properly update install.md

ptha_access/INSTALL.Rmd

@@ -11,47 +11,29 @@ If you don't already have R installed, the you need to get it by following the
 instructions on the [R website](https://www.r-project.org/). Use the most recent
 version.
 
-### **Getting a recent version of netcdf**
+### **Installing netcdf**
 
 You need to install the R package `ncdf4` with OPeNDAP support. This may be
 difficult unless you are running Linux (although you can do this using a
 virtual machine). Non-Linux users are encouraged to install an Ubuntu virtual
 machine (e.g. using [VirtualBox](https://www.virtualbox.org) or some other
-virtualization software) and follow the steps below. If you must run Windows,
-we have heard of people successfully running the PTHA codes by using [this
-package]{https://github.com/pmjherman/r-ncdf4-build-opendap-windows} instead of
-the `ncdf4` package - although the author has not tried this.
-
-A further complication is that to work with the PTHA outputs on the NCI THREDDS
-server you need to be using a recent version of netcdf-c. *NOTE: As of Ubuntu
-18.04, you can use the 'standard' netcdf install obtained with apt-get.*
-There was a bug in netcdf-c versions prior to 4.6.0 (released in early 2018) that
-prevented the remote reading of long character strings with OPeNDAP. We store
-some earthquake event data as (potentially) long character strings, and it is
-essential to be able to read these remotely. 
-
-If you are using an older version of netcdf then you will have to install
-netcdf-c from source. Source-code for a recent release of
-netcdf-c can be obtained from the [netcdf-c github
-page](https://github.com/Unidata/netcdf-c/releases). You need to follow their
-instructions to get it installed. 
-
-Next you need to install R's `ncdf4` package, and specifically tell it to use
-the newly installed netcdf.  This can be done by 
-[downloading the ncdf4 sources from this site](https://cran.r-project.org/web/packages/ncdf4/index.html), 
-and then running a command similar to the following, in the directory where you
-have downloaded the `ncdf4` source package:
-
-    R CMD INSTALL ncdf4_1.16.tar.gz --configure-args="--with-nc-config=/home/username/PATH_TO_YOUR_NETCDF_INSTALL/bin/nc-config"
-
-On Ubuntu you might need to prepend `sudo` to the above command, depending on
-where you do the installation. Also, you may need to adjust the numbers in the
-`ncdf4_1.16.tar.gz` term above to match those of the package you download.
-Furthermore, you definitely need to change the path to nc-config to match the
-one on your machine.
-
-To confirm that your `ncdf4` installation is using a suitably recent netcdf-c
-library, please run the following code:
+virtualization software). 
+
+On recent versions of Ubuntu (18.04 and greater) you can probably install netcdf libraries like this
+```
+sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev
+```
+and then install netcdf4 from inside R.
+```r
+# Run this from inside R.
+# You may need to start R with "sudo R" to get permissions to install
+install.packages('ncdf4')
+```
+
+An earlier version of Ubuntu shipped netcdf with an opendap bug, which caused
+problems with ptha data access. To confirm that your `ncdf4` installation is
+using a suitably recent netcdf-c library, please run the following code:
+
 ```{r checkncdf, eval=FALSE}
 library(ncdf4)
 
@@ -89,6 +71,7 @@ etc).
 
 If your internet is not working perfectly, or the NCI server is down, you will see an
 message like this:
+
 ```{r errorMess, eval=FALSE}
 #    Error in Rsx_nc4_get_vara_double: NetCDF: DAP failure
 #    Var: gaugeID  Ndims: 1   Start: 0 Count: 20185
@@ -100,6 +83,7 @@ then check if your internet is working. Also check whether the NCI THREDDS
 server is running (occasionally it goes down for maintainence or technical
 problems).
 
+
 ### **Installing rptha**
 
 Finally you need to install the `rptha` package. This must be built from

ptha_access/INSTALL.md

@@ -34,6 +34,7 @@ An earlier version of Ubuntu shipped netcdf with an opendap bug, which caused
 problems with ptha data access. To confirm that your `ncdf4` installation is
 using a suitably recent netcdf-c library, please run the following code:
 
+
 ```r
 library(ncdf4)
 
@@ -72,6 +73,7 @@ etc).
 If your internet is not working perfectly, or the NCI server is down, you will see an
 message like this:
 
+
 ```r
 #    Error in Rsx_nc4_get_vara_double: NetCDF: DAP failure
 #    Var: gaugeID  Ndims: 1   Start: 0 Count: 20185
@@ -83,6 +85,7 @@ then check if your internet is working. Also check whether the NCI THREDDS
 server is running (occasionally it goes down for maintainence or technical
 problems).
 
+
 ### **Installing rptha**
 
 Finally you need to install the `rptha` package. This must be built from