[vsni.co.uk] Contact us
Author Message
Post new topic

  ASReml  ~  Does ASReml-R work with R-2.9.0?

kiwi
Posted: Tue May 05, 2009 11:32 pm Reply with quote
Joined: 16 Nov 2008 Posts: 22
It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code:
> require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
  libirc.so: cannot open shared object file: No such file or directory
(Note that
Code:
$Rhome
is not literally what's in the message.)
Has anyone used R-2.9.0 with asreml?
Code:
> sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grDevices utils     stats     graphics  methods   base     

other attached packages:
[1] lattice_0.17-22

loaded via a namespace (and not attached):
[1] grid_2.9.0
>
Reverting to R-2.8.1 avoids the problem, but that's not a satisfactory solution..
View user's profile Send private message
david.butler
Posted: Wed May 06, 2009 1:26 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
Dear Kiwi,

I'll check it out as soon as I can - I've not yet installed R 2.9.

dave.


From: ASReml users discussion group [mailto:ASREML-L@dpi.nsw.gov.au] On Behalf Of kiwi
Sent: Wednesday, 6 May 2009 9:33 AM
To: ASREML-L@dpi.nsw.gov.au
Subject: Does ASReml-R work with R-2.9.0?



It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code: > require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory

(Note that Code: $Rhome

is not literally what's in the message.)
Has anyone used R-2.9.0 with asreml? Code: > sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grDevices utils stats graphics methods base

other attached packages:
[1] lattice_0.17-22

loaded via a namespace (and not attached):
[1] grid_2.9.0

Reverting to R-2.8.1 avoids the problem, but that's not a satisfactory solution..








This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


********************************DISCLAIMER****************************
The information contained in the above e-mail message or messages
(which includes any attachments) is confidential and may be legally
privileged. It is intended only for the use of the person or entity
to which it is addressed. If you are not the addressee any form of
disclosure, copying, modification, distribution or any action taken
or omitted in reliance on the information is unauthorised. Opinions
contained in the message(s) do not necessarily reflect the opinions
of the Queensland Government and its authorities. If you received
this communication in error, please notify the sender immediately
and delete it from your computer system network.



This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
luansheng
Posted: Wed May 06, 2009 1:51 am Reply with quote
Joined: 05 Aug 2008 Posts: 45
Dear david:Will asreml-r3package be also released when distributing the asreml 3 ?
Luan sheng
----------------------------------------
Yellow Sea Fisheries Research Institute
Chinese Academy of Fisheries Sciences
Nanjing Road 106
Qingdao 266071
China
luansheng@gmail.com (luansheng@gmail.com)
luansheng@ysfri.ac.cn (luansheng@ysfri.ac.cn)
----------------------------------------



2009/5/6 Butler, David <David.Butler@dpi.qld.gov.au (David.Butler@dpi.qld.gov.au)>
Quote:
Dear Kiwi,

I'll check it out as soon as I can - I've not yet installed R 2.9.

dave.


From: ASReml users discussion group [mailto:ASREML-L@dpi.nsw.gov.au (ASREML-L@dpi.nsw.gov.au)] On Behalf Of kiwi
Sent: Wednesday, 6 May 2009 9:33 AM
To: ASREML-L@dpi.nsw.gov.au (ASREML-L@dpi.nsw.gov.au)
Subject: Does ASReml-R work with R-2.9.0?




It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code: > require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory

(Note that Code: $Rhome

is not literally what's in the message.)
Has anyone used R-2.9.0 with asreml? Code: > sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grDevices utils stats graphics methods base

other attached packages:
[1] lattice_0.17-22

loaded via a namespace (and not attached):
[1] grid_2.9.0

Reverting to R-2.8.1 avoids the problem, but that's not a satisfactory solution..








Thismessageisintendedfortheaddresseenamedandmaycontainconfidentialinformation.Ifyouarenottheintendedrecipient,pleasedeleteitandnotifythesender.Viewsexpressedinthismessagearethoseoftheindividualsender,andarenotnecessarilytheviewsoftheirorganisation.




********************************DISCLAIMER****************************
Theinformationcontainedintheabovee-mailmessageormessages
(whichincludesanyattachments)isconfidentialandmaybelegally
privileged.Itisintendedonlyfortheuseofthepersonorentity
towhichitisaddressed.Ifyouarenottheaddresseeanyformof
disclosure,copying,modification,distributionoranyactiontaken
oromittedinrelianceontheinformationisunauthorised.Opinions
containedinthemessage(s)donotnecessarilyreflecttheopinions
oftheQueenslandGovernmentanditsauthorities.Ifyoureceived
thiscommunicationinerror,pleasenotifythesenderimmediately
anddeleteitfromyourcomputersystemnetwork.



Thismessageisintendedfortheaddresseenamedandmaycontainconfidentialinformation.Ifyouarenottheintendedrecipient,pleasedeleteitandnotifythesender.Viewsexpressedinthismessagearethoseoftheindividualsender,andarenotnecessarilytheviewsoftheirorganisation.








This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
stephen
Posted: Wed May 06, 2009 5:57 am Reply with quote
Joined: 05 Aug 2008 Posts: 4
It works for me with R 2.9 under windows XP.
So perhaps it's a Linux issue?

Cheers
View user's profile Send private message Send e-mail
david.butler
Posted: Wed May 06, 2009 7:03 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
Dear kiwi,

It looks as though the dynamic linker is not finding the asreml dependencies. Depending on your installation, check either the setting of the environment variable LD_LIBRARY_PATH or the path in /etc/ld.so.conf and make sure that which ever of these you have used points to the package sub-directory ('libs') containing the asreml shared object (.so) files.

Dave.

From: ASReml users discussion group [mailto:ASREML-L@dpi.nsw.gov.au] On Behalf Of kiwi
Sent: Wednesday, 6 May 2009 9:33 AM
To: ASREML-L@dpi.nsw.gov.au
Subject: Does ASReml-R work with R-2.9.0?



It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code: > require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory

(Note that Code: $Rhome

is not literally what's in the message.)
Has anyone used R-2.9.0 with asreml? Code: > sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grDevices utils stats graphics methods base

other attached packages:
[1] lattice_0.17-22

loaded via a namespace (and not attached):
[1] grid_2.9.0

Reverting to R-2.8.1 avoids the problem, but that's not a satisfactory solution..








This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


********************************DISCLAIMER****************************
The information contained in the above e-mail message or messages
(which includes any attachments) is confidential and may be legally
privileged. It is intended only for the use of the person or entity
to which it is addressed. If you are not the addressee any form of
disclosure, copying, modification, distribution or any action taken
or omitted in reliance on the information is unauthorised. Opinions
contained in the message(s) do not necessarily reflect the opinions
of the Queensland Government and its authorities. If you received
this communication in error, please notify the sender immediately
and delete it from your computer system network.



This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
kiwi
Posted: Wed May 06, 2009 11:01 pm Reply with quote
Joined: 16 Nov 2008 Posts: 22
Dave Butler writes:
Quote:
It looks as though the dynamic linker is not finding the asreml dependencies. Depending on your installation, check either the setting of the environment variable LD_LIBRARY_PATH or the path in /etc/ld.so.conf and make sure that which ever of these you have used points to the package sub-directory ('libs') containing the asreml shared object (.so) files.
I have that set in ~/.bash_profile and R-2.8.1 is quite happy about it so I can't be far off target. There must be something different in R-2.9.0 which decides against looking there. Are you indicating that I should use /etc/ld.so.conf ? I don't have access to edit it. At present, all it has is:
Code:
include ld.so.conf.d/*.conf
and the directory it's in has these:
Code:
  -rw-r--r--   1 root   root    94960 Mar 25 10:56 ld.so.cache
  -rw-r--r--   1 root   root       28 Oct  9  2006 ld.so.conf
  drwxr-xr-x   2 root   root     4096 Dec  6 06:24 ld.so.conf.d
/etc/ld.so.conf.d: has this:
Code:

  /etc/ld.so.conf.d:
  used 28 available 31464792
  drwxr-xr-x   2 root root  4096 Dec  6 06:24 .
  drwxr-xr-x 101 root root 12288 May  6 04:02 ..
  -rw-r--r--   1 root root    20 Sep 14  2007 qt-i386.conf
qt-i386.conf would have nothing to do with this lot I think would be safe to say.

The ld.so.cache might have something in it which needs updating or something along those lines. I'm totally ignorant of its workings, so all manner of subtleties could be behind the problem I'm experiencing.
Even so, I'd have thought I need to find out what R-2.9.0 is doing differently. It's probably not a question for the Rhelp list since we're using something rather different from what "standard" R packages use.
View user's profile Send private message
david.butler
Posted: Thu May 07, 2009 1:16 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
Dear kiwi,

I'm not suggesting you should use "ld.so.conf", it's just one of the alternatives. It loads fine for me on a 64 bit Fedora 9 machine with R 2.9.0, however, I have not installed asreml in the default R library tree, so a sequence like

LD_LIBRARY_PATH=path/asreml/libs
library(asreml,lib.loc="path")

works. I'm not able to check the 32 bit version with R 2.9 just yet. Can you give me some more background on your installation, such as 32/64 bit, R installation configuration (ie paths to 2.8 and 2.9 if installed in parallel), contents of LD_LIBRARY_PATH etc. Perhaps you could send this directly to me rather than the list.

dave.

From: ASReml users discussion group [mailto:ASREML-L@dpi.nsw.gov.au] On Behalf Of kiwi
Sent: Thursday, 7 May 2009 9:02 AM
To: ASREML-L@dpi.nsw.gov.au
Subject: Re: Does ASReml-R work with R-2.9.0?



Dave Butler writes:
Quote: It looks as though the dynamic linker is not finding the asreml dependencies. Depending on your installation, check either the setting of the environment variable LD_LIBRARY_PATH or the path in /etc/ld.so.conf and make sure that which ever of these you have used points to the package sub-directory ('libs') containing the asreml shared object (.so) files.


I have that set in ~/.bash_profile and R-2.8.1 is quite happy about it so I can't be far off target. There must be something different in R-2.9.0 which decides against looking there. Are you indicating that I should use /etc/ld.so.conf ? I don't have access to edit it. At present, all it has is: Code: include ld.so.conf.d/*.conf

and the directory it's in has these: Code: -rw-r--r-- 1 root root 94960 Mar 25 10:56 ld.so.cache
-rw-r--r-- 1 root root 28 Oct 9 2006 ld.so.conf
drwxr-xr-x 2 root root 4096 Dec 6 06:24 ld.so.conf.d


/etc/ld.so.conf.d: has this: Code:
/etc/ld.so.conf.d:
used 28 available 31464792
drwxr-xr-x 2 root root 4096 Dec 6 06:24 .
drwxr-xr-x 101 root root 12288 May 6 04:02 ..
-rw-r--r-- 1 root root 20 Sep 14 2007 qt-i386.conf

qt-i386.conf would have nothing to do with this lot I think would be safe to say.

The ld.so.cache might have something in it which needs updating or something along those lines. I'm totally ignorant of its workings, so all manner of subtleties could be behind the problem I'm experiencing.
Even so, I'd have thought I need to find out what R-2.9.0 is doing differently. It's probably not a question for the Rhelp list since we're using something rather different from what "standard" R packages use.








This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


********************************DISCLAIMER****************************
The information contained in the above e-mail message or messages
(which includes any attachments) is confidential and may be legally
privileged. It is intended only for the use of the person or entity
to which it is addressed. If you are not the addressee any form of
disclosure, copying, modification, distribution or any action taken
or omitted in reliance on the information is unauthorised. Opinions
contained in the message(s) do not necessarily reflect the opinions
of the Queensland Government and its authorities. If you received
this communication in error, please notify the sender immediately
and delete it from your computer system network.



This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
Xianming Wei
Posted: Tue May 26, 2009 3:44 am Reply with quote
Guest
Hi all,

Has anyone tried to install asreml-R in Ubuntu (9.04)? I got virtually the same problem as described below. Using LD_LIBRARY_PATH=myPath/asreml/libs and then library(asreml, lib.loc=’myPath’) didn’t solve the problem. ASReml stand-alone works fine.

#########
Quote:
sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base
#############

Regards,
Xianming


It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code:
Quote:
require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory




BSES Limited Disclaimer

This email and any files transmitted with it are confidential and intended solely for the person or entity to whom they are addressed.
If you are not the intended recipient of this email, you should not read, copy or otherwise use it, or disclose its contents to anyone else.If you received this email in error please notify BSES Limited immediately by return email, destroy all copies of the email, any delete if from your system.
Recipients should rely on their own systems for detecting computer viruses or other material that may corrupt files or systems.





This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
kiwi
Posted: Tue May 26, 2009 4:54 am Reply with quote
Joined: 16 Nov 2008 Posts: 22
Xianming Wei wrote:
Quote:
Hi all,

Has anyone tried to install asreml-R in Ubuntu (9.04)? I got virtually the same problem as described below. Using LD_LIBRARY_PATH=myPath/asreml/libs and then library(asreml, lib.loc=’myPath’) didn’t solve the problem. ASReml stand-alone works fine.
The quoting codes aren't at all clear, but I get the impression that this is describing a problem similar to the one I experience using CentOS 5.2 and R-2.9.0. It's not clear if you had the problem with R-2.8.1 or with 2.9.0. If it's with the latter and not the former, then it would seem to be the same problem I have. Although there's no problem installing, it won't load.

That would be interesting since I don't get it with Fedora8, nor with Mepis 6.5, the latter being a Debian derivitive, as is Ubuntu (though a somewhat newer version). The only suggestion I get from the CentOS people is to use a newer version (which would use kernel-2.6.18-128.1.10.el5. Currently I'm using 2.6.18-92.1.22.el5. What does Ubuntu 9.04 use?
View user's profile Send private message
david.butler
Posted: Tue May 26, 2009 6:06 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
Xianming,

This seems to have arisen with R2.9 and some flavours of Linux, the environment variable is not "visible" in the R sesion. You could confirm this with the R function "Sys.getenv". I'll investigate as to whether the library dependencies can be eliminated from the licensing software, and hence the need for LD_LIBRARY_PATH.

Dave.


From: ASReml users discussion group [mailto:ASREML-L@DPI.NSW.GOV.AU] On Behalf Of Xianming Wei
Sent: Tuesday, 26 May 2009 12:55 PM
To: ASREML-L@DPI.NSW.GOV.AU
Subject: ASReml-R in Ubuntu9.04 has same problem as in 'Does ASReml-R work with R-2.9.0?'




Hi all,

Has anyone tried to install asreml-R in Ubuntu (9.04)? I got virtually the same problem as described below. Using LD_LIBRARY_PATH=myPath/asreml/libs and then library(asreml, lib.loc=’myPath’) didn’t solve the problem. ASReml stand-alone works fine.

#########
Quote:
sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base
#############

Regards,
Xianming


It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code:
Quote:
require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory




BSES Limited Disclaimer

This email and any files transmitted with it are confidential and intended solely for the person or entity to whom they are addressed.
If you are not the intended recipient of this email, you should not read, copy or otherwise use it, or disclose its contents to anyone else.If you received this email in error please notify BSES Limited immediately by return email, destroy all copies of the email, any delete if from your system.
Recipients should rely on their own systems for detecting computer viruses or other material that may corrupt files or systems.





This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


********************************DISCLAIMER****************************
The information contained in the above e-mail message or messages
(which includes any attachments) is confidential and may be legally
privileged. It is intended only for the use of the person or entity
to which it is addressed. If you are not the addressee any form of
disclosure, copying, modification, distribution or any action taken
or omitted in reliance on the information is unauthorised. Opinions
contained in the message(s) do not necessarily reflect the opinions
of the Queensland Government and its authorities. If you received
this communication in error, please notify the sender immediately
and delete it from your computer system network.



This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
Xianming Wei
Posted: Tue May 26, 2009 6:23 am Reply with quote
Guest
Thanks Kiwi.

I actually replied your first email because I had exact same error message as described in your email (Error in dyn.load …). Because my original email exceeded the length the list permitted so I had to delete your original message.

My setup is different to yours though. I have R-2.8.1 under Ubuntu 9.04, Kernel linux 2.6.28-11-generic, Genome 2.26.1.


Regards,
Xianming


From: ASReml users discussion group [mailto:ASREML-L@DPI.NSW.GOV.AU] On Behalf Of kiwi
Sent: Tuesday, 26 May 2009 2:54 PM
To: ASREML-L@DPI.NSW.GOV.AU
Subject: Re: Does ASReml-R work with R-2.9.0?



Xianming Wei wrote:
Quote:
Hi all,

Has anyone tried to install asreml-R in Ubuntu (9.04)? I got virtually the same problem as described below. Using LD_LIBRARY_PATH=myPath/asreml/libs and then library(asreml, lib.loc=’myPath’) didn’t solve the problem. ASReml stand-alone works fine.


The quoting codes aren't at all clear, but I get the impression that this is describing a problem similar to the one I experience using CentOS 5.2 and R-2.9.0. It's not clear if you had the problem with R-2.8.1 or with 2.9.0. If it's with the latter and not the former, then it would seem to be the same problem I have. Although there's no problem installing, it won't load.

That would be interesting since I don't get it with Fedora8, nor with Mepis 6.5, the latter being a Debian derivitive, as is Ubuntu (though a somewhat newer version). The only suggestion I get from the CentOS people is to use a newer version (which would use kernel-2.6.18-128.1.10.el5. Currently I'm using 2.6.18-92.1.22.el5. What does Ubuntu 9.04 use?









This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


BSES Limited Disclaimer

This email and any files transmitted with it are confidential and intended solely for the person or entity to whom they are addressed.
If you are not the intended recipient of this email, you should not read, copy or otherwise use it, or disclose its contents to anyone else.If you received this email in error please notify BSES Limited immediately by return email, destroy all copies of the email, any delete if from your system.
Recipients should rely on their own systems for detecting computer viruses or other material that may corrupt files or systems.





This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
david.butler
Posted: Tue May 26, 2009 6:28 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
On behalf of Dean Diepeveen:


=============
Xianming, others,
I have hardware with this combination of software (Ubuntu 9.04, Centos
5.3 with R2.9.0) and it works a treat. Check out the documentation that comes with it (ie
http://www.austatgen.org/files/software/asreml/asreml-SRinstall.html) .
I have set mine up with an asreml.conf file in the directory /etc/ld.so.conf.d. containing the locations of the asreml libraries.
Remember to run ldconfig once done.
Cheers,
Dean Diepeveen


From: ASReml users discussion group [mailto:ASREML-L@DPI.NSW.GOV.AU] On Behalf Of Xianming Wei
Sent: Tuesday, 26 May 2009 12:55 PM
To: ASREML-L@DPI.NSW.GOV.AU
Subject: ASReml-R in Ubuntu9.04 has same problem as in 'Does ASReml-R work with R-2.9.0?'




Hi all,

Has anyone tried to install asreml-R in Ubuntu (9.04)? I got virtually the same problem as described below. Using LD_LIBRARY_PATH=myPath/asreml/libs and then library(asreml, lib.loc=’myPath’) didn’t solve the problem. ASReml stand-alone works fine.

#########
Quote:
sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base
#############

Regards,
Xianming


It would appear from my recent experience that R-2.9.0 does something different that is incompatible with the way the asreml package looks for the executable.
Code:
Quote:
require(asreml)
Loading required package: asreml
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '$Rhome/asreml/libs/asreml-R.so':
libirc.so: cannot open shared object file: No such file or directory




BSES Limited Disclaimer

This email and any files transmitted with it are confidential and intended solely for the person or entity to whom they are addressed.
If you are not the intended recipient of this email, you should not read, copy or otherwise use it, or disclose its contents to anyone else.If you received this email in error please notify BSES Limited immediately by return email, destroy all copies of the email, any delete if from your system.
Recipients should rely on their own systems for detecting computer viruses or other material that may corrupt files or systems.





This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.


********************************DISCLAIMER****************************
The information contained in the above e-mail message or messages
(which includes any attachments) is confidential and may be legally
privileged. It is intended only for the use of the person or entity
to which it is addressed. If you are not the addressee any form of
disclosure, copying, modification, distribution or any action taken
or omitted in reliance on the information is unauthorised. Opinions
contained in the message(s) do not necessarily reflect the opinions
of the Queensland Government and its authorities. If you received
this communication in error, please notify the sender immediately
and delete it from your computer system network.



This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of their organisation.

Post generated using Mail2Forum (http://www.mail2forum.com)
View user's profile Send private message
kiwi
Posted: Wed May 27, 2009 4:31 am Reply with quote
Joined: 16 Nov 2008 Posts: 22
Quote:
david.butler Posted: Tue May 26, 2009 7:28 pm
On behalf of Dean Diepeveen:

=============
Xianming, others,
I have hardware with this combination of software (Ubuntu 9.04, Centos
5.3 with R2.9.0) and it works a treat.
I'm still confused. Is that saying BOTH Ubuntu and CentOS work? I have CentOS 5.2 which allows asrem-R to work fine with R2.8.1, but not with 2.9.0 but it appears that Xianming's problem with Ubuntu 9.04 and R 2.8.1. I don't know whether Xianming has it working with any other setup.
Quote:
Check out the documentation that comes with it (ie
http://www.austatgen.org/files/software/asreml/asreml-SRinstall.html) .
I have set mine up with an asreml.conf file in the directory /etc/ld.so.conf.d. containing the locations of the asreml libraries.
Remember to run ldconfig once done.
I see you have the luxury of having root access which I don't have. Obviously, I also can't check to see if the problem disappears with CentOS 5.3 but that fact might get us closer to working out how the problem arises. With both the Fedora 8 and Mepis installations I've checked I have root access. However, I still set the LD_LIBRARY_PATH in the user directory, so I'm still not convinced that is the issue since they work there, even with R-2.9.0.
View user's profile Send private message
kiwi
Posted: Thu Jul 30, 2009 3:45 am Reply with quote
Joined: 16 Nov 2008 Posts: 22
With a bit of help from the Rhelp list, I've discovered that there's a file $Rhome/etc/ldpaths which should have read the appropriate information at the time R was compiled. Copying the missing bit from the corresponding file in the 2.8.1 installation put an end to the problem.

However, I never worked out why the problem seems to appear only with CentOS and even with it, not before R-2.9.0. But now it ain't broke.

HTH
View user's profile Send private message

Display posts from previous:  

All times are GMT
Page 1 of 1
Post new topic

Jump to:  

You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You can attach files in this forum
You can download files in this forum