updte to R console instructions

zehrilatezab · Feb 4, 2014 · 5bb2dec · 5bb2dec
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diff --git a/h2o-docs/source/Ruser/R_studio.rst b/h2o-docs/source/Ruser/R_studio.rst
@@ -8,6 +8,7 @@ These instructions assume you are using R Studio 2.14.0 or later.
 
 **STEP 1**
 
+To use H2O in R, users need a copy of H2O. 
 The download package can be obtained by clicking on the button Download H\ :sub:`2`\ O at `http://0xdata.com/downloadtable <http://0xdata.com/downloadtable/>`_.
 
 Unzip the downloaded H\ :sub:`2`\ O zip file.
@@ -20,32 +21,58 @@ Start an instance of H\ :sub:`2`\ O. For help with this see :ref:`GettingStarted
 Users should be aware that in order for H\ :sub:`2`\ O to successfully run through R, an instance of H\ :sub:`2`\ O must also simultaneously be running. If the instance of H\ :sub:`2`\ O is stopped, the R program will no longer run, and work done will be lost. 
 
 
-**STEP 3**
+**STEP 3** 
 
-Install the H\ :sub:`2`\ O package, and the H\ :sub:`2`\ O client package simultaneously by clicking on **Install Package** 
+For users who may have already installed a prior version of the H2O
+package. New users may skip this step. 
 
-.. image:: Rinstall.png
-   :width: 70%
-
-Walk through the installer helper to the H\ :sub:`2`\ O downloaded folder.  
+For packages to be successfully removed and updated in R studio - they
+must first be detatched from the R environment and then uninstalled. 
+Simply enter the following: 
+
+::
+
+   detach("package:h2o", unload=TRUE) 
+   detach("package:h2oRClient", unload=TRUE) 
+   remove.packages("h2o") 
+   remove.packages("h2oRClient") 
+
+
+Note: users may get warnings of the type "Error in
+detatch("package:h2o", unload = TRUE): invalid 'name' argument. 
+This tells users that there is no h2o package to uninstall. These
+warnings can safely be ignored. 
 
-.. image:: Rfilefinder.png
-   :width: 70%
+.. image:: Rstudioinstall1.jpg
+   :width: 90%
 
 
-Once the correct path has been specified click **Install.** This will install the package in R. 
+**STEP 4**
+
+Install the H\ :sub:`2`\ O package from the H2ORepo, the H2O cran that
+functions exactly like the usual R cran, but is managed and maintained
+by H2O. 
+Simply enter the call: 
 
+::
 
-Start the H\ :sub:`2`\ O package by clicking the check box next to the package name **h2o**. 
-
+  install.packages("h2o", repos=(c("http://h2o-release.s3.amazonaws.com/h2o/rel-jacobi/2/R", getOption("repos"))))
+ 
+as shown here:
 
-.. image:: Rcheckbox.png
-   :width: 70%
+.. image:: Rstudioinstall2.jpg
+   :width: 90%
+
 
 
 
 **STEP 4**
 
+If you have not started an instance of H2O from your command line
+terminal, R will start an instance for you automatically. If you have
+already started an instance, H2O R will connect to this instance, and
+no other instance will be started. 
+
 Get R Studio talking to your instance of H\ :sub:`2`\ O by typing in the call: 
 
 ::
@@ -60,8 +87,9 @@ Upgrading the H\ :sub:`2`\ O R Packages
 """""""""""""""""""""""""""""""""""""""
 
 
-Users may wish to manually upgrade their R packages. For instance, if you are running the bleeding edge developer build, it’s possible that the code has changed, but that the revision number has not, in which case manually upgrading ensures the most current version of not only the H\ :sub:`2`\ O code, but the corresponding R code as well.
-It is highly recommended that users close and restart R, manually remove (by clicking the x next to BOTH h2o packages, as shown in the picture above), and reinstall. 
+Users may wish to manually upgrade their R packages. They can do this
+by returning to STEP 3, and following the instructions through
+STEP 4. 
 
 
 

diff --git a/h2o-docs/source/Ruser/Rcheckbox.png b/h2o-docs/source/Ruser/Rcheckbox.png
diff --git a/h2o-docs/source/Ruser/Rfilefinder.png b/h2o-docs/source/Ruser/Rfilefinder.png
diff --git a/h2o-docs/source/Ruser/Rinstall.png b/h2o-docs/source/Ruser/Rinstall.png
diff --git a/h2o-docs/source/Ruser/Rinstall.rst b/h2o-docs/source/Ruser/Rinstall.rst
@@ -26,38 +26,68 @@ program will no longer run, and work done will be lost.
 
 **STEP 3:**
 
-Install the H\ :sub:`2`\ O package, and the H\ :sub:`2`\ O client
-package simultaneously by entering the following call into your R
-console with an instance of H\ :sub:`2`\ O already running (if H\ :sub:`2`\ O is not
-running, an instance will be started automatically at ip=LocalHost and
-port=54321).  
-
-**DO NOT CUT AND PASTE THIS CALL.** Please replace "foo" and the
-revision number  with the appropriate file path and revision number
-specifying your downloaded and unzipped H\ :sub:`2`\ O file. 
+New uses can safely skip this step, while users who have previously
+installed the  H\ :sub:`2`\ O R packages should uninstall them by entering the
+following commands to the R console:  
 
 ::
 
-  install.packages("foo/R/h2o_2.1.0.99999.tar.gz", repos = NULL, type = "source")
- 
-Once the correct path has been specified, the H\ :sub:`2`\ O package will be
-installed. 
+   detach("package:h2o", unload=TRUE) 
+   detach("package:h2oRClient", unload=TRUE) 
+   remove.packages("h2o") 
+   remove.packages("h2oRClient") 
+
+
+Note: users may get warnings of the type "Error in
+detatch("package:h2o", unload = TRUE): invalid 'name' argument. 
+This tells users that there is no h2o package to uninstall. These
+warnings can safely be ignored. 
 
 **STEP 4:**
 
-Call:
+Install the H\ :sub:`2`\ O package, and the H\ :sub:`2`\ O client
+package via the  H\ :sub:`2`\ O cran. This repository functions exactly like the R
+repository, but is maintained by  H\ :sub:`2`\ O. 
 
 ::
 
-  library(h2o)
-  localH2O<- h2o.init()
+  install.packages("h2o", repos=(c("http://h2o-release.s3.amazonaws.com/h2o/rel-jacobi/2/R", getOption("repos"))))
+ 
+  
 
+**STEP 4:**
+
+Once the  H\ :sub:`2`\ O R package has been installed, call the
+package, and establish a connection to a running instance of  H\
+:sub:`2`\ O. 
+
+If there is no running instance of  H\ :sub:`2`\ O prior to using
+the command "h2o.init()",  H\ :sub:`2`\ O in R will start an instance
+automatically for the user. 
 Note that in the call "localH2O<- h2o.init()" the h2o.init object is
 being named localH2O in the R environment for use later in model
 specification. Users who wish to specify a different IP, port, or heap
 size can do so by entering the appropriate information within the
 call. Entering the call exactly as it is written above assumes the
-user wishes to connect to IP localhost and port: 54321. 
+user wishes to connect to IP localhost and port: 54321.
+
+::
+
+  library(h2o)
+  localH2O<- h2o.init()
+
+
+Users who wish to specify a connection
+with a server (rather than local host at port 54321) must explicity
+state the IP address and port number in the h2o.init call. 
+An example is given below, but **do not cut and paste**; users should
+specify the IP and port number appropriate to their specific
+environment. 
+
+::
+
+  library(h2o)
+  localH2O = h2o.init(ip = "192.555.1.123", port = 12345, startH2O = FALSE, silentUpgrade = TRUE) 
 
 This call *may* return the output:
 
@@ -77,22 +107,9 @@ the code has changed, but that the revision number has not, in which
 case manually upgrading ensures the most current version of not only
 the H\ :sub:`2`\ O code, but the corresponding R code as well.
 
-This can be done using the following commands.
-
-**IMPORTANT**
-Before you cut and paste these commands please check that the file path to 
-the version of H\ :sub:`2`\ O R you would like to install is correct. Replace **foo** with the correct file path. 
+This can be done by returning to STEP 3, and following the commands
+through STEP 4.
 
-::
-  
-  detach("h2oRClient”)
-  detach("h2oRClient”)
-  remove.packages("h2oRClient")
-  remove.packages("h2o")
-  install.packages("foo/R/h2o_2.1.0.99999.tar.gz", repos = NULL, 
-        type = "source")
-  library(h2o)
-  localH2O=h2o.init()
 
 
 

diff --git a/h2o-docs/source/Ruser/Ripandport.png b/h2o-docs/source/Ruser/Ripandport.png
diff --git a/h2o-docs/source/Ruser/Rstudioinstall1.jpg b/h2o-docs/source/Ruser/Rstudioinstall1.jpg
diff --git a/h2o-docs/source/Ruser/Rstudioinstall1.png b/h2o-docs/source/Ruser/Rstudioinstall1.png
diff --git a/h2o-docs/source/Ruser/Rstudioinstall2.jpg b/h2o-docs/source/Ruser/Rstudioinstall2.jpg
diff --git a/h2o-docs/source/Ruser/Rstudioinstall2.png b/h2o-docs/source/Ruser/Rstudioinstall2.png
diff --git a/h2o-docs/source/deployment/multinode.rst b/h2o-docs/source/deployment/multinode.rst
@@ -8,7 +8,7 @@ an H\ :sub:`2`\ O multi-node cluster. Begin by locating a set of hosts to make u
 **STEP 1**
 
 To download H\ :sub:`2`\ O, including the .jar, go to
-`the H\ :sub: `2` O downloads page <http://0xdata.com/downloadtable/>`_ and choose the version that is right for your environment. 
+the H\ :sub:`2`\ O `downloads page <http://0xdata.com/downloadtable/>`_ and choose the version that is right for your environment. 
 
 
 **STEP 2**
@@ -52,8 +52,8 @@ memory.
 For best performance, we recommend you size your cluster to be about
 four times the size of your data (but to avoid swapping, Xmx must not
 be larger than physical memory on any given node).  Giving all nodes
-the same amount of memory is strongly recommended (H\ :sub:`2`\ O works best with
-symmetric nodes).
+the same amount of memory is strongly recommended (H\ :sub:`2`\ O
+works best withsymmetric nodes).
 
 Note the optional -ip (not shown in the example below) and -port
 options tell this H\ :sub:`2`\ O node what IP address and ports (port and port+1
@@ -62,7 +62,7 @@ that have multiple network interfaces.
 
 ::
 
-  $ java -Xmx20g -jar h2o.jar -flatfile flatfile.txt -port 54321 -name MyClusterName
+  $ java -Xmx20g -jar h2o.jar -flatfile flatfile.txt -port 54321
 
 You will see output similar to the following:
 
@@ -80,7 +80,9 @@ You will see output similar to the following:
   08:35:33.559 main      INFO WATER: Java heap maxMemory: 17.78 gb
   08:35:33.559 main      INFO WATER: ICE root: '/tmp/h2o-tomk'
   08:35:33.580 main      INFO WATER: Internal communication uses port: 54322
-  +                                  Listening for HTTP and REST traffic on  http://192.168.1.163:54321/
+  +                                  Listening for HTTP and REST
+				     traffic 
+                                     on  http://192.168.1.163:54321/
   08:35:33.613 main      INFO WATER: H2O cloud name: 'MyClusterName'
   08:35:33.613 main      INFO WATER: (v1.7.0.520) 'MyClusterName' on /192.168.1.163:54321, static configuration based on -flatfile flatfile.txt
   08:35:33.615 main      INFO WATER: Cloud of size 1 formed [/192.168.1.163:54321]

diff --git a/h2o-docs/source/misc/troubleshoot.rst b/h2o-docs/source/misc/troubleshoot.rst
@@ -1,16 +1,3 @@
-H\ :sub:`2`\ O Troubleshooting
-------------------------------
-
-
-**How to Send Logs:** Reporting Errors in H\ :sub:`2`\ O
----------------------------------------------------------
-
-**Errors in Browser Based GUI**
-
-  When you encounter an error while working in the web based GUI for
-  H\ :sub:`2`\ O, following the instructions below will assist H\ :sub:`2`\ O developers in
-  giving you the best possible solution. 
-
 **Step 1** 
 
   Through the drop down menu **Admin** go to **Log View**. 
@@ -194,15 +181,3 @@ on 192.168.1.173:55599
 
 .. Image:: Clusterstattunnel.png
    :width: 70%
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/h2o-docs/source/newuser/quickstart_jar.rst b/h2o-docs/source/newuser/quickstart_jar.rst
@@ -6,7 +6,8 @@ Getting Started from a Downloaded Zip File
 
 Quick Step-by-step
 """"""""""""""""""
-1. Download the latest release of H\ :sub:`2`\ O as a .zip file from H\ :sub:`2`\ O `website <http://0xdata.com/h2O/>`_.
+1. Download the latest release of H\ :sub:`2`\ O as a .zip file from
+   H\ :sub:`2`\ O `downloads page <http://0xdata.com/downloadtable//>`_.
 
 2. From your terminal change your working directory to the same directory where your .zip file is saved.
 
@@ -23,25 +24,39 @@ Quick Step-by-step
   cd h2o-1.7.0.520  #change working directory to the downloaded file
   java -Xmx1g -jar h2o.jar 
 
-5. Wait a few moments and the following output will appear in your terminal window:
+5. Wait a few moments and output similar to the following will appear in your terminal window:
 
 ::
 
-  03:05:45.311 main      INFO WATER: ----- H2O started -----
-  03:05:45.312 main      INFO WATER: Build git branch: master
-  03:05:45.312 main      INFO WATER: Build git hash: f253798433c109b19acd14cb973b45f255c59f3f
-  03:05:45.312 main      INFO WATER: Build git describe: f253798
-  03:05:45.312 main      INFO WATER: Build project version: 1.7.0.520
-  03:05:45.313 main      INFO WATER: Built by: 'jenkins'
-  03:05:45.313 main      INFO WATER: Built on: 'Thu Sep 12 00:01:52 PDT 2013'
-  03:05:45.313 main      INFO WATER: Java availableProcessors: 8
-  03:05:45.321 main      INFO WATER: Java heap totalMemory: 0.08 gb
-  03:05:45.321 main      INFO WATER: Java heap maxMemory: 0.99 gb
-  03:05:45.322 main      INFO WATER: ICE root: '/tmp/h2o-tomk'
-  03:05:45.364 main      INFO WATER: Internal communication uses port: 54322
-  +                                  Listening for HTTP and REST traffic on  http://192.168.1.52:54321/
-  03:05:45.409 main      INFO WATER:  03:05:45.411 main      INFO WATER: Cloud of size 1 formed [/192.168.1.52:54321]
-  03:05:45.543 main      INFO WATER: Log dir: '/tmp/h2o-tomk/h2ologs'
+  Irenes-MacBook-Pro:target Irene$ java -Xmx3g -jar h2o.jar 
+09:54:05.400 main      INFO WATER: ----- H2O started -----
+09:54:05.402 main      INFO WATER: Build git branch: master
+09:54:05.402 main      INFO WATER: Build git hash: e44ee2cec508140fc6312e3d6874df8069eac669
+09:54:05.402 main      INFO WATER: Build git describe: nn-2-3032-ge44ee2c-dirty
+09:54:05.402 main      INFO WATER: Build project version: 2.1.0.99999
+09:54:05.402 main      INFO WATER: Built by: 'Irene'
+09:54:05.402 main      INFO WATER: Built on: 'Tue Feb  4 09:45:26 PST 2014'
+09:54:05.402 main      INFO WATER: Java availableProcessors: 8
+09:54:05.403 main      INFO WATER: Java heap totalMemory: 0.24 gb
+09:54:05.403 main      INFO WATER: Java heap maxMemory: 2.67 gb
+09:54:05.404 main      INFO WATER: Java version: Java 1.7.0_51 (from Oracle Corporation)
+09:54:05.404 main      INFO WATER: OS   version: Mac OS X 10.9.1 (x86_64)
+09:54:05.404 main      INFO WATER: ICE root: '/tmp/h2o-Irene'
+09:54:05.407 main      INFO WATER: Possible IP Address: en0 (en0), fe80:0:0:0:6203:8ff:fe91:950a%4
+09:54:05.407 main      INFO WATER: Possible IP Address: en0 (en0), 192.168.0.4
+09:54:05.408 main      INFO WATER: Possible IP Address: lo0 (lo0), fe80:0:0:0:0:0:0:1%1
+09:54:05.408 main      INFO WATER: Possible IP Address: lo0 (lo0), 0:0:0:0:0:0:0:1
+09:54:05.408 main      INFO WATER: Possible IP Address: lo0 (lo0), 127.0.0.1
+09:54:05.431 main      INFO WATER: Internal communication uses port: 54322
++                                  Listening for HTTP and REST traffic on  http://192.168.0.4:54321/
+09:54:05.471 main      INFO WATER: H2O cloud name: 'Irene'
+09:54:05.472 main      INFO WATER: (v2.1.0.99999) 'Irene' on
+                       /192.168.0.4:54321, discovery address /229.58.14.243:58682
+09:54:05.472 main      INFO WATER: If you have trouble connecting, try SSH tunneling from your local machine (e.g., via port 55555):
++                                    1. Open a terminal and run 'ssh -L 55555:localhost:54321 [email protected]'
++                                    2. Point your browser to http://localhost:55555
+09:54:05.475 main      INFO WATER: Cloud of size 1 formed [/192.168.0.4:54321]
+09:54:05.475 main      INFO WATER: Log dir: '/tmp/h2o-Irene/h2ologs'
 
 5. Point your web-browser to: