cmd <- unname(Sys.which("rasdial"))
cmd_args <- c('"VPN Name"', "user","password")
system2(command = cmd, args = cmd_args)
When I run the above it gives me the error:
sh: 1: : Permission denied
Warning message:
In system2(command = cmd, args = cmd_args) : error in running command
I am trying to do this with openvpn. Any help would be much appreciated.
This is my code:
pkgs <- c("rvest", "urltools")
sapply(pkgs, library, character.only = T)
name <- 'cry'
url1 = URLencode(paste0('https://www.google.co.za/search?q=',name))
htmlpage <- html_session(url1)
Unfortunately, I get the following error:
Error in curl::curl_fetch_memory(url, handle = handle) :
Failed to connect to www.google.co.za port 443: Connection refused
What can I do about the error?
I have a connection with an ftp server with the following code:
url <- "ftp://MyServer"
userpwd <- "MyUser:MyPass"
filenames <- getURL(url, userpwd = userpwd, ftp.use.epsv = FALSE, dirlistonly = TRUE, port = 22)
filen <- "MyFile.csv"
rawdata <- getURL(paste(url, filen, sep = ""), userpwd = userpwd, crlf = TRUE)
The file will be moved to an SFTP server, so I need to change the input. This new SFTP server is accessed via port 22 instead of the standard port 21. At the moment the connection fails with the following error
Error in function (type, msg, asError = TRUE) :
Failed to connect to MyServer port 21: Connection refused
It takes the wrong port, but how do I tell R to choose port 22?
You need to specify the SFTP protocol in the URL, so the line
url <- "ftp://MyServer"
should become
url <- "sftp://MyServer"
getUrl will then use the SSH port (22).
I am trying to access to a database HWSD.md which can be downloaded here : http://webarchive.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/HWSD_Data.html?sb=4
I have a linux machine and I tried this command line but I have a message error
require(MonetDB.R)
Mydb <- src_monetdb("*/HWSD.mdb")
Error in socketConnection(host = host, port = port, blocking = TRUE, open = "r+b", :
cannot open the connection
In addition: Warning message:
In socketConnection(host = host, port = port, blocking = TRUE, open = "r+b", :
localhost:50000 cannot be opened
Anyone can help me out with it?
Recently I found out about great dplyr.spark.hive package that enables dplyr frontend operations with spark or hive backend .
There is an information on how to install this package in package's README :
options(repos = c("http://r.piccolboni.info", unlist(options("repos"))))
install.packages("dplyr.spark.hive")
and there are also many examples on how to work with dplyr.spark.hive when one is already connected to hiveServer - check this.
But I am not able to connect to hiveServer, so I can not benefit from the great power of this package...
I've tried such commands, but they did not work out. Does anyone have any solution or comment on what am I doing wrong?
> library(dplyr.spark.hive,
+ lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning: changing locked binding for ‘over’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘partial_eval’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘default_op’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’
>
> Sys.setenv(SPARK_HOME = "/opt/spark-1.5.0-bin-hadoop2.4")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
>
> my_db = src_SparkSQL()
Error in .jfindClass(as.character(driverClass)[1]) : class not found
>
> my_db = src_SparkSQL(host = 'jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl',
+ port = 10000)
Error in .jfindClass(as.character(driverClass)[1]) : class not found
>
> my_db = src_SparkSQL(start.server = TRUE)
Error in start.server() :
Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1
>
> my_db = src_SparkSQL(start.server = TRUE,
+ list(spark.num.executors='5', spark.executor.cores='5', master="yarn-client"))
Error in start.server() :
Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1
EDIT 2
I have set more paths to system variables like this but now I receive a warning telling me that some kind of Java logging-configuration is not specified bu I think it is
> library(dplyr.spark.hive,
+ lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’
3: package ‘SparkR’ was built under R version 3.2.1
>
> Sys.setenv(SPARK_HOME = "/opt/spark-1.5.0-bin-hadoop2.4")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
> Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
> Sys.setenv(HADOOP_HOME="/usr/share/hadoop")
> Sys.setenv(HADOOP_CONF_DIR="/etc/hadoop")
> Sys.setenv(PATH='/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/share/hadoop/bin:/opt/hive/bin')
>
>
> my_db = src_SparkSQL()
log4j:WARN No appenders could be found for logger (org.apache.hive.jdbc.Utils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
My log properties are not empty.
-bash-4.2$ wc /etc/hadoop/log4j.properties
179 432 6581 /etc/hadoop/log4j.properties
EDIT 3
My exact call to the scr_SparkSQL() is
> detach("package:SparkR", unload=TRUE)
Warning message:
package ‘SparkR’ was built under R version 3.2.1
> detach("package:dplyr", unload=TRUE)
> library(dplyr.spark.hive, lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning: changing locked binding for ‘over’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘partial_eval’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘default_op’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’
> Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
> my_db = src_SparkSQL()
log4j:WARN No appenders could be found for logger (org.apache.hive.jdbc.Utils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
And then the proces does not stop (never).
Where those settings work for beeline with such params:
beeline -u "jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl" -n mkosinski --outputformat=tsv --incremental=true -f sql_statement.sql > sql_output
but I am not able to pass user name and dbname to src_SparkSQL()
so I have tried to manual use the code from inside that function but I receive the sam problem that the below code also does not finish
host = 'tools-1.hadoop.srv'
port = 10000
driverclass = "org.apache.hive.jdbc.HiveDriver"
Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
library(RJDBC)
dr = JDBC(driverclass, Sys.getenv("HADOOP_JAR"))
url = paste0("jdbc:hive2://", host, ":", port)
class = "Hive"
con.class = paste0(class, "Connection") # class = "Hive"
# dbConnect_retry =
# function(dr, url, retry){
# if(retry > 0)
# tryCatch(
# dbConnect(drv = dr, url = url),
# error =
# function(e) {
# Sys.sleep(0.1)
# dbConnect_retry(dr = dr, url = url, retry - 1)})
# else dbConnect(drv = dr, url = url)}
#################
##con = new(con.class, dbConnect_retry(dr, url, retry = 100))
#################
con = new(con.class, dbConnect(dr, url, user = "mkosinski", dbname = "loghost"))
Maybe the url should containg also /loghost - the dbname?
I now see that you tried multiple things with multiple errors. Let me comment error by error.
my_db = src_SparkSQL()
Error in .jfindClass(as.character(driverClass)[1]) : class not found
The RJDBC object could not be created. Unless we solve this, nothing else will work, workarounds or not. Have you set HADOOP_JAR with, for instance,
Sys.setenv(HADOOP_JAR = "../spark/assembly/target/scala-2.10/spark-assembly-1.5.0-hadoop2.6.0.jar"). Sorry I seem to have skipped this in the instructions. Will fix.
my_db = src_SparkSQL(host = 'jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl',
+ port = 10000)
Error in .jfindClass(as.character(driverClass)[1]) : class not found
Same problem. Please note host port argument do not accept URL syntax, just host and port. URL is formed internally.
my_db = src_SparkSQL(start.server = TRUE)
Error in start.server() :
Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1
Stop thriftserver first or connect to existing one, but you still have to fix the class not found problem.
my_db = src_SparkSQL(start.server = TRUE,
+ list(spark.num.executors='5', spark.executor.cores='5', master="yarn-client"))
Error in start.server() :
Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1
Same as above.
Plan:
Set HADOOP_JAR. Find host and port of running thriftserver, if not default. Try src_SparkSQL with start.server = FALSE. If happy quit, else goto step 2
Stop existing thriftserver. Try again src_SparkSQL with start.server = TRUE
Let me know how things go.
There was a problem that I did't specify the proper classPath that was needed inside JDBC function that created a driver. Parameters to classPath in dplyr.spark.hive package are passed via HADOOP_JAR global variable.
To use JDBC as a driver to hiveServer2 (through the Thrift protocol) one need to add at least those 3 .jars with Java classes to create a proper driver
hive-jdbc-1.0.0-standalone.jar
hadoop/common/lib/commons-configuration-1.6.jar
hadoop/common/hadoop-common-2.4.1.jar
versions are arbitrary and should be compatible with the installed version of local hive, hadoop and hiveServer2.
They need to be set with the .Platform$path.sep (as described here)
classPath = c("system_path1_to_hive/hive/lib/hive-jdbc-1.0.0-standalone.jar",
"system_path1_to_hadoop/hadoop/common/lib/commons-configuration-1.6.jar",
"system_path1_to_hadoop/hadoop/common/hadoop-common-2.4.1.jar")
Sys.setenv(HADOOP_JAR= paste0(classPath, collapse=.Platform$path.sep)
Then when HADOOP_JAR is set one have to be carefull with hiveServer2 url. In my case it had to be
host = 'tools-1.hadoop.srv'
port = 10000
url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")
and finally the proper connection with hiveServer2 using RJDBC package is
Sys.setenv(HADOOP_HOME="/usr/share/hadoop/share/hadoop/common/")
Sys.setenv(HIVE_HOME = '/opt/hive/lib/')
host = 'tools-1.hadoop.srv'
port = 10000
url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")
driverclass = "org.apache.hive.jdbc.HiveDriver"
library(RJDBC)
.jinit()
dr2 = JDBC(driverclass,
classPath = c("/opt/hive/lib/hive-jdbc-1.0.0-standalone.jar",
#"/opt/hive/lib/commons-configuration-1.6.jar",
"/usr/share/hadoop/share/hadoop/common/lib/commons-configuration-1.6.jar",
"/usr/share/hadoop/share/hadoop/common/hadoop-common-2.4.1.jar"),
identifier.quote = "`")
url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")
dbConnect(dr2, url, username = "mkosinski") -> cont