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Use sendmailR with Windows
(4 answers)
Closed 8 years ago.
I am trying to use sendemailR package in R but I am getting an error I don't know how to fix.
When trying the default parameters:
library(sendmailR)
from <- "your_email"
to <- "your_email"
subject <- "Test send email in R"
body <- "It works!"
mailControl=list(smtpServer="smtp.gmail.com")
sendmail(from=from,to=to,subject=subject,msg=body,control=mailControl)
I get the error
Error in socketConnection(host = server, port = port, blocking = TRUE) :
cannot open the connection
In addition: Warning message:
In socketConnection(host = server, port = port, blocking = TRUE) :
Gmail SMTP Server:25 cannot be opened
So I change the port to 465 and it seems to work
library(sendmailR)
from <- "your_email"
to <- "your_email"
subject <- "Test send email in R"
body <- "It works!"
mailControl=list(smtpServer="smtp.gmail.com", smtpPort="465")
sendmail(from=from,to=to,subject=subject,msg=body,control=mailControl)
but then I get the following error
Error in if (code == lcode) { : argument is of length zero
Any idea what's happening?
This is the version of R and Windows
R version 3.0.3 (2014-03-06) -- "Warm Puppy"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
Thanks!
There are two things that need attention in your example:
As #David Arenburg commented, to should contain a valid email address.
The second thing is the smtp server you are using: smtp.gmail.com. This server need authentication which is not supported by sendmailR.
You can use an smtp server that does not require authentication (e.g. the restricted gmail smtp server: aspmx.l.google.com, port 25, see here for details)
The other option is to use the mailR package that allows authentication.
Try something like (of course you have to put valid email addresses and user.name and passwd to work):
library(mailR)
sender <- "SENDER#gmail.com"
recipients <- c("RECIPIENT#gmail.com")
send.mail(from = sender,
to = recipients,
subject="Subject of the email",
body = "Body of the email",
smtp = list(host.name = "smtp.gmail.com", port = 465,
user.name="YOURUSERNAME#gmail.com", passwd="YOURPASSWORD", ssl=TRUE),
authenticate = TRUE,
send = TRUE)
Hope it helps,
alex
Related
I'm having issues using the SFTP functionality of this package. Here is the issue I'm running into.
If I enter my credential information as such:
sftp_con <- sftp_connect(server = "sftp.name.com",
username = "username",
password = "password",
protocol = "sftp://",
port = 2222)
sftp_download("*")
I get the following error message:
Error in function (type, msg, asError = TRUE) :
Protocol "sftp" not supported or disabled in libcurl
Is there a way around this? If it helps, I'm on a Mac Book running this.
I've got a postgres database hosted on Digital Ocean. On a server, I use the below R code without error and am able to connect. However, on my local machine (Mac, M1, 11.2.3) I get an error. Any ideas?
library(DBI)
library(RPostgres)
library(dbplyr)
library(dbx)
con <- dbxConnect(adapter = "postgres",
host = "db-postgresql-XXX.ondigitalocean.com",
port = 11111,
dbname = "XXXX",
user = "XXXX",
password = "XXXXX")
The error I get is:
Error: FATAL: no pg_hba.conf entry for host "XXX", user "XXXX", database "XXXX", SSL off
p.s. I've replaced sensitive stuff in the above with XXX etc.
That is often a sign that you do are being barred from access by Postgres configurations.
You need to add your IP address to the pg_hba.conf file (or your administrator does) and label it as trusted. Once this is done, you will likely not have that problem.
It is a security feature.
The is a problem with the newest version of the RPostgres library. Downgrading worked for me:
install.packages("RPostgres", repos = "https://r-dbi.r-universe.dev")
More info here:
https://github.com/r-dbi/RPostgres/issues/291
I am running into
Error: could not receive data from server: Software caused connection abort (0x00002745/10053)
upon trying to connect to a postgres database using the DBI package in R. Note that i am in a work environment, so subject to a corporate firewall. Can that explain the error or is there something else that could be happening?
Here is the code I'm using
# Connect to trayaway dev
con <- DBI::dbConnect(
RPostgres::Postgres(),
host = host, port = 5432, dbname = "postgres",
user = user, password = password
)
error below:
Error: could not receive data from server: Software caused connection abort (0x00002745/10053)
solution was found- i tried the same code using wiFi and the code works - when hardwired, connection string fails to connect to database - so this is a corporate firewall issue - thank you,
I am attempting to connect to an SFTP site to pull data. It used to work, but for some reason, it stopped working a couple of weeks ago. The owners of the SFTP say nothing has changed on their end, and I can pull data easily without error using WinSCP.
protocol <- "sftp"
server <- "sftp.xxxx.net"
userpwd <- "user:password"
file <- "/public/bpus_dailytx.csv"
url <- paste0(protocol, "://", server, file)
data <- getURL(url = url, userpwd=userpwd, verbose = TRUE)
When I run this, I now get the following info:
* Trying xxx.xx.xx.xxx...
* Connected to sftp.xxxx.net (xxx.xx.xx.xxx) port 22 (#0)
* SSH MD5 fingerprint: 34rh3ie93hhr39hhdik3
* SSH authentication methods available: publickey,keyboard-interactive
* Using SSH public key file '(nil)'
* Using SSH private key file ''
* SSH public key authentication failed: Unable to extract public key from private key file: Unable to open private key file
* No identity would match
* Authentication failure
* Closing connection 0
Error in function (type, msg, asError = TRUE) : Authentication failure
It connects OK but then the authentication fails. Any ideas what could be going on here? Again, this code used to work but something has changed. What are some other ways I can attempt to pull the data other than this?
Edit: WinSCP screenshots:
It is difficult to say why your code stopped working because we do not have enough information about configurations (both on your machine and on the server) when it was working.
Because your keyfile was not in the proper format for RCurl, my leading hypothesis is that although the server folks said nothing changed on their end, I think they removed the password authentication option. That is because your code attempts password authentication only. If password authentication were still available, the one line in your output would look something like this:
SSH authentication methods available: publickey,password,keyboard-interactive
It is, as you noted, now:
SSH authentication methods available: publickey,keyboard-interactive
Therefore, the solution here was to convert your keyfile from PuTTY to OpenSSH format using PuTTYgen and then use the following RCurl code pointing to your new keyfile:
protocol <- "sftp"
server <- "sftp.xxxx.net"
file <- "/public/bpus_dailytx.csv"
url <- paste0(protocol, "://", server, file)
keypasswd <- "your_keypasswd"
ssh.private.keyfile = "your_path_to_keyfile"
username <- "your_username"
data <- getURL(url = url, keypasswd = keypasswd, ssh.private.keyfile = ssh.private.keyfile, username = username, verbose = TRUE)
And I will add a special thanks to #Tensibai for the assistance. It would have taken me way longer to arrive at this solution without their insight with the keyfile format.
I'm writing a R package for the first time. Its called aactr and is hosted on my GitHub: https://github.com/jasonbaik94/aactr
Right now, the package only has one function, aact_connect:
aact_connect <- function(user, password) {
drv <- DBI::dbDriver('PostgreSQL')
con <- DBI::dbConnect(drv,
dbname="aact",
host="aact-db.ctti-clinicaltrials.org",
port=5432,
user=user,
password=password)
}
My concern is that users of my package wouldn't like to input their username and password in their R script for privacy reasons.
What would be a nice workaround to ensure user privacy?
One thought I had: When the user types aact_connect(), a window pops up where the user can input username and password and press Enter, after which the connection would be made. Also, for those without a username or password, I'd put a parameter, init_connection = TRUE, after which this sign up page would load: https://aact.ctti-clinicaltrials.org/users/sign_up
Any others suggestions are greatly welcome!
There are many ways to securely handle database credentials in scripts. See few examples below:
Use configuration files such as yaml saves securely on user's machines for R to read into needed variables. See #Spacedman's answer.
config.yaml
db:
host : localhost
port : 5432
name : mypgdb
user : pg_useR
pwd : ***
R
library(yaml)
config = yaml.load_file("/path/to/config.yml")
dbConnect(drv, host = config$db$host, port = config$db$port,
dbname = config$db$name,
user = config$db$user, password = config$db$pwd)
Use environmental variables that are linked to user or system profiles:
db_creds <- Sys.getenv(c("DB_HOST", "DB_PORT", "DB_NAME", "DB_USER", "DB_PWD"))
con <- DBI::dbConnect(drv,
dbname = db_creds[['DB_NAME']],
host = db_creds[['DB_HOST']],
port = db_creds[['DB_PORT,']],
user = db_creds[['DB_USER']],
password = db_creds[['DB_PWD']])
Use DSNs that maintains connection parameters but requires an ODBC connection which can be run with the generalized odbc package (part of same DBI family as RPostgreSQL). Postgres maintains up-to-date odbc drivers for most operating systems. See R-bloggers post.
odbc.ini
[myPG_DSN]
Driver = PostgreSQL Unicode
Database = mypg_db
Servername = localhost
UserName = pg_useR
Password = ***
R
db <- dbConnect(odbc::odbc(), "myPG_DSN")