[Bioc-devel] ccfindR install fails

[Manders-2, F.M.]

Hi all,

I’m trying to install the devel version of the ccfindR package to test my package (MutationalPatterns).
It passed the nightly build tests, so I thought it should work.
I used the development docker container to try and install the package, but it fails because its dependency “Rmpi” fails to install. I pasted the errors  I got below.
I found some information on how to install this dependency, but can’t get it to work. (http://fisher.stats.uwo.ca/faculty/yu/Rmpi/install.htm)
I tried to install open-mpi, but this is apparently already installed in the docker. However, I couldn’t find its path. I found several files starting with mpi in /usr/bin/ , but I have no idea if these are the correct ones.

Does anybody know what you need to do to install the ccfindR package?

The issue can be reproduced by running (requires docker):
docker pull bioconductor/bioconductor_docker:devel
docker run -it --user rstudio bioconductor/bioconductor_docker:devel R
BiocManager::install("ccfindR")

With kind regards,
Freek Manders


Errors:
** testing if installed package can be loaded from temporary location
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
--------------------------------------------------------------------------
The value of the MCA parameter "plm_rsh_agent" was set to a path
that could not be found:

  plm_rsh_agent: ssh : rsh

Please either unset the parameter, or check that the path is correct
--------------------------------------------------------------------------
[abf30c1267ab:00745] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 582
[abf30c1267ab:00745] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 166
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_ess_init failed
  --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[abf30c1267ab:745] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/Rmpi’
Warning in install.packages :
  installation of package ‘Rmpi’ had non-zero exit status


	[[alternative HTML version deleted]]