Login

News

Installation Assistance for the Closed Beta

Posted on
Picture of user. Jeff Joined: 07/31/2009
Forums
OpenMx Installation
Welcome to the OpenMx Installation Forum. If you're here, you may be having problems installing OpenMx, but we're here to help. The first step is install R (http://r-project.org). You need to make sure that you have version 2.9.1 or the latest version as of August 2, 2009. Next, you need to run the command that Steve included in his email. That will install the dependencies required for OpenMx, namely Snowfall, and download and install the version of OpenMx that will work with your system. If you didn't receive any errors, then you're all set to try your first model (start with the User Guide in Documentation). If you did receive an error, be sure to create a new forum topic in this forum, and copy and paste the output (including the error) that you received from R along with the output when you run the following command in R:

R.Version()

For example, my R.Version() outputs the following:

> R.Version()
$platform
[1] "i386-apple-darwin8.11.1"

$arch
[1] "i386"

$os
[1] "darwin8.11.1"

$system
[1] "i386, darwin8.11.1"

$status
[1] ""

$major
[1] "2"

$minor
[1] "9.1"

$year
[1] "2009"

$month
[1] "06"

$day
[1] "26"

$`svn rev`
[1] "48839"

$language
[1] "R"

$version.string
[1] "R version 2.9.1 (2009-06-26)"

Good luck!

Replied on Thu, 08/06/2009 - 07:05
Picture of user. smedland Joined: 08/04/2009

Sorry to post the first error
when I pasted in the command from Steve's email it yielded the following output - there is an obvious issue with the path

also installing the dependency ‘snow’

trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.9/snow_0.3-3.zip'
Content type 'application/zip' length 83667 bytes (81 Kb)
opened URL
downloaded 81 Kb

trying URL 'http://cran.ms.unimelb.edu.au/bin/windows/contrib/2.9/snowfall_1.70.zip'
Content type 'application/zip' length 272684 bytes (266 Kb)
opened URL
downloaded 266 Kb

package 'snow' successfully unpacked and MD5 sums checked
package 'snowfall' successfully unpacked and MD5 sums checked
Error in normalizePath(path) :
path[1]="C:\Program Files\R\R-2.9.1\library/snowfall": The system cannot find the file specified
>

> R.Version()
$platform
[1] "i386-pc-mingw32"

$arch
[1] "i386"

$os
[1] "mingw32"

$system
[1] "i386, mingw32"

$status
[1] ""

$major
[1] "2"

$minor
[1] "9.1"

$year
[1] "2009"

$month
[1] "06"

$day
[1] "26"

$`svn rev`
[1] "48839"

$language
[1] "R"

$version.string
[1] "R version 2.9.1 (2009-06-26)"

Log in or register to post comments
Replied on Fri, 08/07/2009 - 03:36
Picture of user. Jeff Joined: 07/31/2009

Hmm, that's an interesting one. Let's check if things got installed anyway:

Try typing,

grep("snow", installed.packages()[,1])
grep("OpenMx", installed.packages()[,1])

And paste the output from each.

If you get "integer(0)" for each, then we'll have to figure out how to get snow. One thing you could try, although I'm not sure the result will be different, is by going to the Package Installer under the GUI menu "Packages and Data", selecting "CRAN binaries", "Get List", search for "snow", selecting the packages and then "Install Selected".

Log in or register to post comments
Replied on Fri, 08/07/2009 - 06:34
Picture of user. tbates Joined: 07/31/2009

Did it look like the problem was that the first part of the path was specified in DOS (/) and the last part in Unix/Mac OS "/", then the path normalizer barfed?

It would have worked on anything other than a Windows box, because the user's machine would have supplied the first portion in "/" delimited format

Log in or register to post comments
Replied on Fri, 08/07/2009 - 06:39
Picture of user. mspiegel Joined: 07/31/2009

Typically the Windows environment is fairly robust in the presence of forward-slash deliminators as directory separators. I think the paths generated by the OpenMx Makefile have both types of slashes, and they work successfully. I'm not saying this isn't the problem (maybe R still freaks out when it sees both types), only that I've seen Windows process this correctly in other cases.
Log in or register to post comments
Replied on Fri, 08/07/2009 - 09:02
Picture of user. Ryne Joined: 07/31/2009

In my windows install, R will recognize both single forward slashes and double backslashes as directory separators. Single backslashes give me the following error in a setwd() command:

1: '\c' is an unrecognized escape in a character string
2: unrecognized escape removed from "C:/Documents and Settings\cre2w/"

Log in or register to post comments
Replied on Fri, 08/07/2009 - 13:54
Picture of user. mspiegel Joined: 07/31/2009

I was able to run the installer on a Windows XP machine. Are you running Windows Vista? That would suggest some kind of permissions error. See the following link if you are running Vista: http://cran.wustl.edu/bin/windows/base/rw-FAQ.html#I-don_0027t-have-permission-to-write-to-the-R_002d2_002e9_002e1_005clibrary-directory
Log in or register to post comments
Replied on Sun, 08/09/2009 - 09:13
Picture of user. smedland Joined: 08/04/2009

Snow appears to be installed

> grep("snow", installed.packages()[,1])
[1] 20
> grep("OpenMx", installed.packages()[,1])
integer(0)

I reinstalled R (clean install) using the default install and got the same error. I also tried another clean install using the -internet2 option and got the same error

Error in normalizePath(path) :
path[1]="C:\Program Files\R\R-2.9.1\library/snowfall": The system cannot find the file specified

However, it did install successfully on my work machine also xp

Log in or register to post comments
Replied on Sun, 08/09/2009 - 10:25
Picture of user. Steve Joined: 07/30/2009

How about a really basic check.

Does C:\Program Files\R\R-2.9.1\library exist? Maybe your Program Files directory is on a D: drive? I'm trying to figure out why it would work on one of your machines and not on another.

Another possibility is that you don't have permissions to access that directory and so R put the snowfall package somewhere else.

Log in or register to post comments
Replied on Mon, 08/10/2009 - 07:15
Picture of user. smedland Joined: 08/04/2009

yes the folder C:\Program Files\R\R-2.9.1\library does exist
this is my personal laptop and I am the administrator

the issue is not the snowfall package which is successfully installed
it is the OpenMx package which is not installing - the command is searching for the folder

"C:\Program Files\R\R-2.9.1\library/OpenMx"

There is no OpenMx folder in C:\Program Files\R\R-2.9.1\library

Obviously I can download the zip file and do a local install however, the issue is whether this can be resolved for future users

Log in or register to post comments
Replied on Mon, 08/10/2009 - 10:51
Picture of user. mspiegel Joined: 07/31/2009

It's good to hear that you've got OpenMx working on at least one computer. Let's consider our options for fixing the installation on the other machine. Jeff is more of the expert in configuring R packages, but what if you tried source(SECRET-URL-FROM-EMAIL, echo = TRUE), where you replace SECRET-URL-FROM-EMAIL with the url from Steve's email. And then copy/paste the output into the forums. Except if you don't mind deleting the URL when you paste the output on the forums, we'd like to keep OpenMx in closed beta until we are ready for a larger release.
Log in or register to post comments
Replied on Mon, 08/10/2009 - 12:21
Picture of user. neale Joined: 07/31/2009

Agreed, this seems like a good way to go to help debug. I am also wondering if one or other of you who might be able to fix it should Skype Sarah to figure out wtf is going on, so as to speed up the bugfix cycle. It's obviously an inconvenience for her to be able to use it only at the office (where she's probably being paid to do other things...) and she's a really capable tester.
Log in or register to post comments
  Login

News