R Client Bootstrap

R Client Development

Install the R Client

Follow the instructions to install the current production version of the R client, this will automatically install most dependencies
Installation:
1. If needed, install R from http://cran.r-project.org/
2. From the R command prompt, install the following packages:
  source('http://depot.sagebase.org/CRAN.R') pkgInstall("synapseClient") # If you plan to use a private SFTP server for hosting data, install the optional Rsftp library: pkgInstall("Rsftp")
  At a later date, we anticipate that these packages will be available via Bioconductor or CRAN
3. Also possibly need to install these:
  pkgInstall("RCurl") pkgInstall("rjson") pkgInstall("digest") pkgInstall("RUnit")
Supported Platforms:
- Windows
- Mac OSX
- Any Linux/Unix platform will use the source of the package and compile/install as-needed
Common Installation Problems
RCurl package cannot be installed
If you see an error like:
- installing source package ‘RCurl’ ...
  - package ‘RCurl’ correctement décompressé et sommes MD5 vérifiées
    checking for curl-config... no
    Cannot find curl-config
    ERROR: configuration failed for package ‘RCurl’
then there are missing dependencies for the RCurl package, upon which the Synapse R client depends. For information on resolving these missing dependencies, please see: http://www.omegahat.org/RCurl/FAQ.html
Install any additional required dependences, from the R prompt
- install.packages(c("RUnit","rJava"))
Install the developer tools needed for R Developer Tools#R

Make sure your maven settings file is pointing to the 64bit version of R

Mac OSX

<properties>
        <local.r.path>/usr/bin/r</local.r.path>
...
      </properties>

Windows

<properties>
        <local.r.path>C:\Program Files\R\R-2.13.0\bin\x64\R.exe</local.r.path>
...
      </properties>

You now need to checkout and build the entire Synapse code tree since the R client now depends upon the Java client, Get the Maven Build working
Build the Sage Bionetworks R package, from the shell
- Rcmd INSTALL rSynapseClient
If you see a loading error for rJava, include $JAVA_HOME$/jre/bin/server in your PATH.
Now you are ready to use it, from the R prompt
- library (synapseClient)

Note that every time you change the Java Synapse Client and want to pick up those changes in the R client, you'll need to do an mvn install in each.

How to run the R client against staging

synSetEndpoints('https://repo-staging.prod.sagebase.org/repo/v1',
                'https://auth-staging.prod.sagebase.org/auth/v1',
                'https://file-staging.prod.sagebase.org/file/v1', 
                'https://staging.synapse.org/')

How to run the R unit tests

How to run the installed R unit tests

> synapseAuthServiceEndpoint("https://auth-staging.sagebase.org/auth/v1")
> synapseRepoServiceEndpoint("https://repo-staging.sagebase.org/repo/v1")
> synapseClient:::.test()

RUNIT TEST PROTOCOL -- Wed May 25 15:24:15 2011
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0


1 Test Suite :
synapseClient RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0

How to run your local copy of the R unit tests

> synapseAuthServiceEndpoint("https://auth-staging.sagebase.org/auth/v1")
> synapseRepoServiceEndpoint("https://repo-staging.sagebase.org/repo/v1")
> synapseClient:::.test('/Users/deflaux/platform/trunk/client/rSynapseClient/inst/unitTests')
Error: object '*tmp*' not found
Timing stopped at: 0 0 0
Error in func() : could not find function "synapseQuery"


RUNIT TEST PROTOCOL -- Wed May 25 15:16:24 2011
***********************************************
Number of test functions: 5
Number of errors: 1
Number of failures: 0


1 Test Suite :
synapseClient RUnit Tests - 5 test functions, 1 error, 0 failures
ERROR in unitTestJsonCorretlyParsed: Error in func() : could not find function "synapseQuery"

Test files with failing tests

   test_synapseQuery.R
     unitTestJsonCorretlyParsed


Error in synapseClient:::.test("/Users/deflaux/platform/trunk/client/rSynapseClient/inst/unitTests") :
  unit tests failed for package synapseClient
>

How to run the R integration tests

How to run the installed integration tests

> synapseAuthServiceEndpoint("https://auth-staging.sagebase.org/auth/v1")
> synapseRepoServiceEndpoint("https://repo-staging.sagebase.org/repo/v1")
> synapseLogin("YourUsername", "YourPassword")
> synapseClient:::.integrationTest()
Error: attempt to apply non-function
Error: attempt to apply non-function
Error: attempt to apply non-function
Error: attempt to apply non-function


RUNIT TEST PROTOCOL -- Wed May 25 15:25:52 2011
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0


1 Test Suite :
synapseClient RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>

How to run your local copy of the R integration tests

> synapseAuthServiceEndpoint("https://auth-staging.sagebase.org/auth/v1")
> synapseRepoServiceEndpoint("https://repo-staging.sagebase.org/repo/v1")
> synapseLogin("YourUsername", "YourPassword")
> synapseClient:::.integrationTest('/Users/deflaux/platform/trunk/client/rSynapseClient/inst/integrationTests')
Error: attempt to apply non-function
Error: attempt to apply non-function
Error in parse(n = -1, file = file) : 27:84: unexpected ')'
26: integrationTestPaging <- function() {
27:   firstPagePackets <- synapseQuery('select * from dataset where limit=20 offset=1'))
                                                                                       ^


RUNIT TEST PROTOCOL -- Wed May 25 15:27:38 2011
***********************************************
Number of test functions: 5
Number of errors: 1
Number of failures: 0


1 Test Suite :
synapseClient RUnit Tests - 5 test functions, 1 error, 0 failures
ERROR in /Users/deflaux/platform/trunk/client/rSynapseClient/inst/integrationTests/test_synapseQuery.R: Error while sourcing  /Users/deflaux/platform/trunk/client/rSynapseClient/inst/integrationTests/test_synapseQuery.R : Error in parse(n = -1, file = file) : 27:84: unexpected ')'
26: integrationTestPaging <- function() {
27:   firstPagePackets <- synapseQuery('select * from dataset where limit=20 offset=1'))
                                                                                       ^

Test files with failing tests

   test_synapseQuery.R
     /Users/deflaux/platform/trunk/client/rSynapseClient/inst/integrationTests/test_synapseQuery.R


Error in synapseClient:::.integrationTest("/Users/deflaux/platform/trunk/client/rSynapseClient/inst/integrationTests") :
  integration tests failed for package synapseClient
>

How to run the R integration tests against your local stack

The wiki generator and several of our integration tests expect a subset of prod SageBioCurated data to exist in the service. To populate a local stack with that data, do this by
1. running the following single integration tests:
  ~/platform/trunk/integration-test>mvn -Dit.test=IT100BackupRestoration verify
2. and then once the database is populated we can restart the local stack in debug mode:
  ~/platform/trunk/integration-test>mvn cargo:run

Run the R unit and/or integration tests interactively. Remember to tell R to hit your local stack and use the integration test user account:

library(synapseClient)
synapseAuthServiceEndpoint(endpoint='http://localhost:8080/services-authentication-0.10-SNAPSHOT/auth/v1')
synapseRepoServiceEndpoint(endpoint='http://localhost:8080/services-repository-0.10-SNAPSHOT/repo/v1')
synapseLogin(username='devUser1@sagebase.org', password='password')

How to enable verbose mode

Some what verbose:

synapseClient:::.setCache("debug", TRUE)

Really, really verbose:

synapseClient:::.setCache("debug", TRUE)
synapseClient:::.setCache("curlOpts", list(ssl.verifypeer = FALSE, verbose = TRUE))

How to import the project into Eclipse

Install StatET: http://www.walware.de/goto/statet
In Eclipse: Window > Open Perspective > Other... > StatET
File > New > R-Project
Type project name: "rSynapseClient"
Unclick 'use default location'
Enter name of folder where you checked out the project from SVN, e.g. ...\eclipse projects\trunk\SynapseClient\
Click 'finish'

You will then have the project in Eclipse.