.CSV.gz"
When I copy paste this link in Firefox I can download the file, but with R I cannot. I tried download.file, GET, writeBin, getURL. All failed: getURL gives the following error:
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
embedded nul in string: '\037‹\b\bøÙx_\0\003AGLO_00001_03-0_GDBX_1000077_202010032206_860101.CSV\0¬\\M³£¸’Ý¿_Áîº\002I Xɶ®*\fn>nÔMÇ›\231·èͼ\210î×\021óóç¤\004\006#¹.Œ§+¢ë’צŽ’TæÉ\017¡ÎUS*üï·\030ÿ±ßbñKüÛùtøþ\033#A–ýÆc\036ãgÁy,\177Ë%~f_ŽÝ{é~,é\v%}¡\\~ÐIN¿ÿùï?~ÿ\217¿þýÏ¿þ(\017±\034oY¾ýë¯?þû÷?ÿ$qù·Å/p\v÷\177{£òð]U½.umÊ¿\235»¦/{s~ƒ”\220–7ÓŸ¢Ã¿þø¯\177þã¯ÿ)ó¸ÈŠ\022_eEœã·îúz-K\031—í £¯ZÕÑW5´º+…H9/{Uéú¨K^BfNôsT©è]·n\215ŽÊ2\021œ©²¦¯”e/æ»7e\fIy‹\231Ä_"ayF?ÈñÏýsåQUGüâ3ô¼H’d\t\177\024Hàgœ•ê=ºªópR„\235笼\002á¹VÇ\aðºRFy°y\b6Ç_xz¹d¯Àf<—I2Â.\030›\004\f°3\002ZÓõ#\027\035Z£ê\023ÀDz(+\\7CwT}ÉJ\215¿»nè£þ¢\201\230Ô^>"§\033×ø3#çLäž¾éc›õ\035§‰`wàr\022\020pg-êøë »èÖjØCï\003çeý÷\037j\210êoM}n"ÝG׫ÆCÂ:£úï]S«è¢a_*°\034¹Z\016\036C\034XŽÜ¼œBð8YX\217»&ã‘\t=†›êz=´X…`yyÓ]g-G\177é¾Ü¾(ü颶9`\235Ñ\031ÎXË\016\033*RÚwÏmèûgàešf|\001Þ]\023xžYËï/F·\235}\004p\tM{Òj\200·);ݾ\033\230ýE\003úY_u\215‡`j,´Û¾\0^°8}iëf<\023Kå\217\002,àP2aÉß\006‚%åM\r¦ªì“¸Ý`jã%°“{ú±AùiÊ_s;ô_ºÄî\004Öí0\vý4ÜTÿá+ÿÚœL5þv‡¹0ž’ÃxÁ夒\025l\
There is no proxy problem whatsoever since to get the u url I am searching in the FTP directory.
How can I download this fing file ?
Also another way I could eventially work around this is using:
browseURL(u,
browser = "C:/Program Files (x86)/Mozilla Firefox/firefox.exe")
The issue with this is that it will open a Firefox browser that will:
Ask me if I am sure I want to go to this site and then
Ask me what I want to do with this file (not so much of a problem since I can choose a default to always download, but still I do not want to)
The issue with this is that simply I do not want to open a browser and I do not want to be asked if I want to go to the site and if I want to download. There are many files on this server so I want to do all of this automatically and I will need to be working in parllel, so having a browser pop up is not great, but if all else fails I can accept.
I am so desperate that I can give you the user name and password in private.
Apparently downloading the file to disk using httr solved the problem. It is possible to combine write_disk and httr::GET to download files to disk in the following way:
library(httr)
to_download <- "https://www.w3.org/WAI/ER/tests/xhtml/testfiles/resources/pdf/dummy.pdf"
# Download pdf to disk
GET(to_download, write_disk("dummy.pdf"))
I'm trying to publish an R Shiny app. It works when run locally, but once published to shinyapps.io produces the following error.
Warning in gzfile(file, "wb") :
cannot open compressed file '/key.rda', probable reason 'Permission denied'
Error in value[[3L]](cond) : cannot open the connection
Calls: local ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
You can also see the actual page with the error here: https://povertylab.shinyapps.io/ACS-Map-Dashboard/
Though I have tried to reproduce this error it doesn't appear when I publish other apps, and my searches haven't turned up anything. Other things I've tried: publishing from other computers, publishing only global.R, server.R, and ui.R files, and copying files to a new project and publishing from there.
You can find all code for the app here: https://github.com/Poverty-Lab/ACS-Map-Dashboard
I would appreciate any input, even if it's just guidance on what gzfile is and what the error message could mean. Thank you!
Where is the key.rda file supposed to be? I've looked through your repo and I don't see it, which is probably causing the "cannot open the connection" error.
As a side note, you should probably ignore the .Renviron file; right now anyone can use see and use your key. Make sure you remove it from the history as well.
Thanks all. Turns out this was a problem with the way we were handing the api key for the acs package. We were using api.key.install to install the api key inside the app, and one of api.key.install's default arguments is file = "key.rda", and that file apparently could not be found. I'm still not sure why this problem only came up when we published the app, but we got around it by supplying the actual api key to the acs.fetch function in server.R.
Is there some way to source an R script from the web?
e.g. source('http://github.com/project/R/file.r')
Reason: I currently have a project that I'd like to make available for use but isn't ready to be packaged yet. So it would be great to give people a single file to source from the web (that will then source all the individual function files).
On closer inspection, the problem appears to be https. How would I source this file?
https://raw.github.com/hadley/stringr/master/R/c.r
You can use the source_url in the devtools library
library(devtools)
source_url('https://raw.github.com/hadley/stringr/master/R/c.r')
This is a wrapper for the RCurl method by #ROLO
Yes you can, try running this R tutorial:
source("http://www.mayin.org/ajayshah/KB/R/tutorial.R")
(Source)
Https is only supported on Windows, when R is started with the --internet2 command line option (see FAQ):
> source("https://pastebin.com/raw.php?i=zdBYP5Ft")
> test()
[1] "passed"
Without this option, or on linux, you will get the error "unsupported URL scheme". In that case resort to the solution suggested by #ulidtko, or:
Here is a way to do it using RCurl, which also supports https:
library(RCurl)
eval( expr =
parse( text = getURL("http://www.mayin.org/ajayshah/KB/R/tutorial.R",
ssl.verifypeer=FALSE) ))
(You can remove the ssl.verifypeer if the ssl certificate is valid)
Yes, it is possible and worked for me right away.
R> source("http://pastebin.com/raw.php?i=zdBYP5Ft")
R> test()
[1] "passed"
Regarding the HTTPS part, it isn't supported by internal R code. However, R can use external utilities like wget or curl to fetch https:// URLs. One will need to write additional code to be able to source the files.
Sample code might be like this:
wget.and.source <- function(url) {
fname <- tempfile()
download.file(url, fname, method="wget")
source(fname)
unlink(fname)
}
There is a Windows-only solution too: start R with --internet2 commandline option. This will switch all the internet code in R to using IE, and consequently HTTPS will work.
Windows:
If Internet Explorer is configured to access the web using your organization's proxy, you can direct R to use these IE settings instead of the default R settings. This change can be made once by the following steps:
Save your work and close all R sessions you may have open.
Edit the following file. (Note: Your exact path will differ based on your R installation)
C:\Program Files\R\R-2.15.2\etc\Rprofile.site
Open this "Rprofile.site" file in Notepad and add the following line on a new line at the end of the file:
utils::setInternet2(TRUE)
You may now open a new R session and retry your "source" command.
Linux alikes:
Use G. Grothendieck's suggestion. At the command prompt within R type:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url/here.r")))
You may get an error saying:
cannot verify certificate - - - - Self-signed certificate encountered.
At this point it is up to you to decide whether you trust the person issuing the self-signed certificate and proceed or to stop.
If you decide to proceed, you can connect insecurely as follows:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url.r", "--no-check-certificate")))
For more details, see the following:
See section 2.19
CRAN R Documentation 2.19
wget documentation section 2.8 for "no-check-certificate"
Similar questions here:
Stackoverflow setInternet2 discussion
Stackoverflow Proxy configuration discussion
The methods here were giving me the following error from github:
OpenSSL: error:14077458:SSL routines:SSL23_GET_SERVER_HELLO:reason(1112)
I used the following function to resolve it:
github.download = function(url) {
fname <- tempfile()
system(sprintf("curl -3 %s > %s", url, fname))
return(fname)
}
source(github.download('http://github.com/project/R/file.r'))
Hope that helps!
This is working for me on windows:
library(RCurl)
# load functions and scripts from github ----------------------------
fn1 <- getURL("https://raw.githubusercontent.com/SanjitNarwekar/Advanced-R-Programming/master/fn_factorial_loop.R", ssl.verifypeer = FALSE)
eval(parse(text = fn1))
I try to install packages (pdbDEMO actually and all the dependencies) and I am encountering an issue, that I cannot solve and I haven't found any solution about it.
I use the R command :
>install.packages("pbdDEMO", lib="C:/Users/xavier_520285/Desktop", type = "source")
Then all the 6 packages are downloaded, but not installed since I get 6 error messages :
Error in getOctD(x, offset, len) : invalid octal digit
I have absolutely no clue about how to fix it.
I would be very grateful with any helpful answer.
As the post above suggests, your tar file is probably corrupt, or it's not a tar file at all.
The easiest way to check it on Linux is to use file <filename> command, a proper .tar.gz file will return something like this:
rJava_0.9-4.tar.gz: gzip compressed data, from Unix, last modified: Tue Mar 12 09:54:30 2013
When you are behind a proxy or a firewall and you don't have it properly configured on your computer, oftentimes you will download a html file or a proxy script instead of the file that you are looking for. You can even try to read it as text with head or less:
# head rhdfs_1.0.5.tar.gz
/* NCSC PAC v1.271 */
var Pt;
var Pc;
var ihost;
var NAPROXY="133.183.234.11";
...
Are you doing this with a firewall perhaps? In my case the company's firewall was filtering the download, and ultimately, wget http://cran.fhcrc.org/src/contrib/gdata_2.17.0.tar.gz was downloading an html page from the firewall saying the download was blocked, but install.packages wasn't aware, it just knew that the file was not a valid tarball.
I've come across this issue when using an incompatible (older) version of R/Rstudio. It's worth trying to install an older version of the package via devtools::install_version()
Is there some way to source an R script from the web?
e.g. source('http://github.com/project/R/file.r')
Reason: I currently have a project that I'd like to make available for use but isn't ready to be packaged yet. So it would be great to give people a single file to source from the web (that will then source all the individual function files).
On closer inspection, the problem appears to be https. How would I source this file?
https://raw.github.com/hadley/stringr/master/R/c.r
You can use the source_url in the devtools library
library(devtools)
source_url('https://raw.github.com/hadley/stringr/master/R/c.r')
This is a wrapper for the RCurl method by #ROLO
Yes you can, try running this R tutorial:
source("http://www.mayin.org/ajayshah/KB/R/tutorial.R")
(Source)
Https is only supported on Windows, when R is started with the --internet2 command line option (see FAQ):
> source("https://pastebin.com/raw.php?i=zdBYP5Ft")
> test()
[1] "passed"
Without this option, or on linux, you will get the error "unsupported URL scheme". In that case resort to the solution suggested by #ulidtko, or:
Here is a way to do it using RCurl, which also supports https:
library(RCurl)
eval( expr =
parse( text = getURL("http://www.mayin.org/ajayshah/KB/R/tutorial.R",
ssl.verifypeer=FALSE) ))
(You can remove the ssl.verifypeer if the ssl certificate is valid)
Yes, it is possible and worked for me right away.
R> source("http://pastebin.com/raw.php?i=zdBYP5Ft")
R> test()
[1] "passed"
Regarding the HTTPS part, it isn't supported by internal R code. However, R can use external utilities like wget or curl to fetch https:// URLs. One will need to write additional code to be able to source the files.
Sample code might be like this:
wget.and.source <- function(url) {
fname <- tempfile()
download.file(url, fname, method="wget")
source(fname)
unlink(fname)
}
There is a Windows-only solution too: start R with --internet2 commandline option. This will switch all the internet code in R to using IE, and consequently HTTPS will work.
Windows:
If Internet Explorer is configured to access the web using your organization's proxy, you can direct R to use these IE settings instead of the default R settings. This change can be made once by the following steps:
Save your work and close all R sessions you may have open.
Edit the following file. (Note: Your exact path will differ based on your R installation)
C:\Program Files\R\R-2.15.2\etc\Rprofile.site
Open this "Rprofile.site" file in Notepad and add the following line on a new line at the end of the file:
utils::setInternet2(TRUE)
You may now open a new R session and retry your "source" command.
Linux alikes:
Use G. Grothendieck's suggestion. At the command prompt within R type:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url/here.r")))
You may get an error saying:
cannot verify certificate - - - - Self-signed certificate encountered.
At this point it is up to you to decide whether you trust the person issuing the self-signed certificate and proceed or to stop.
If you decide to proceed, you can connect insecurely as follows:
source(pipe(paste("wget -O -", "https://github.com/enter/your/url.r", "--no-check-certificate")))
For more details, see the following:
See section 2.19
CRAN R Documentation 2.19
wget documentation section 2.8 for "no-check-certificate"
Similar questions here:
Stackoverflow setInternet2 discussion
Stackoverflow Proxy configuration discussion
The methods here were giving me the following error from github:
OpenSSL: error:14077458:SSL routines:SSL23_GET_SERVER_HELLO:reason(1112)
I used the following function to resolve it:
github.download = function(url) {
fname <- tempfile()
system(sprintf("curl -3 %s > %s", url, fname))
return(fname)
}
source(github.download('http://github.com/project/R/file.r'))
Hope that helps!
This is working for me on windows:
library(RCurl)
# load functions and scripts from github ----------------------------
fn1 <- getURL("https://raw.githubusercontent.com/SanjitNarwekar/Advanced-R-Programming/master/fn_factorial_loop.R", ssl.verifypeer = FALSE)
eval(parse(text = fn1))