Summary: | dev-lang/R with >sys-cluster/openmpi-1.4.3 - Rmpi fails to install because of undefined symbol: mca_base_param_reg_int in /usr/lib64/openmpi/mca_paffinity_linux.so | ||
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Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | [OLD] Unspecified | Assignee: | Gentoo Science Mathematics related packages <sci-mathematics> |
Status: | RESOLVED WONTFIX | ||
Severity: | normal | ||
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
URL: | https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14526 | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Juergen Rose
2011-03-09 12:23:37 UTC
Is this dev-lang/R failing to install? Attach the build log, please, and also explain to me why you need to be asked every time - it's standard procedure. Hi Jeroen, dev-lang/R (R-2.12.2) installes without problems. Mostly I add build.log to my bug messages. Sometimes I thought, that build.log is not helpful. But for this bug there is no build.log, because Rmpi is not installed by emerge, it is installed inside R with 'install.packages("Rmpi")' or at the bash prompt with 'R CMD INSTALL /path_to/Rmpi_0.5-9.tag.gz'. I think the issue is caused by not matching R, Rmpi or openmpi. Downgrading to openmpi-1.4.3 solves the issue for me. (In reply to comment #3) > Downgrading to openmpi-1.4.3 solves the issue for me. sys-cluster/openmpi-1.4.3 is the latest version in the tree. Any newer version must be from an overlay. Hi Jurgen, Please submit your bug to the Rmpi developers. We will not try to fix it because it is neither in the tree nor in the science overlay where openmpi-1.5.2 is. Thanks Hi Sébastien, for me openmpi-1.5.2 is in the science-overlay: root@lynx:/root(2)# emerge -pvuDN world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] sys-apps/hwloc-1.1.1 USE="X cairo svg xml -static-libs" 2,306 kB [0] [ebuild U ] sys-cluster/openmpi-1.5.2 [1.4.3] USE="cxx fortran ipv6 romio threads -heterogeneous -infiniband% -mpi-threads -pbs -vt" 7,402 kB [0=>1] Total: 2 packages (1 upgrade, 1 new), Size of downloads: 9,707 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/science As I wrote in my original posting, I reported this issue also https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14526 and meanwhile also to the maintainer of the Rmpi package <hyu at stats.uwo.ca>. |