Problems installing package

[lazariv]

I have the following error when installing a package:

.....
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘pbdMPI-guide.Rnw’ 
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘pbdMPI’:
 .onLoad failed in loadNamespace() for 'pbdMPI', details:
  call: fun(libname, pkgname)
  error: ignoring SIGPIPE signal
Error: Load failed
* removing ‘/******/pbdMPI’

R configuration is following

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS/LAPACK: /software/haswell/OpenBLAS/0.3.5-GCC-8.2.0-2.31.1/lib/libopenblas_haswellp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] compiler_3.6.0

with OpenMPI/3.1.3-GCC-8.2.0-2.31.1

Do you have any hints?

[snoweye]

Try newer R such as 4.0.3.

[lazariv]

Try newer R such as 4.0.3.

We do have R/4.0.0-foss-2020a on our HPC, but it does not work either. Same error.

[snoweye]

You may have to try to use --no-test-load or so to avoid the loading during the installation. However, you may have a test run manually by yourself. The dynamical libraries built by R may link to different locations for whatever reasons R wants to test, or the ld in the system can not find or load the required libraries as other systems. It would be over my ability to fix if this is or is not the reason.

[bkmgit]

If using a cluster, try the following

#!/bin/bash

module load OpenMPI
module load R
mkdir R_libs
Rscript installPackages.R
 

where installPackages.R contains

# Script to install pbdMPI

install.packages("pbdMPI", repos="http://cran.r-project.org", lib="R_libs/",dependencies=TRUE)

[go-ski]

While install and load of pbdMPI works on most cluster login nodes, some allow MPI runs only on compute nodes, thus requiring --no-test-load installs. Others may just need a module load to use MPI.