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Warning: dependencies ‘digest’, ‘RcppEigen’ are not available

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karobro's picture
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Joined: 01/16/2013 - 10:41
Warning: dependencies ‘digest’, ‘RcppEigen’ are not available

Hi,
I am getting a warning that some dependencies are not available each time I download the beta. Is this sth to worry about? The analysis will still run.

> source('https://openmx.ssri.psu.edu/getOpenMxBeta.R')
Installing package into ‘M:/pc/Dokumenter/R/win-library/3.1’
(as ‘lib’ is unspecified)
Warning: dependencies ‘digest’, ‘RcppEigen’ are not available
trying URL 'https://openmx.ssri.psu.edu/testing/bin/windows/contrib/3.1/OpenMx_2.0.0-3838.zip'
Content type 'application/zip' length 3404044 bytes (3.2 Mb)
opened URL
downloaded 3.2 Mb

package ‘OpenMx’ successfully unpacked and MD5 sums checked

Thanks,
Karoline

mhunter's picture
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Joined: 07/31/2009 - 15:26
Hmm ...

Hmm ... try

install.packages(c('RcppEigen', 'digest'))
source('http://openmx.psyc.virginia.edu/getOpenMxBeta.R')

Do you still get the same warning?

karobro's picture
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Joined: 01/16/2013 - 10:41
Yes I get the same warning. I

Yes I get the same warning.

I also occasionally encounter this warning: cannot remove prior installation of package ‘OpenMx’. It usually works if I close R and retry once or twice or change to another -bit.

I have attached the output.

Thanks,
Karoline

karobro's picture
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Joined: 01/16/2013 - 10:41
cannot remove prior installation of OpenMx

Hi again,

Today I get the warning: cannot remove prior installation of package ‘OpenMx’ after several tries with source('http://openmx.psyc.virginia.edu/getOpenMxBeta.R').

I tried remove.packages("OpenMx"), but get the following message: Error in find.package(pkgs, lib) : there is no package called ‘OpenMx’.

I would greatly appreciate any suggestions for a solution to this problem.

Many thanks,
Karoline

AdminRobK's picture
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Joined: 01/24/2014 - 12:15
You run Windows, correct?

You run Windows, correct? Try this. In the file explorer, navigate to the R library folder into which you're installing OpenMx. It's probably the path you would see if you enter .libPaths()[1] at the R prompt. Once you're looking at the contents of the folder, look for a file called "OpenMx" that has no file extension. Delete that file, and try installing again.

karobro's picture
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Joined: 01/16/2013 - 10:41
Yes, I'm running windows. It

Yes, I'm running windows. It worked now, so thank you!

I'm still getting that the dependency RcppEigen is not available when I download the beta. Should I worry about this with regard to the correctness of the results?

Thanks for the help,
Karoline

AdminRobK's picture
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Joined: 01/24/2014 - 12:15
I think you'll be OK(?)

I suspect that the warning you're seeing about RcppEigen is spurious. Much of OpenMx's C++ code links to RcppEigen's compiled code for matrix objects and operations, so if the warning were genuine, I would guess that even if installation of OpenMx somehow succeeded, running analyses would probably fail.

Do you have package RcppEigen installed??

karobro's picture
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Joined: 01/16/2013 - 10:41
Yes, RcppEigen is in the

Yes, RcppEigen is in the library, so I guess there is nothing to worry about then. Thanks!

mhunter's picture
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Joined: 07/31/2009 - 15:26
Try an example

Like Rob and other have indicated, we're pretty sure that everything is working fine with your install, and the warning is nothing to worry about. However, if you'd like to check for yourself then you can run some models from our test suite. These scripts contain code that checks to make sure the parameters (and sometimes standard errors or other statistics) match what we know they should be. Here's one example.

http://openmx.psyc.virginia.edu/svn/trunk/models/passing/IntroSEM-MultiRegRaw.R

The end should say something like "blah and blah are equal to within blah". If it prints an error, then there's a problem and let us know!

karobro's picture
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Joined: 01/16/2013 - 10:41
I ran your example, and

I ran your example, and everything looked fine! Thank you for that!

tbates's picture
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Joined: 07/31/2009 - 14:25
not looking in the right place for RcppEigen?

I wonder if we're not looking in the right place for RcppEigen?

I just installed OpenMx 2.0 on a student's machine (OS X 10.8.1) and got the error RcppEigen unavailable warning

> source('http://openmx.psyc.virginia.edu/getOpenMx2.R')
...
Warning: dependency ‘RcppEigen’ is not available

It is, however, available for this R (sock it to me) and installs fine on the same OS X machine

> install.packages("RcppEigen")
trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/RcppEigen_0.3.2.2.0.tgz'
Content type 'application/x-gzip' length 3321066 bytes (3.2 Mb)
opened URL
==================================================
downloaded 3.2 Mb
tbates's picture
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Joined: 07/31/2009 - 14:25
not available = not found for your platform/R version

install.packages by default installs packages we c("Depends", "Imports", "LinkingTo")

Warning: dependencies ‘digest’, ‘RcppEigen’ are not available

means R couldn't find versions of those packages for your platform/R version.

try looking at the package requirements and see if you meet them
http://cran.r-project.org/web/packages/RcppEigen

http://cran.r-project.org/web/packages/digest

It might be also that RcppEigen needs compiling, in which case I think you need devtools installed? ...

The warning "cannot remove prior installation of package ‘OpenMx’ " occurs because R doesn't have a great mechanism for pulling loaded packages out of memory in order to load in the new version. Even specialised tools like devtools struggle to get this to work all the time, esp. if packages are used by other packages. It's safest to quit and restart R when you update a package that you've already loaded in that session (either that or do the update before calling library(OpenMx)

t