Error in newXMLTextNode(title) : CHAR() can only be applied to a 'CHARSXP', not a 'NULL'

[xiaowei3223]

Hi, I am a master student from Guangzhou Medical University of China.

This is a good R package for building R function tools in the Galaxy.
I am using this package for build an Galaxy tools. But I has some problem in this process.

Following this package Vignettes, I tried to build R function tool to Galaxy. As its written: build a function and the man page (I thought the man page is a RDucumentaion, and the name of this RDucumentation should be the same of this function name.)

My galaxy downloaded using command git clone -b release_20.05 https://github.com/galaxyproject/galaxy.git , it work.

1. Now, I try to use the comand:

galaxy("addTwoNumbers",
       manpage = "/home/xiaowei/Galaxy/R_test/addTwoNumbers.Rd",
       galaxyConfig=
         GalaxyConfig("/home/xiaowei/Galaxy/Galaxy_20.05/galaxy/config/", "mytool", "Test Section",
                      "testSectionId")
)

It shows the error:

Error in newXMLTextNode(title) : 
  CHAR() can only be applied to a 'CHARSXP', not a 'NULL'
In addition: Warning message:
Not enough information to create a functional test. 

And it didn't build the mytool directory in tools.

2. In fact, the Galaxy home should be /home/xiaowei/Galaxy/Galaxy_20.05/galaxy/. If I set galaxyHome was /home/xiaowei/Galaxy/Galaxy_20.05/galaxy/ at function GalaxyConfig, it show me ERROR:

Error: Invalid galaxyHome, no tool_conf.xml file!
In addition: Warning message:
 Error: Invalid galaxyHome, no tool_conf.xml file! 

And it build the mytool directory in tools, but mytool directory not has this tool XML file.

So, can you help solve this problem. Also, if you can tell me how to build the XML file for R function, I will sincerely appreciate your help.

Thank you.

Regard,
Huang Xiaowei

Guangzhou Medical University, Guangdong Province, China
email: h15016211223@163.com

[nturaga]

Hi,

I'm unable to reproduce your error using the RGalaxy package.

However, I did notice an issue with the way you are calling the GalaxyConfig function. The first argument in the GalaxyConfig(galaxyHome = "/home/xiaowei/Galaxy/Galaxy_20.05/galaxy/", ... should be just the galaxy home directory (just like you point it out in your point number two)

galaxyHome: *Required.* The full path to your Galaxy distribution.

And as far as the tool_conf.xml, you need to have a tool_conf.xml file in your galaxyHome. There is a dummy tool_conf.xml if you'd like to take a look in the RGalaxy package,

print(system.file("galaxy", "tool_conf.xml", package="RGalaxy"))

But the more comprehensive tool_conf.xml is located here in the Galaxy config directory galaxyHome/config/tool_conf.xml.main

     galaxyHome <- "/home/xiaowei/Galaxy/Galaxy_20.05/galaxy/"
     file.copy(file.path(galaxyHome, "config", "tool_conf.xml.main"), file.path(galaxyHome, "tool_conf.xml"), overwrite=FALSE)

If you need more help, be sure to mention all the steps you took, so we can reproduce your error.