[R] Segmentation Fault when Installing Some Packages

Lorenzo Isella lorenzo.isella at gmail.com
Wed Jun 21 21:20:42 CEST 2017


Dear All,
I have a fresh Debian Stretch (now the official Debian stable)
installation on my machine.
Based on what written here

https://cran.r-project.org/bin/linux/debian/#debian-jessie-stable

I added the line

deb https://stat.ethz.ch/CRAN/bin/linux/debian stretch-cran34/

to my sources in order to have a backport of R 3.4.

The issue is that I am now experiencing some troubles to install some
packages from cran which did not give me any trouble in the past.
The worst is that all I get is an uninformative segmentation fault
error.
For instance, consider the RJSDMX package

> install.packages("RJSDMX")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://lib.ugent.be/CRAN/src/contrib/RJSDMX_1.7.tar.gz'
Content type 'application/x-gzip' length 155642 bytes (151 KB)
==================================================
downloaded 151 KB

* installing *source* package ‘RJSDMX’ ...
** package ‘RJSDMX’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Segmentation fault
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/RJSDMX’

The downloaded source packages are in
	‘/tmp/RtmpkjeaiB/downloaded_packages’
Warning message:
In install.packages("RJSDMX") :
  installation of package ‘RJSDMX’ had non-zero exit status



or the openNLP data

> install.packages("openNLPdata")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://lib.ugent.be/CRAN/src/contrib/openNLPdata_1.5.3-2.tar.gz'
Content type 'application/x-gzip' length 7318681 bytes (7.0 MB)
==================================================
downloaded 7.0 MB

* installing *source* package ‘openNLPdata’ ...
** package ‘openNLPdata’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
No man pages found in package  ‘openNLPdata’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
Segmentation fault
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/openNLPdata’

The downloaded source packages are in
	‘/tmp/RtmpkjeaiB/downloaded_packages’
Warning message:
In install.packages("openNLPdata") :
  installation of package ‘openNLPdata’ had non-zero exit status


I enclose also my sessionInfo data

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

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

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0    tcltk_3.4.0   


Is anybody else having similar troubles?
I would like to add that I can install other fairly complicated
packages (like tidyverse), so I am really puzzled.
Any suggestion is welcome.
Many thanks

Lorenzo



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