Mac Pro Server Installation Problem
pdeboeck
Joined: 08/04/2009
Am I missing a step? Did source('http://...'), library(OpenMx) and problems came up.
> source('REDACTED')
trying URL 'http://cran.wustl.edu/bin/macosx/universal/contrib/2.9/snowfall_1.70.tgz'
Content type 'application/x-tar' length 221764 bytes (216 Kb)
opened URL
==================================================
downloaded 216 Kb
The downloaded packages are in
/var/folders/4P/4PjGpUneHz4ihgwMhvzYPE+++TI/-Tmp-//RtmpN2blBk/downloaded_packages
trying URL 'REDACTED'
Content type 'application/x-gzip' length 2356993 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb
The downloaded packages are in
/var/folders/4P/4PjGpUneHz4ihgwMhvzYPE+++TI/-Tmp-//RtmpN2blBk/downloaded_packages
> library(OpenMx)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so
Reason: image not found
Error in library(OpenMx) : .First.lib failed for 'OpenMx'
> 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)"
OpenMx does show up under
OpenMx does show up under installed.packages(), but I'm not doing something right because:
> mxMatrix()
Error: could not find function "mxMatrix"
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In reply to OpenMx does show up under by pdeboeck
I wonder if this is a
I wonder if this is a permissions problem since you're using OS X Server
Are you logged in as an account that has permissions to write to
/Library/Frameworks/R.framework/Resources/library/
You might need to do the install as an administrator, depending on how your OS X Server is set up.
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In reply to I wonder if this is a by Steve
Turns out --- Not just a
Turns out --- Not just a server issue. Similar issues on my laptop (Mac Pro)
> source('http:...')
trying URL 'http://cran.mtu.edu/bin/macosx/universal/contrib/2.9/snowfall_1.70.tgz'
Content type 'application/x-gzip' length 221764 bytes (216 Kb)
opened URL
==================================================
downloaded 216 Kb
The downloaded packages are in
/var/folders/96/96lirKLcEKeAKV3pKF6Y2E+++TI/-Tmp-//RtmpkKyMfC/downloaded_packages
trying URL 'http:...'
Content type 'application/x-gzip' length 2356993 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb
The downloaded packages are in
/var/folders/96/96lirKLcEKeAKV3pKF6Y2E+++TI/-Tmp-//RtmpkKyMfC/downloaded_packages
> library(OpenMx)
Loading required package: snowfall
Loading required package: snow
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so
Reason: image not found
Error in library(OpenMx) : .First.lib failed for 'OpenMx'
> 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"
$version.string
[1] "R version 2.9.1 (2009-06-26)"
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In reply to I wonder if this is a by Steve
p.s. I'm admin on both
p.s. I'm admin on both computers.
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Hi, Pascal, Let's start out
Hi, Pascal,
Let's start out in terminal:
> ls /usr/local/lib/libgfortran.2.dylib
Is it there? If it is, it's a permission issue to that file. If it's not, then you probably need to do a clean install of R for all users. But let's do a quick search first:
> locate libgfortran.2.dylib
If it doesn't find it, then, if you have time:
> /usr/libexec/locate.updatedb
> locate libgfortran.2.dylib
The first will update your "locate" databases.
If it did find it, then you can do an "ln -s" to the file in /usr/local/lib or just cp it there.
As Steve pointed out, the fact that it's server may be causing some problems.
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In reply to Hi, Pascal, Let's start out by Jeff
Both computers --- here's the
Both computers --- here's the problem.
ComputerName:~ pascal$ ls /usr/local/lib/libgfortran.2.dylib
ls: /usr/local/lib/libgfortran.2.dylib: No such file or directory
ComputerName:~ pascal$ locate libgfortran.2.dylib
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
What's the best way to fix this?
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In reply to Both computers --- here's the by pdeboeck
Give this a try: > sudo ln
Give this a try:
That should be all on one line.
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In reply to Give this a try: > sudo ln by Jeff
Terminal: ComputerName:~
Terminal:
ComputerName:~ localadmin$ sudo ln -s /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib /usr/local/lib/libgfortran.2.dylib
Password:
ComputerName:~ localadmin$
R:
> library(OpenMx)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so
Reason: image not found
Error in library(OpenMx) : .First.lib failed for 'OpenMx'
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In reply to Terminal: ComputerName:~ by pdeboeck
Let's see output from: > ls
Let's see output from:
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In reply to Let's see output from: > ls by Jeff
lrwxr-xr-x 1 root wheel 78
lrwxr-xr-x 1 root wheel 78 Aug 21 09:30 /usr/local/lib/libgfortran.2.dylib -> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
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In reply to Let's see output from: > ls by Jeff
Same thing, both computers.
Same thing, both computers. (MacBook Pro & Mac Pro Server)
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In reply to Same thing, both computers. by pdeboeck
Let's try a clean install of
Let's try a clean install of R on the MacBook Pro. Is that possible, Pascal?
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In reply to Let's try a clean install of by AdminJeff
Will do. First let me throw
Will do. First let me throw out something else. In the other forum, tbates refers to version 714. Using installed.packages() in R, OpenMx is listed with version "0.1.2-708." Is this a separate/additional potential issue?
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In reply to Will do. First let me throw by pdeboeck
That refers to using the
That refers to using the latest SVN version, instead of an "official" release. If you'd like to have the most up-to-date version, we can point you to the svn repository. But, for this problem, it's unrelated.
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In reply to Let's try a clean install of by AdminJeff
Tried it --- still having
Tried it --- still having problems.
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Library/Frameworks/R.framework/Resources/library/OpenMx/libs/i386/OpenMx.so
Reason: image not found
Error in library(OpenMx) : .First.lib failed for 'OpenMx'
In the terminal, I tried locating the file and got:
ComputerName:~ pascal$ ls /usr/local/lib/libgfortran.2.dylib
/usr/local/lib/libgfortran.2.dylib
ComputerName:~ pascal$
permissions are: lrwxr-xr-x
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In reply to Let's see output from: > ls by Jeff
What do you think of
What do you think of this?
ComputerName:~ localadmin$ ls -la /usr/local/lib/libgfortran.2.dylib
lrwxr-xr-x 1 root wheel 78 Aug 21 09:30 /usr/local/lib/libgfortran.2.dylib -> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
ComputerName:~ localadmin$ ls -la /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
ls: /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib: No such file or directory
ComputerName:~ localadmin$ locate libgfortran.2.dylib
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
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In reply to What do you think of by pdeboeck
I think there's some bad
I think there's some bad magic going on there. Did you try a reinstall yet? You might want to
sudo rm usr/local/lib/libgfortran.2.dylibfirst.Log in or register to post comments
In reply to I think there's some bad by Jeff
That was after the reinstall.
That was after the reinstall. I'll try again, after using the command you listed.
I wouldn't find this so odd, except that both computers seem to be doing the same thing.
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In reply to I think there's some bad by Jeff
So... I can't remove it,
So... I can't remove it, because "No such file or directory"
yet it turns up with ls -la
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In reply to Hi, Pascal, Let's start out by Jeff
I'm guessing this is due, in
I'm guessing this is due, in some way, to how I updated my R version. We might want to include this fix in a Troubleshooting part of the documentation.
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In reply to I'm guessing this is due, in by pdeboeck
Might help to ask people to
Might help to ask people to start with a fresh install of R, and if they don't, then make that the first port of call for trouble?
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In reply to Might help to ask people to by tbates
If they have the latest
If they have the latest version, then we should see if we can fix first, as these issues could pop up when we have to support earlier versions of R as well, that is, when R 2.9.2 comes out.
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Poor Solution: I made a copy
Poor Solution:
I made a copy of R.framework/Versions/2.9 and relabeled it 2.7. Now when it goes to
/usr/local/lib/libgfortran.2.dylib
it finds
/Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libgfortran.2.dylib
However, when I try to
sudo ln -s /Library/Frameworks/R.framework/Versions/2.9/Resources/lib/libgfortran.2.dylib /usr/local/lib/libgfortran.2.dylib
It complains the file exists. When I try to remove /usr/local/lib/libgfortran.2.dylib, it complains that no such file exists. So ugly solution, and some bad voodoo, but it is working. Question is what is the underlying problem? These are two very different machines --- one OS X 10.5.8 server, the other just OS X 10.5.8. I can see if the problem will replicate with one of my machines downstairs, but I suspect the result will be the same.
On a tangent, I get the complaint from R:
> library(OpenMx)
Created directory: /var/localadmin/.sfCluster/restore
snowfall 1.70 initialized: sequential execution, one CPU.
Warning message:
In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
Unknown option on commandline: --gui
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In reply to Poor Solution: I made a copy by pdeboeck
That last message is a
That last message is a warning from snowfall. It's not our fault. And it doesn't indicate that something is wrong.
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In reply to That last message is a by mspiegel
Thanks!
Thanks!
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In reply to Poor Solution: I made a copy by pdeboeck
Thanks for your hard work on
Thanks for your hard work on this, Pascal. If you want, I can remote desktop in sometime to see if I can figure out what's happening, it no one else can come up with anything, but I agree: some bad voodoo.
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In reply to Poor Solution: I made a copy by pdeboeck
This looks to me like a
This looks to me like a permissions problem.
Someplace on the directory tree you likely don't have permission to read anything further up the tree (for trees that grow up from their roots).
That's the only thing I know of that can create the symptoms you are describing: a file exists some times (especially when sudo'ing) and doesn't appear to exist at other times.
If your user is named "pdeboeck", you might try
cd /Library/Frameworks
chown -R pdeboeck R.framework
That will make "all your base belong to you".
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In reply to This looks to me like a by Steve
Might also be time for
Might also be time for cmd-space "Disk Utility"
First Aid:Repair Disk Permissions
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