Rstudio:
Link to download the Software:
http://www.rstudio.com/products/rstudio/download-server/
Installation:
sudo yum install --nogpgcheck <rstudio-server-package.rpm>
Here we need to cross check all the dependencies in-order to install successfully.
Ex: openssl098e-0.9.8e-18.el6_5.2.x86_64
gcc41-libgfortran-4.1.2 ( I didn't install this but it's working for me)
Rstudio restart:
sudo rstudio-server restart/start/stop OR
sudo /usr/sbin/rstudio-server restart
Logs:
/var/log/message --for CentOS
Configuration Files:
/etc/rstudio/
Javaconf/Renviron/ldpath Location:
/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc/Renviron
Managing Active Sessions:
sudo rstudio-server active-sessions
Suspend all running sessions:
sudo rstudio-server suspend-all
sudo rstudio-server force-suspend-session <pid>
sudo rstudio-server force-suspend-all
List open files:
lsof -u <divakar>
RStudio taking backup for every 1 min.
Solution:
Go to /etc/rstudio and below property in rsession.conf( create a new file if file doesn't exit)
cat rsession.conf
session-timeout-minutes=60
limit-file-upload-size-mb=10240 (not required, this property to put limit in upload size)
RHive:
Installation Location:
/lib64/Revo-7.3/R-3.1.1/lib64/R/library/
Required Packages:
Required Packages:
Command to Un-install Packages:
R CMD REMOVE RHive OR
> uninstall.packages("rJava")
Command to Install any package:
R CMD INSTALL <RHive_2.0-0.10.tar.gz> &
>install.packages("rJava")
To find Environmental Variable related to R:
just run env from Linux command line and typical env variables should be like:
------------------------
[root@abc ~]# env
MANPATH=/opt/teradata/client/14.10/odbc_32/help/man:
HOSTNAME=abc.com
SHELL=/bin/bash
TERM=xterm
HISTSIZE=1000
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
USER=root
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib64:/opt/teradata/client/14.10/tbuild/lib:/usr/lib
NLSPATH=/opt/teradata/client/14.10/tbuild/msg/%N:/opt/teradata/client/14.10/odbc_32/msg/%N:
MAIL=/var/spool/mail/root
PATH=/opt/teradata/client/14.10/tbuild/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
TD_ICU_DATA=/opt/teradata/client/14.10/tdicu/lib
PWD=/root
LANG=en_US.UTF-8
COPLIB=/opt/teradata/client/14.10/lib
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
ODBCINI=/home/root/.odbc.ini
TWB_ROOT=/opt/teradata/client/14.10/tbuild
COPERR=/opt/teradata/client/14.10/lib
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
CVS_RSH=ssh
LESSOPEN=||/usr/bin/lesspipe.sh %s
G_BROKEN_FILENAMES=1_=/bin/env
OLDPWD=/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc
----------------------------------------------------------
Typical Environmental Variables for R,Revo64,RHive,HIveR & Rstudio:
echo $LD_LIBRARY_PATH=
/usr/local/lib:/usr/local/lib64:/opt/teradata/client/14.10/tbuild/lib:/usr/lib
-------------------------------
R CMD javareconf: This needs to be run after after changing/creation of any soft links which are related to libjar( this doesn't cause any issue, just to refresh Env Variables)
[root@adcp22nxhwx01 ~]# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.7.0_71
Java home path : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI progam
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L/usr/lib64 -ljvm
gcc -std=gnu99 -I/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib64 -ljvm -L/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/lib -lR
----------------------------------------------
JAVA_HOME : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre
Java library path: /usr/lib64
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L/usr/lib64 -ljvm
Updating Java configuration in /usr/lib64/Revo-7.3/R-3.1.1/lib64/R
Done.
Error Messages:
Problem:
* installing to library ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library’
ERROR: dependency ‘rJava’ is not available for package ‘RHive’
* removing ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library/RHive’
Solution: Install rJava
Problems:
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library/rJava’
The downloaded source packages are in
‘/tmp/RtmpY0FHgS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
Solution:
Here java libs are pointing incorrect location, ideally should display like:
ln -s /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server/libjvm.so /usr/lib64/libjvm.so
run R CMD javareconf ( To refresh java config after creation of soft link)
To find:
Location: /usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc/ --check for any files updated by today
find /usr/ | grep libjvm.so
rm /usr/lib64/libjvm.so
ls -la /usr/lib64/libhdfs.so
/usr/lib64/libhdfs.so -> /usr/hdp/2.2.0.0-2041/usr/lib/libhdfs.so.0.0.0 ( Incorrect Link)
--------------------
Problem:
rhive.connect(host="00.000.00.00",port=10000,defaultFS="hdfs://00.000.00.00:8020")
[Fatal Error] hadoop-env.sh.xml:2:1: Content is not allowed in prolog.
2015-06-20 22:09:16,608 FATAL [main] conf.Configuration (Configuration.java:loadResource(2518)) - error parsing conf file:/etc/hadoop/conf/hadoop-env.sh.xml
org.xml.sax.SAXParseException; systemId: file:/etc/hadoop/conf/hadoop-env.sh.xml; lineNumber: 2; columnNumber: 1; Content is not allowed in prolog.
org.apache.hadoop.security.UserGroupInformation.setConfiguration(UserGroupInformation.java:299)
file:/etc/hadoop/conf/hadoop-env.sh.xml; lineNumber: 2; columnNumber: 1; Content is not allowed in prolog.
Solution: remove unwanted hadoop-env.sh.xml from /etc/hadoop/conf/
-----------
> install.packages("RCurl", repos="http://cran.r-project.org")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/RCurl_1.95-4.7.tar.gz'
Content type 'application/x-gzip' length 916897 bytes (895 KB)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/lib64/R/library/RCurl’
The downloaded source packages are in
‘/tmp/Rtmp0CKyl3/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("RCurl", repos = "http://cran.r-project.org") :
installation of package ‘RCurl’ had non-zero exit status
>
Link to download the Software:
http://www.rstudio.com/products/rstudio/download-server/
Installation:
sudo yum install --nogpgcheck <rstudio-server-package.rpm>
Here we need to cross check all the dependencies in-order to install successfully.
Ex: openssl098e-0.9.8e-18.el6_5.2.x86_64
gcc41-libgfortran-4.1.2 ( I didn't install this but it's working for me)
Rstudio restart:
sudo rstudio-server restart/start/stop OR
sudo /usr/sbin/rstudio-server restart
Logs:
/var/log/message --for CentOS
Configuration Files:
/etc/rstudio/
Javaconf/Renviron/ldpath Location:
/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc/Renviron
Managing Active Sessions:
sudo rstudio-server active-sessions
Suspend all running sessions:
sudo rstudio-server suspend-all
sudo rstudio-server force-suspend-session <pid>
sudo rstudio-server force-suspend-all
List open files:
lsof -u <divakar>
RStudio taking backup for every 1 min.
Solution:
Go to /etc/rstudio and below property in rsession.conf( create a new file if file doesn't exit)
cat rsession.conf
session-timeout-minutes=60
limit-file-upload-size-mb=10240 (not required, this property to put limit in upload size)
RHive:
Installation Location:
/lib64/Revo-7.3/R-3.1.1/lib64/R/library/
Required Packages:
yum
install -y java-1.70.-openjdk-devel.x86_64
yum
install -y mesa-libGL-devel
yum
install -y mesa-libGLU-devel
Required Packages:
install.packages("rJava")
install.packages("HiveR")
install.packages("png")
install.packages("Rserve")
Command to Un-install Packages:
R CMD REMOVE RHive OR
> uninstall.packages("rJava")
Command to Install any package:
R CMD INSTALL <RHive_2.0-0.10.tar.gz> &
>install.packages("rJava")
To find Environmental Variable related to R:
just run env from Linux command line and typical env variables should be like:
------------------------
[root@abc ~]# env
MANPATH=/opt/teradata/client/14.10/odbc_32/help/man:
HOSTNAME=abc.com
SHELL=/bin/bash
TERM=xterm
HISTSIZE=1000
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
USER=root
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib64:/opt/teradata/client/14.10/tbuild/lib:/usr/lib
NLSPATH=/opt/teradata/client/14.10/tbuild/msg/%N:/opt/teradata/client/14.10/odbc_32/msg/%N:
MAIL=/var/spool/mail/root
PATH=/opt/teradata/client/14.10/tbuild/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
TD_ICU_DATA=/opt/teradata/client/14.10/tdicu/lib
PWD=/root
LANG=en_US.UTF-8
COPLIB=/opt/teradata/client/14.10/lib
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
ODBCINI=/home/root/.odbc.ini
TWB_ROOT=/opt/teradata/client/14.10/tbuild
COPERR=/opt/teradata/client/14.10/lib
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
CVS_RSH=ssh
LESSOPEN=||/usr/bin/lesspipe.sh %s
G_BROKEN_FILENAMES=1_=/bin/env
OLDPWD=/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc
----------------------------------------------------------
Typical Environmental Variables for R,Revo64,RHive,HIveR & Rstudio:
echo $LD_LIBRARY_PATH=
/usr/local/lib:/usr/local/lib64:/opt/teradata/client/14.10/tbuild/lib:/usr/lib
-------------------------------
R CMD javareconf: This needs to be run after after changing/creation of any soft links which are related to libjar( this doesn't cause any issue, just to refresh Env Variables)
[root@adcp22nxhwx01 ~]# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.7.0_71
Java home path : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI progam
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L/usr/lib64 -ljvm
gcc -std=gnu99 -I/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/include -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib64 -ljvm -L/usr/lib64/Revo-7.3/R-3.1.1/lib64/R/lib -lR
----------------------------------------------
JAVA_HOME : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre
Java library path: /usr/lib64
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L/usr/lib64 -ljvm
Updating Java configuration in /usr/lib64/Revo-7.3/R-3.1.1/lib64/R
Done.
Error Messages:
Problem:
* installing to library ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library’
ERROR: dependency ‘rJava’ is not available for package ‘RHive’
* removing ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library/RHive’
Solution: Install rJava
Problems:
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/lib64/Revo-7.3/R-3.1.1/lib64/R/library/rJava’
The downloaded source packages are in
‘/tmp/RtmpY0FHgS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rJava") :
installation of package ‘rJava’ had non-zero exit status
Solution:
Here java libs are pointing incorrect location, ideally should display like:
ln -s /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server/libjvm.so /usr/lib64/libjvm.so
run R CMD javareconf ( To refresh java config after creation of soft link)
To find:
Location: /usr/lib64/Revo-7.3/R-3.1.1/lib64/R/etc/ --check for any files updated by today
find /usr/ | grep libjvm.so
rm /usr/lib64/libjvm.so
ls -la /usr/lib64/libhdfs.so
/usr/lib64/libhdfs.so -> /usr/hdp/2.2.0.0-2041/usr/lib/libhdfs.so.0.0.0 ( Incorrect Link)
--------------------
Problem:
rhive.connect(host="00.000.00.00",port=10000,defaultFS="hdfs://00.000.00.00:8020")
[Fatal Error] hadoop-env.sh.xml:2:1: Content is not allowed in prolog.
2015-06-20 22:09:16,608 FATAL [main] conf.Configuration (Configuration.java:loadResource(2518)) - error parsing conf file:/etc/hadoop/conf/hadoop-env.sh.xml
org.xml.sax.SAXParseException; systemId: file:/etc/hadoop/conf/hadoop-env.sh.xml; lineNumber: 2; columnNumber: 1; Content is not allowed in prolog.
org.apache.hadoop.security.UserGroupInformation.setConfiguration(UserGroupInformation.java:299)
file:/etc/hadoop/conf/hadoop-env.sh.xml; lineNumber: 2; columnNumber: 1; Content is not allowed in prolog.
Solution: remove unwanted hadoop-env.sh.xml from /etc/hadoop/conf/
-----------
> install.packages("RCurl", repos="http://cran.r-project.org")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/RCurl_1.95-4.7.tar.gz'
Content type 'application/x-gzip' length 916897 bytes (895 KB)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/lib64/R/library/RCurl’
The downloaded source packages are in
‘/tmp/Rtmp0CKyl3/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("RCurl", repos = "http://cran.r-project.org") :
installation of package ‘RCurl’ had non-zero exit status
>
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