SOS! R Console crashed after loading RODBC... Update: Re: How to set up RODBC? Diff between R Console and RStudio?
I think it would be useful to first understand how your RStudio environment is working. You should not need both "/pp64/odbc/5.3/lib" and "/pp64/odbc/5.1/lib" on your LD_LIBRARY_PATH. One can guess what is being used, but it would be better to be certain. So if you can get a relatively clean RStudio environment that works, then deciding what to use in the console session would be easier. Once again, while the crash to the shell with no error messages may not happen until you execute some R commands, this behaviour is almost certainly related to loading a bad binary file or library. (Also, be certain you are getting the same version of R and package libraries when you run RStudio and your console session.) Paul
On 12-05-27 09:59 PM, Michael wrote:
Even more weirdly... Now I open the R-Console again, and manually typed:
>
library(RODBC)
>
require(RODBC)
And it seems to be fine, no crash at all.
But when I run my original program(the same program ran perfectly fine
in RStudio), it crashed again quietly...
The problem seems to be lying in the commands/functions after loading
the RODBC library, but it's related to RODBC...
On Sun, May 27, 2012 at 8:46 PM, Michael <comtech.usa at gmail.com
<mailto:comtech.usa at gmail.com>> wrote:
Thank you!
I dug into the RStudio, since the RODBC worked perfectly fine inside
RStudio.
I did Sys.getenv("ODBC_HOME"), it returned:
/pp64/odbc/5.3/
I then looked into that fold and found "libodbc.so" in that directory.
When I set the LD_LIBRARY_PATH, I actually have copied everything
related to "odbc" and "ODBC" on the environments from RStudio.
There, inside RStudio, I found the following in LD_LIBRARY_PATH:
"/pp64/unixODBC/2.3.1/lib" "/pp64/unixODBC/2.3.1/lib"
"/pp64/unixODBC/2.3.1/lib"
"/pp64/unixODBC/2.3.1/lib"
"/pp64/odbc/5.3/lib" "/pp64/odbc/5.1/lib"
"/pp64/odbcpp/0.2.5-unixodbc/lib" "/pp64/odbcpp/0.2.5-unixodbc/lib"
"/pp64/odbc/5.3/lib" "/pp64/odbc/5.1/lib"
"/pp64/odbcpp/0.2.5-unixodbc/lib" "/pp64/odbcpp/0.2.5-unixodbc/lib"
There are some repetitions, so I copied only those non-repitives to
the global shell environment before calling the R-Console.
My goal was to replicate the exactly same environment variables for
R-Console... so that RODBC could work in R-Console.
Also following exactly what I see from RStudio, using Sys.getenv(),
I copied over and set up for R-Console the following:
ODBC_HOME
ODBCINI
ODBC_INI
PATH
PYTHONPATH
They all have "odbc" or "ODBC" in them...
As reported, initially it was the file "libodbc.so" couldn't be
found; later it became crash after I set up the paths...
Any more thoughts?
Thanks a lot!
On Sun, May 27, 2012 at 7:37 PM, Paul Gilbert <pgilbert902 at gmail.com
<mailto:pgilbert902 at gmail.com>> wrote:
If they are both installed, I think they are in directories like
/usr/lib/i386-linux-gnu/ and /usr/lib/x86_64-linux-gnu/. If they
are not both installed, then that could not be the problem. Try
locate libodbc.so
to see what you have installed.
On 12-05-27 07:58 PM, Michael wrote:
Thank you Paul.
How do I judge/check which lib is 32 and which is 64?
Thanks again!
On Sun, May 27, 2012 at 6:45 PM, Paul Gilbert
<pgilbert902 at gmail.com <mailto:pgilbert902 at gmail.com>
<mailto:pgilbert902 at gmail.com
<mailto:pgilbert902 at gmail.com>>__> wrote:
(Cross posting should not be done!)
A crash to the shell prompt suggests a bad .so got
loaded. Maybe you
are picking up a 32 bit version instead of 64 bit, or
the reverse. I
am surprised you need to set LD_LIBRARY_PATH, and if
you set it
wrong it might cause this. (Just guessing.)
Paul
On 12-05-27 01:26 PM, Michael wrote:
On Sun, May 27, 2012 at 11:32 AM,
Michael<comtech.usa at gmail.com <mailto:comtech.usa at gmail.com>
<mailto:comtech.usa at gmail.com
<mailto:comtech.usa at gmail.com>>__> wrote:
Help! The R Console very quietly closed and
exited without
giving any
errors/warnings...after I loaded the RODBC
library...
Loading required package: RODBC
On Sat, May 26, 2012 at 10:27 PM,
Michael<comtech.usa at gmail.com
<mailto:comtech.usa at gmail.com>
<mailto:comtech.usa at gmail.com
<mailto:comtech.usa at gmail.com>>__> wrote:
Hi all,
It's very strange. In RStudio, I can
successfully
load("RODBC"). But in
the plain R Console, I just couldn't get it
work:
(For some special and important reasons, I
have to make
the RODBC work in
R Console, not the RStudio.)
At first, the some shared library
"libodbc.so" couldn't
be found... it's
right there, but R Console just couldn't
find it.
I then find that the
Sys.getenv("LD_LIBRARY_PATH") is different
for R Console
vs. RStudio.
Weirdly, the LD_LIBRARY_PATH in RStudio even
doesn't
have any "ODBC"
terms/words in its long string...
I guess RStudio has some special
configuration for
RODBC, so it doesn't
require LD_LIBRARY_PATH to be set up for
ODBC at all.
I then added the ODBC library path into the
LD_LIBRARY_PATH in R Console.
I found that this problem is solved...
But then the R Console complained that the
"ODBCINI" was
set up correctly.
So I compared the "ODBCINI" in RStudio vs.
"ODBCINI" in
R Console, found
the R Console one seems to be missing.
I then copied the "ODBCINI" from RStudio and
pasted it
into R Console.
Now the load("RODBC") can run in the plain R
Console,
but then the whole
R console crashed without giving any
errors/warnings...
It exited back to the shell prompt...
What can I do? Anybody please shed some
lights on me on
this?
Thanks a lot!
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