When running R CMD check I get the following note:
checking for future file timestamps ... NOTE
unable to verify current time
I have seen this discussed here, but I am not sure which files it is checking for timestamps, so I'm not sure which files I should look at. This happens locally on my windows and remotely on different systems (using github actions).
Take a look at https://svn.r-project.org/R/trunk/src/library/tools/R/check.R
The check command relies on an external web resource:
now <- tryCatch({
foo <- suppressWarnings(readLines("http://worldclockapi.com/api/json/utc/now",
warn = FALSE))
This resource http://worldclockapi.com/ is currently not available.
Hence the following happens (see same package source):
if (is.na(now)) {
any <- TRUE
noteLog(Log, "unable to verify current time")
See also references:
https://community.rstudio.com/t/r-devel-r-cmd-check-failing-because-of-time-unable-to-verify-current-time/25589
So, unfortunately this requires a fix in the check function by the R development team ... or the web-resource coming online again.
To add to qasta's answer, you can silence this check by setting the _R_CHECK_SYSTEM_CLOCK_ environment variable to zero e.g Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0)
To silence this in a persistent manner, you can set this environment variable on R startup. One way to do so is through the .Renviron file, in the following manner:
install.packages("usethis") (If not installed already)
usethis::edit_r_environ()
Add _R_CHECK_SYSTEM_CLOCK_=0 to the file
Save, close file, restart R
Related
Typically, when starting up an renv project, one gets a message that looks something like this:
* Project '~/path/to/project' loaded. [renv 0.10.0]
I am trying to suppress this message, particularly when non-interactively running a script from this project.
Checking the package help, I noted ?config i.e. User-Level Configuration of renv. Specifically, I found synchronized.check, of which the document states is for controlling how renv lockfile synchronization is checked (this is also outputted to the console). However, I couldn't find how to control the main startup message. I also checked the ?settings but found nothing relevant either.
I've tried fiddling with options and Sys.setenv without luck so far.
So, is it possible to suppress the message, seeing that the renv script activate.R controls how the package itself is loaded?
You are correct that there isn't a specific documented way to configure this in renv. For now, you can set:
options(renv.verbose = FALSE)
before renv is loaded. (You may want to turn it back to TRUE if you want renv to display other messages as part of its normal work.)
You can suppress library startup messages with suppressPackageStartupMessages, e.g.
suppressPackageStartupMessages(library(igraph))
There is also suppressMessages for arbitrary function calls.
I want to deploy a basic trained R model as a webservice to AzureML. Similar to what is done here:
http://www.r-bloggers.com/deploying-a-car-price-model-using-r-and-azureml/
Since that post the publishWebService function in the R AzureML package was has changed it now requires me to have a workspace object as first parameter thus my R code looks as follows:
library(MASS)
library(AzureML)
PredictionModel = lm( medv ~ lstat , data = Boston )
PricePredFunktion = function(percent)
{return(predict(PredictionModel, data.frame(lstat =percent)))}
myWsID = "<my Workspace ID>"
myAuth = "<my Authorization code"
ws = workspace(myWsID, myAuth, api_endpoint = "https://studio.azureml.net/", .validate = TRUE)
# publish the R function to AzureML
PricePredService = publishWebService(
ws,
"PricePredFunktion",
"PricePredOnline",
list("lstat" = "float"),
list("mdev" = "float"),
myWsID,
myAuth
)
But every time I execute the code I get the following error:
Error in publishWebService(ws, "PricePredFunktion", "PricePredOnline", :
Requires external zip utility. Please install zip, ensure it's on your path and try again.
I tried installing programs that handle zip files (like 7zip) on my machine as well as calling the utils library in R which allows R to directly interact with zip files. But I couldn't get rid of the error.
I also found the R package code that is throwing the error, it is on line 154 on this page:
https://github.com/RevolutionAnalytics/AzureML/blob/master/R/internal.R
but it didn't help me in figuring out what to do.
Thanks in advance for any Help!
The Azure Machine Learning API requires the payload to be zipped, which is why the package insists on the zip utility being installed. (This is an unfortunate situation, and hopefully we can find a way in future to include a zip with the package.)
It is unlikely that you will ever encounter this situation on Linux, since most (all?) Linux distributions includes a zip utility.
Thus, on Windows, you have to do the following procedure once:
Install a zip utility (RTools has one and this works)
Ensure the zip is on your path
Restart R – this is important, otherwise R will not recognize the changed path
Upon completion, the litmus test is if R can see your zip. To do this, try:
Sys.which("zip")
You should get a result similar to this:
zip
"C:\\Rtools\\R-3.1\\bin\\zip.exe"
In other words, R should recognize the installation path.
On previous occasions when people told me this didn’t work, it was always because they thought they had a zip in the path, but it turned out they didn’t.
One last comment: installing 7zip may not work. The reason is that 7zip contains a utility called 7zip, but R will only look for a utility called zip.
I saw this link earlier but the additional clarification which made my code not work was
1. Address and Path of Rtools was not as straigt forward
2. You need to Reboot R
With regards to the address - always look where it was installed . I also used this code to set the path and ALWAYS ADD ZIP at the end
##Rtools.bin="C:\\Users\\User_2\\R-Portable\\Rtools\\bin"
Rtools.bin="C:\\Rtools\\bin\\zip"
sys.path = Sys.getenv("PATH")
if (Sys.which("zip") == "" ) {
system(paste("setx PATH \"", Rtools.bin, ";", sys.path, "\"", sep = ""))
}
Sys.which("zip")
you should get a return of
" C:\\RTools|\bin\zip"
From looking at Andrie's comment here: https://github.com/RevolutionAnalytics/AzureML/commit/9cf2c5c59f1f82b874dc7fdb1f9439b11ab60f40
Implies we can just download RTools and be done with it.
Download RTools from:
https://cran.r-project.org/bin/windows/Rtools/
During installation select the check box to modify the PATH
At first it didn't work. I then tried R32bit, and that seemed to work. Then R64 bit started working again. Honestly, not sure if I did something in the middle to make it work. Only takes a few minutes so worth a punt.
Try the following
-Download the Rtools file which usually contains the zip utility.
-Copy all the files in the "bin" folder of "Rtools"
-Paste them in "~/RStudio/bin/x64" folder
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))
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'm trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.