Ubuntu installation problem

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smedland's picture
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Joined: 08/04/2009

Hi
I'm running into a glitch when installing under Ubuntu 9.04 (64 bit) with R 2.9.2
- I used the source statement from the email dated Aug 17
Error and R.version() are included below
-Sarah

Loading Tcl/Tk interface ... done
Warning in install.packages("snowfall") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
Warning in install.packages("snowfall") :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
'~/R/x86_64-pc-linux-gnu-library/2.9'
to install packages into? (y/n) y
also installing the dependency ‘snow’

trying URL 'http://cran.mtu.edu/src/contrib/snow_0.3-3.tar.gz'
Content type 'application/x-gzip' length 18618 bytes (18 Kb)
opened URL
==================================================
downloaded 18 Kb

trying URL 'http://cran.mtu.edu/src/contrib/snowfall_1.70.tar.gz'
Content type 'application/x-gzip' length 184206 bytes (179 Kb)
opened URL
==================================================
downloaded 179 Kb

* Installing *source* package ‘snow’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'snow'
Formats: text html latex example
snow-cluster text html latex example
snow-internal text html latex
snow-parallel text html latex example
snow-rand text html latex example
snow-startstop text html latex example
** building package indices ...
* DONE (snow)
* Installing *source* package ‘snowfall’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
>>> Building/Updating help pages for package 'snowfall'
Formats: text html latex example
snowfall-a-package text html latex example
snowfall-b-init text html latex example
snowfall-c-calculation text html latex example
snowfall-d-tools text html latex example
snowfall-e-data text html latex
** building package indices ...
* DONE (snowfall)

The downloaded packages are in
‘/tmp/RtmpqUuI7K/downloaded_packages’
Warning in install.packages(pkgs = c("OpenMx"), repos = repos) :
argument 'lib' is missing: using '/home/indigo/R/x86_64-pc-linux-gnu-library/2.9'
trying URL 'http://openmx.psyc.virginia.edu/packages/src/contrib/OpenMx_0.1.3-776.tar.gz'
Content type 'application/x-gzip' length 2920075 bytes (2.8 Mb)
opened URL
==================================================
downloaded 2.8 Mb

* Installing *source* package ‘OpenMx’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc is installed... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.3.3
checking for gawk... /usr/bin/awk
checking for inst/npsol/linux/x86_64/gcc4.3/libnpsol.a... no
configure: error: npsol library not found
ERROR: configuration failed for package ‘OpenMx’
* Removing ‘/home/indigo/R/x86_64-pc-linux-gnu-library/2.9/OpenMx’

The downloaded packages are in
‘/tmp/RtmpqUuI7K/downloaded_packages’
Warning message:
In install.packages(pkgs = c("OpenMx"), repos = repos) :
installation of package 'OpenMx' had non-zero exit status

##################################################

> R.Version()
$platform
[1] "x86_64-pc-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "2"

$minor
[1] "9.2"

$year
[1] "2009"

$month
[1] "08"

$day
[1] "24"

$`svn rev`
[1] "49384"

$language
[1] "R"

$version.string
[1] "R version 2.9.2 (2009-08-24)"

mspiegel's picture
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Joined: 07/31/2009
See

See http://www.macworld.com/article/142379/2009/08/snow_leopard_64_bit.html, there's a difference between your kernel running in 32-bit mode (not happening) and running your applications in 64-bit mode (is happening). You could use the Makefile target "make build64" instead of "make install" to force a x86_64 compile of OpenMx. There is the additional step of taking the .tar.gz file produced in the /build directory and installing that using the R GUI "Install from local file" option.

neale's picture
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Joined: 07/31/2009
Agreed. However, if you hold

Agreed. However, if you hold down the 6 and 4 keys when booting an intel mac, it is possible to coerce the kernel into running in 64-bit mode. Not that this really makes much difference to the present thread, nor to applications which can run in 64-bit mode regardless of the kernel's bit-ness. I've found R64.App to be reasonably decent.

Steve's picture
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Joined: 07/30/2009
Note that the R 2.10 kernel

Note that the R 2.10 kernel is "fat" in that it has both the 32 bit and 64 bit portions compiled in. To force 64 bit behavior from the Mac command line (for those of us who don't use the R GUI....)

R --arch x86_64

or, if you still have a PPC G5 machine:

R --arch ppc64

R 2.10 defaults to 32 bit from the command line. These 64 bit coercions work both on OS X 10.5 and 10.6 as long as your processor is 64 bit addressing capable.

mspiegel's picture
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Joined: 07/31/2009
Ah, I did not know that the

Ah, I did not know that the installation script could install the OpenMx source package. That is useful information to know. WRT your problem, yes it looks like we need to compile NPSOL for gcc 4.4. Hopefully that will be done within a few days.

ecmerkle's picture
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Joined: 03/08/2010
Here is a related (but

Here is a related (but unique) Ubuntu issue: I am running the latest LTS version (Hardy), which as far as I can tell only has gcc 4.2.4. I get the same error message as the others (below); probably the solution is to upgrade to the next LTS coming out soon, but I thought I'd document it here in case anyone knows of other solutions.

* installing *source* package ‘OpenMx’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc is installed... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.2.4
checking for gawk... /usr/bin/awk
checking for inst/npsol/linux/x86/gcc4.2/libnpsol.a... no
configure: error: npsol library not found
ERROR: configuration failed for package ‘OpenMx’
* removing ‘/usr/local/lib/R/site-library/OpenMx’

mspiegel's picture
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Joined: 07/31/2009
Yup. We have npsol compiled

Yup. We have npsol compiled for x86 on gcc 4.1, 4.3, and 4.4 but not 4.2. I'll send an email to our team member with rights to the npsol source and see if we can build a binary for gcc 4.2.

tbates's picture
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Joined: 07/31/2009
just got a new iMac,

just got a new iMac, compiling OpenMx fine but in R64.app I get
> library(OpenMx)
Error: package 'OpenMx' is not installed for 'arch=x86_64'

> gcc --version
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) (dot 1)

Runs fine under R.app

Is there a way to get both 32 and 64 bit working?

t

Steve's picture
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Joined: 07/30/2009
OS X 10.5 or 1.6? 32 bit or

OS X 10.5 or 1.6?

32 bit or 64 bit Intel?

On my macbook pro with 10.6, 64 bit is compiled automatically.

tbates's picture
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Joined: 07/31/2009
OS X 10.6.2 System Software

OS X 10.6.2
System Software Overview
System Version: Mac OS X 10.6.2 (10C2234)
Kernel Version: Darwin 10.2.0
...
64-bit Kernel and Extensions: No

The iMac came with OS X installed... perhaps 64 bit is an option at install time?

My Laptop is, like yours 64 auto and only (R.app won't run OpenMx - only R64).

R64 boots for me on this iMac though, hence I was (and still am, I guess) unsure what was going on.

Steve's picture
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Joined: 07/30/2009
I'm guessing your iMac

I'm guessing your iMac doesn't have a 64 bit processor. AFAIK, Apple is still shipping some 32/64 bit processors. You should be able to coerce GCC to create 64 bit code (with the -arch flag), but it likely won't run as fast as the 32 bit code. I believe you can still get 64 bit addressing if that's what you need 64 bit for. I expect that's how R64 is running on your iMac.

izahn's picture
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Joined: 09/02/2009
Great, I will check back next

Great, I will check back next week.

mspiegel's picture
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Joined: 07/31/2009
The latest release

The latest release (0.2.2-951) works with gcc 4.4 on 32-bit and 64-bit linux systems.

izahn's picture
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Joined: 09/02/2009
I have the same problem with

I have the same problem with 32-bit versions of ubuntu 9.10 beta. Same problem occurs for me on my desktop machine as well as my Asus netbook. By the way, what exactly is the problem? Is it a missing system library, or something missing from OpenMx? I can't find much mention of npsol library anywhere.

mspiegel's picture
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Joined: 07/31/2009
The original thread concerns

The original thread concerns an installation of OpenMx from the source library. There is no binary install of OpenMx on linux. To perform a source install, follow the directions here: http://openmx.psyc.virginia.edu/wiki/howto-build-openmx-source-repository. Anonymous subversion access has been enabled, so you should omit the the "--username" flag. NPSOL is a software package for solving constrained optimization problems (nonlinear programs). We have the rights to distribute the NPSOL binary, which is included with the OpenMx source install.

izahn's picture
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Joined: 09/02/2009
Well OK. I tried to install

Well OK. I tried to install using

source('http://openmx.psyc.virginia.edu/getOpenMx.R')

and got the same error reported in this thread. This method worked in the past (before I upgraded to ubuntu 9.10 beta) but no longer does. Since the error I received is the same as the one reported here I figured I would post in this thread rather than opening a new one.

mspiegel's picture
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Joined: 07/31/2009
Oh I noticed you're installed

Oh I noticed you're installed on the beta release of Ubuntu. Are you performing a source installation? Type gcc --version and copy/paste the output to a forum post. We probably have not compiled npsol for that release of gcc.

izahn's picture
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Joined: 09/02/2009
gcc --version gcc (Ubuntu

gcc --version
gcc (Ubuntu 4.4.1-4ubuntu8) 4.4.1
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

yrosseel's picture
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Joined: 09/20/2009
There seems to be no x86_64

There seems to be no x86_64 gcc4.2 version of the npsol lib either, causing the installation to fail on the LTS version of (k)ubuntu 8.04 (64bit):

* Installing *source* package ‘OpenMx’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc is installed... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.2.4
checking for gawk... /usr/bin/awk
checking for inst/npsol/linux/x86_64/gcc4.2/libnpsol.a... no
configure: error: npsol library not found
ERROR: configuration failed for package ‘OpenMx’
* Removing ‘/opt/R/library/OpenMx’

> R.version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 9.2
year 2009
month 08
day 24
svn rev 49384
language R
version.string R version 2.9.2 (2009-08-24)

mspiegel's picture
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Joined: 07/31/2009
Yeah, at the moment we have

Yeah, at the moment we have NPSOL x86_64 linux compiles for gcc 3.4., 3.9, 4.1. We're in the process of compiling for the more recent revisions.

mspiegel's picture
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Joined: 07/31/2009
Ah. It looks like npsol for

Ah. It looks like npsol for linux on x86_64 was not compiled for gcc 4.3. I can open a ticket for that issue.

smedland's picture
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Joined: 08/04/2009
great thanks very much (and

great thanks very much (and yes I'm still seeing how many operating systems I can get this running on)
Sarah