The sysadmin just made SSL connection compulsory and since then I'm not able to access the mysql db anymore from R (even if I'm able to access it through Workbench) using the package RMysql. I tried multiple options without success and here is the error I get in R Studio:
Error in .local(drv, ...) :
Failed to connect to database: Error: Access denied for user 'blabla'#'host.blablabla' (using password: YES)
I read that I should modify my cnf file, but as I could not find it I created one in the /etc folder and still did not work. Should I save it somewhere else? Am I missing something?
Solved using the RMySql version that is on GitHub at the moment.
Related
I am struggling with installing a package from a GitLab repository on a Windows computer.
I found different hints but still have problems to install my package from GitLab. First of all, I generated a public and private key with puttygen.exe. The files need to be changed afterwards, I had to remove comments and stuff so they look like my the file on my Unix system. So now, both public and private key files have just a single line.
I tried to install my package via devtools::install_git which takes very long and I get the error message
Error: Failed to install 'unknown package' from Git:
Error in 'git2r_remote_ls': Failed to authenticate SSH session: Unable to send userauth-publickey request
And with devtools::install_gitlab I get a different error message and I somehow have the feeling, the link which gets generated doesn't fit to my GitLab server.
Error: Failed to install 'unknown package' from GitLab:
cannot open URL 'https://gitlab.rlp.net/api/v4/projects/madejung%2FMQqueue.git/repository/files/DESCRIPTION/raw?ref=master'
My complete code to test at the moment is
creds <- git2r::cred_ssh_key(publickey="~/.ssh/id_rsa_gitlab.pub",
privatekey="~/.ssh/id_rsa_gitlab")
devtools::install_git(
url='git#gitlab.rlp.net:madejung/MQqueue.git',
quiet=FALSE,
credentials=creds)
devtools::install_gitlab(
repo='madejung/MQqueue.git',
host='gitlab.rlp.net',
quiet=FALSE,
credentials=creds
)
My id_rsa_gitlab.pub file looks like this and is just a single line:
ssh-rsa AAAA....fiwbw== rsa-key-20200121
The id_rsa_gitlab file has just the code:
AAABA.....3WNSIAGE=
Update
On my Mac system it works as expected after installing the libssh2 library via homebrew and and recompiling git2r with install.packages("git2r", type = "source").
So the working code on my machine is:
creds <- git2r::cred_ssh_key(publickey="~/.ssh/id_rsa_gitlab.rlp.net.pub",
privatekey="~/.ssh/id_rsa_gitlab.rlp.net")
devtools::install_git(
url='git#gitlab.rlp.net:madejung/MQqueue.git',
quiet=FALSE,
credentials=creds
)
For some strange reason, the devtools::install_git call needs about a minute to fail in the end. I have no idea where the problem here is.
After struggling for almost a day, I found a solution I can live with...
I first created a PAT (Personal Access Token) in my gitlab account and granted full API access. For some reason the read_only access didn't worked and I am now tired to figure out what the problem is.
After this I had still problems to install my package and for some reason, the wininet setting for downloading doesn't work.
I used the command capabilities("libcurl") to check if libcurl is available on my windows, which was and tried to overwrite wininet to libcurl by using method='libcurl' in the install function. Somehow, this was not enough so I overwrote the options variable download.file.method directly.
options("download.file.method"='libcurl')
devtools::install_gitlab(
repo='madejung/MQqueue',
auth_token='Ho...SOMETHING...xugzb',
host='gitlab.rlp.net',
quiet=FALSE, force=TRUE
)
After installing sparklyr package I followed the instruction here ( http://spark.rstudio.com/ ) to connect to spark. But faced with this error. Am I doing something wrong. Please help me.
sc = spark_connect( master = 'local' )
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file 'C:\Users\USER\AppData\Local\Temp\RtmpYb3dq4\fileff47b3411ae_spark.log':
Permission denied
But I am able to find the file at the stated location. And on opening, I found it to be empty.I
First of all, did you install sparklyr from github devtools::install_github("rstudio/sparklyr") or CRAN?
There were some issues some time ago with Windows installations.
The issue you have seems to be related to TEMP and TMP folder level permission on Windows or to file creation permission. Every time you start sc <- spark_connect(), it tries to create a folder and file to write the log files.
Make sure you have a write access to these locations.
I could observe the same error message with version 2.4.3 and 2.4.4
in different cases:
When trying to connect to a non "local" master, using spark_connect(master="spark://192.168.0.12:7077", ..),
if the master is not started or not responding at the specified master url.
when setting a specific incomplete configuration
in my case trying to set dynamicAllocation to true, without other required dynamicAllocation settings:
conf <- spark_config()
conf$spark.dynamicAllocation.enabled <- "true"
I am working on deploying a shiny application in a Docker container onto Bluemix. I am using the rocker/shiny Docker image (https://hub.docker.com/r/rocker/shiny/) as my initial starting point. I have installed unixODBC-dev, RODBC, ibm data server driver package, the ibmdbR library for R, and all needed dependencies. My only problem is that when I try to access the shiny app from a web browser it fails to execute, the error is:
Warning in odbcDriverConnect("DSN=BLUDB", :
[RODBC] ERROR: state 01000, code 0, message [unixODBC][Driver Manager]Can't open lib '/root/db2_cli_odbc_driver/dsdriver/odbc_cli_driver/linuxamd64/clidriver/lib/libdb2o.so' : file not found
Warning in odbcDriverConnect("DSN=BLUDB; :
ODBC connection failed
Error in idaInit(con) : con is not an open connection, please use idaConnect() to create an open connection to the data base.
Initially I had this same problem whenever I would try to use isql to connect to the database or try to connect from RStudio, I used ldd on that library file and found what was missing and that fixed making connections from the command line and RStudio, however my Shiny-Server still gives me the same error, is there anything I am missing?
I ended up solving the problem myself, turns out the libraries were not accessible by the shiny-server which was running as a service. I moved the db2 odbc drivers over to /usr/local/lib to make it accessible, I also ran the "ldd" command on the library mentioned in the error message and found that I had to install libxml2 as well. After doing that I simply changed my odbcinst.ini file at /etc to reference the new location of the db2 library and now it all works! Hopefully anyone else trying to deploy Shiny Apps that rely on connecting to a DB2 database will find this useful.
Using the following for just connection pooling no master_slave or replication: rhel 6, postgresql 9.1.9, & pgpool-II 3.1.3 (also tried 3.2.5)
Followed solution suggested in http://www.pgpool.net/pipermail/pgpool-general/2013-May/001773.html
After following the instructions for MD5 I also tried setting both pg_hba.conf and pool_hba.conf to trust for local and subnet, but still get the following error when attempting to connect to the pool locally:
ERROR: "MD5" authentication with pgpool failed for user foo
Tried locally on Fedora 18 with pg9.2 and pgpool from Fedora repo and worked right out of the box.
At the end of all routes suggested everywhere I could find.
Help would be greatly appreciated.
After having hit the same problem the solution was to change ownership of the pool_passwd file to postgres.
Even though this file has a 644 permission, if owner isn't postgres you'll always get the aforementioned error. I guess this file's owner and the user running pgpool must match.
I'm running PosgreSQL 9.2 and pgpool-II 3.3.2, BTW.
I'm using the RPostgreSQL 0.4 library (compiled on R 2.15.3) on R 2.15.2 under Windows 7 64-bit to interface to PostgreSQL. This works fine when connecting to my PostgreSQL databases on localhost. I'm trying to get my R code to run with a remote PostgreSQL database on Heroku. I can connect to Heroku's PostgreSQL database from the psql command shell on my machine, and it connects without a problem. I get the message:
psql (9.2.3, server 9.1.9)
WARNING: psql version 9.2, server version 9.1.
Some psql features might not work.
WARNING: Console code page (437) differs from Windows code page (1252)
8-bit characters might not work correctly. See psql reference
page "Notes for Windows users" for details.
SSL connection (cipher: DHE-RSA-AES256-SHA, bits: 256)
Clearly, psql uses SSL to connect. When I try to connect using the RPostgreSQL library routine dbConnect(), however, supplying exactly the same credentials using dname=, host=, port=, user=, password=, the connection fails with the complaint:
Error in postgresqlNewConnection(drv, ...) :
RS-DBI driver: (could not connect <user>#<hostname> on dbname <dbname>)
Calls: source ... .valueClassTest -> is -> is -> postgresqlNewConnection -> .Call
Execution halted
I know that Heroku insists on an SSL connection if you want to access their database remotely, so it seems likely that the R interface routine dbConnect() isn't trying SSL. Is there something else that I can do to get a remote connection from R to PostgreSQL on Heroku to work?
To get the JDBC URL for your heroku instance:
Get your hostname, username and password using [pg:credentials].
Your jdbc URL is going to be:
jdbc:postgresql://[hostname]/[database]?user=[user]&password=[password]&ssl=true&sslfactory=org.postgresql.ssl.NonValidatingFactory
Proceed as you would normally with JDBC.
Apparently there is a way using RJDBC. See:
http://ryepup.unwashedmeme.com/blog/2010/11/17/working-with-r-postgresql-ssl-and-mssql/
Please note that in order to connect to Heroku database with JDBC externally, it is important to set the sslfactory parameter as well. Hope Heroku team goes through it and modifies their documentation.
String dbUri = "jdbc:postgresql://ec2-54-243-202-174.compute-1.amazonaws.com:5432/**xxxxxxx**";
Properties props = new Properties();
props.setProperty("user", "**xxxxx**");
props.setProperty("password", "**xxxxx**");
props.setProperty("ssl", "true");//ssl to be set true
props.setProperty("sslfactory", "org.postgresql.ssl.NonValidatingFactory");// sslfactory to be set as shown above
Connection c=DriverManager.getConnection(dbUri,props);
See answer to related Q at https://stackoverflow.com/a/38942581. The suggestion of using RPostgres (https://github.com/rstats-db/RPostgres) instead of RPostgreSQL resolved this same issue for me.