Message-ID: <20170621192042.5n3pncj5fau3evbt@chicca>
Date: 2017-06-21T19:20:42Z
From: Lorenzo Isella
Subject: Segmentation Fault when Installing Some Packages
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