We have a cluster running squeeze (amd64) that uses CRAN (squeeze-cran directory) to get more recent versions of R packages. Unfortunately, many cluster-related packages, including rmpi and rsprng are missing. The basic squeeze version of rmpi won't load because it doesn't have a namespace. Any suggestions about how to deal with this? Thanks. Ross Boylan
rmpi backports?
5 messages · Ross Boylan, Dirk Eddelbuettel, Johannes Ranke
On 14 February 2013 at 13:42, Ross Boylan wrote:
| We have a cluster running squeeze (amd64) that uses CRAN (squeeze-cran | directory) to get more recent versions of R packages. | | Unfortunately, many cluster-related packages, including rmpi and rsprng | are missing. The basic squeeze version of rmpi won't load because it | doesn't have a namespace. | | Any suggestions about how to deal with this? Install into /usr/local, that is what it is for: edd at max:~$ ls -1 /usr/local/lib/R/site-library/ | wc -l 256 edd at max:~$ Dirk
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
On 2/14/2013 1:59 PM, Dirk Eddelbuettel wrote:
On 14 February 2013 at 13:42, Ross Boylan wrote: | We have a cluster running squeeze (amd64) that uses CRAN (squeeze-cran | directory) to get more recent versions of R packages. | | Unfortunately, many cluster-related packages, including rmpi and rsprng | are missing. The basic squeeze version of rmpi won't load because it | doesn't have a namespace. | | Any suggestions about how to deal with this? Install into /usr/local, that is what it is for: edd at max:~$ ls -1 /usr/local/lib/R/site-library/ | wc -l 256 edd at max:~$ Dirk
Is rebuilding the debian package for testing or sid from source likely to work? I'm thinking that with all the nodes to update it might be easier to go with a deb. If we do that, is there anywhere, e.g., backports or cran, we could make it available for others? Ross
Hi Ross, as the maintainer of the Debian squeeze debs on CRAN, I have to admit that I have no clue about MPI. But the first thing I would try is to get the build dependencies of the Debian squeeze Rmpi package apt-get build-dep r-cran-rmpi and then try installing Rmpi from within R as Dirk suggested. Johannes Am Freitag, 15. Februar 2013, 02:49:01 schrieb Ross Boylan:
On 2/14/2013 1:59 PM, Dirk Eddelbuettel wrote:
On 14 February 2013 at 13:42, Ross Boylan wrote: | We have a cluster running squeeze (amd64) that uses CRAN (squeeze-cran | directory) to get more recent versions of R packages. | | Unfortunately, many cluster-related packages, including rmpi and rsprng | are missing. The basic squeeze version of rmpi won't load because it | doesn't have a namespace. | | Any suggestions about how to deal with this? Install into /usr/local, that is what it is for: edd at max:~$ ls -1 /usr/local/lib/R/site-library/ | wc -l 256 edd at max:~$ Dirk
Is rebuilding the debian package for testing or sid from source likely to work? I'm thinking that with all the nodes to update it might be easier to go with a deb. If we do that, is there anywhere, e.g., backports or cran, we could make it available for others? Ross
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8 days later
Dear all, meanwhile I have tested the following procedure to get Rmpi to work on a multicore Debian squeeze box with a kernel from backports.org: I installed the squeeze version of the package r-cran-rmpi. This does not load because of the missing namespace. But it pulls in all dependencies needed at runtime. I then installed the build dependencies by apt-get build-dep. Within R, I then used install.packages() to install Rmpi. This installed the package and it loaded fine. Kind regards, Johannes Am Freitag, 15. Februar 2013, 18:06:35 schrieb Johannes Ranke:
Hi Ross, as the maintainer of the Debian squeeze debs on CRAN, I have to admit that I have no clue about MPI. But the first thing I would try is to get the build dependencies of the Debian squeeze Rmpi package apt-get build-dep r-cran-rmpi and then try installing Rmpi from within R as Dirk suggested. Johannes Am Freitag, 15. Februar 2013, 02:49:01 schrieb Ross Boylan:
On 2/14/2013 1:59 PM, Dirk Eddelbuettel wrote:
On 14 February 2013 at 13:42, Ross Boylan wrote: | We have a cluster running squeeze (amd64) that uses CRAN | (squeeze-cran directory) to get more recent versions of R packages. | | Unfortunately, many cluster-related packages, including rmpi and | rsprng are missing. The basic squeeze version of rmpi won't load | because it doesn't have a namespace. | | Any suggestions about how to deal with this? Install into /usr/local, that is what it is for: edd at max:~$ ls -1 /usr/local/lib/R/site-library/ | wc -l 256 edd at max:~$ Dirk
Is rebuilding the debian package for testing or sid from source likely to work? I'm thinking that with all the nodes to update it might be easier to go with a deb. If we do that, is there anywhere, e.g., backports or cran, we could make it available for others? Ross
_______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
_______________________________________________ R-SIG-Debian mailing list R-SIG-Debian at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian