Thread: pl/R problem
Hi list,
Information first:
gds2=# select version();
version
----------------------------------------------------------------------------------------------------------
PostgreSQL 8.1.4 on i686-pc-linux-gnu, compiled by GCC gcc (GCC) 3.2.3
20030502 (Red Hat Linux 3.2.3-20)
(1 row)
pl/R 0.6.2
R.2.3 (compiled from source)
R_HOME is defined (before starting postmaster)
gds2=# select * from pg_language;
lanname | lanispl | lanpltrusted | lanplcallfoid | lanvalidator | lanacl
-----------+---------+--------------+---------------+--------------+--------
internal | f | f | 0 | 2246 |
c | f | f | 0 | 2247 |
sql | f | t | 0 | 2248 |
plpgsql | t | t | 16393 | 16394 |
plperl | t | t | 18064 | 18065 |
plpythonu | t | f | 18067 | 0 |
plperlu | t | f | 18064 | 18065 |
plr | t | f | 24576 | 0 |
Now, for the problem:
gds2=# create function sd(_float8) returns float as '' language 'plr';
CREATE FUNCTION
gds2=# select round(sd('{1.23,1.31,1.42,1.27}'::_float8)::numeric,8);
server closed the connection unexpectedly
This probably means the server terminated abnormally
before or while processing the request.
The connection to the server was lost. Attempting reset: Failed.
Relevant server log piece:
cannot find system Renviron
Fatal error: unable to open the base package
LOG: server process (PID 6792) exited with exit code 2
So, the question: what am I missing that enables it to find the "Renviron"
Thank you.
Don
On Tue, Aug 22, 2006 at 04:24:46PM -0500, Don Isgitt wrote:
> gds2=# create function sd(_float8) returns float as '' language 'plr';
> CREATE FUNCTION
>
> gds2=# select round(sd('{1.23,1.31,1.42,1.27}'::_float8)::numeric,8);
> server closed the connection unexpectedly
> This probably means the server terminated abnormally
> before or while processing the request.
> The connection to the server was lost. Attempting reset: Failed.
>
> Relevant server log piece:
>
> cannot find system Renviron
> Fatal error: unable to open the base package
>
> LOG: server process (PID 6792) exited with exit code 2
I can reproduce this on Solaris 9 with PL/R 0.6.2-alpha and R 2.2.1
if I rename $R_HOME/etc/Renviron to something else. I don't get
the "unable to open the base package" error but I do get "cannot
find system Renviron" and several other errors like "Error in
options(...) : invalid editor parameter" followed by a segmentation
fault.
> So, the question: what am I missing that enables it to find the "Renviron"
Does the file $R_HOME/etc/Renviron or $R_HOME/etc/<architecture>/Renviron
exist and have permissions such that the PostgreSQL server can read
it? The error "cannot find system Renviron" comes from the R
function process_system_Renviron() in src/main/Renviron.c in response
to process_Renviron() returning 0, which it does if its filename
argument is NULL or if it can't open that file.
--
Michael Fuhr
Michael Fuhr wrote:
> On Tue, Aug 22, 2006 at 04:24:46PM -0500, Don Isgitt wrote:
>
>> gds2=# create function sd(_float8) returns float as '' language 'plr';
>> CREATE FUNCTION
>>
>> gds2=# select round(sd('{1.23,1.31,1.42,1.27}'::_float8)::numeric,8);
>> server closed the connection unexpectedly
>> This probably means the server terminated abnormally
>> before or while processing the request.
>> The connection to the server was lost. Attempting reset: Failed.
>>
>> Relevant server log piece:
>>
>> cannot find system Renviron
>> Fatal error: unable to open the base package
>>
>> LOG: server process (PID 6792) exited with exit code 2
>>
>
> I can reproduce this on Solaris 9 with PL/R 0.6.2-alpha and R 2.2.1
> if I rename $R_HOME/etc/Renviron to something else. I don't get
> the "unable to open the base package" error but I do get "cannot
> find system Renviron" and several other errors like "Error in
> options(...) : invalid editor parameter" followed by a segmentation
> fault.
>
>
>> So, the question: what am I missing that enables it to find the "Renviron"
>>
>
> Does the file $R_HOME/etc/Renviron or $R_HOME/etc/<architecture>/Renviron
> exist and have permissions such that the PostgreSQL server can read
> it? The error "cannot find system Renviron" comes from the R
> function process_system_Renviron() in src/main/Renviron.c in response
> to process_Renviron() returning 0, which it does if its filename
> argument is NULL or if it can't open that file.
>
>
Hi Michael,
Thanks for the reply and the research. The relevant file is
[djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron
-rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42
/home/djisgitt/R-2.3.0/etc/Renviron
so I don't see that as the problem.
I use R quite a lot, so I know the installation of R itself is good, but
this is the first time I have tried pl/R. Also, pgsql works, so I assume
there is something incorrect between pgsql and R. I just don't know what!
If you have any more suggestions, or need more information, let me know.
Don
Don Isgitt wrote: > Thanks for the reply and the research. The relevant file is > > [djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron > -rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42 > /home/djisgitt/R-2.3.0/etc/Renviron > > so I don't see that as the problem. > > > I use R quite a lot, so I know the installation of R itself is good, but > this is the first time I have tried pl/R. Also, pgsql works, so I assume > there is something incorrect between pgsql and R. I just don't know what! > > If you have any more suggestions, or need more information, let me know. I just got back from a business trip, and am trying to get caught up -- give me a few days and I'll see if I can help (i.e. I should be able to find time on the weekend)... Joe
On Wed, Aug 23, 2006 at 08:38:01AM -0500, Don Isgitt wrote: > Thanks for the reply and the research. The relevant file is > > [djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron > -rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42 > /home/djisgitt/R-2.3.0/etc/Renviron > > so I don't see that as the problem. Have you checked the permissions on all of the directories in the file's path? Have you verified that PostgreSQL is using the same $R_HOME? You can check the environment with plr_environ(): SELECT * FROM plr_environ() ORDER BY name; -- Michael Fuhr
Adam Witney wrote:
> Don Isgitt wrote:
>
>> Michael Fuhr wrote:
>>
>>> On Tue, Aug 22, 2006 at 04:24:46PM -0500, Don Isgitt wrote:
>>>
>>>
>>>> gds2=# create function sd(_float8) returns float as '' language 'plr';
>>>> CREATE FUNCTION
>>>>
>>>> gds2=# select round(sd('{1.23,1.31,1.42,1.27}'::_float8)::numeric,8);
>>>> server closed the connection unexpectedly
>>>> This probably means the server terminated abnormally
>>>> before or while processing the request.
>>>> The connection to the server was lost. Attempting reset: Failed.
>>>>
>>>> Relevant server log piece:
>>>>
>>>> cannot find system Renviron
>>>> Fatal error: unable to open the base package
>>>>
>>>> LOG: server process (PID 6792) exited with exit code 2
>>>>
>>>>
>>> I can reproduce this on Solaris 9 with PL/R 0.6.2-alpha and R 2.2.1
>>> if I rename $R_HOME/etc/Renviron to something else. I don't get
>>> the "unable to open the base package" error but I do get "cannot
>>> find system Renviron" and several other errors like "Error in
>>> options(...) : invalid editor parameter" followed by a segmentation
>>> fault.
>>>
>>>
>>>
>>>> So, the question: what am I missing that enables it to find the
>>>> "Renviron"
>>>>
>>>>
>>> Does the file $R_HOME/etc/Renviron or $R_HOME/etc/<architecture>/Renviron
>>> exist and have permissions such that the PostgreSQL server can read
>>> it? The error "cannot find system Renviron" comes from the R
>>> function process_system_Renviron() in src/main/Renviron.c in response
>>> to process_Renviron() returning 0, which it does if its filename
>>> argument is NULL or if it can't open that file.
>>>
>>>
>>>
>> Hi Michael,
>>
>> Thanks for the reply and the research. The relevant file is
>>
>> [djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron
>> -rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42
>> /home/djisgitt/R-2.3.0/etc/Renviron
>>
>> so I don't see that as the problem.
>>
>>
>> I use R quite a lot, so I know the installation of R itself is good, but
>> this is the first time I have tried pl/R. Also, pgsql works, so I assume
>> there is something incorrect between pgsql and R. I just don't know what!
>>
>> If you have any more suggestions, or need more information, let me know.
>>
>
> Hi Don,
>
> your functions work fine on my linux system. Just wondering, could the
> fact that your R_HOME is installed under your home directory be causing
> the problem? Postgesql will be running as a different user...
>
> adam
>
>
Hi Adam,
Thanks for checking that. There is world read access to R_HOME, so I
hope that is sufficient.
Don
Michael Fuhr wrote: > On Wed, Aug 23, 2006 at 08:38:01AM -0500, Don Isgitt wrote: > >> Thanks for the reply and the research. The relevant file is >> >> [djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron >> -rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42 >> /home/djisgitt/R-2.3.0/etc/Renviron >> >> so I don't see that as the problem. >> > > Have you checked the permissions on all of the directories in the > file's path? Have you verified that PostgreSQL is using the same > $R_HOME? You can check the environment with plr_environ(): > > Yes. At least world read all the way. gds2=# select * from plr_environ() order by name; R_HOME | /home/djisgitt/R-2.3.0 > SELECT * FROM plr_environ() ORDER BY name; > > Thank you, Michael. I appreciate your help. Don
Don Isgitt wrote: > Michael Fuhr wrote: > >On Wed, Aug 23, 2006 at 08:38:01AM -0500, Don Isgitt wrote: > > > >>Thanks for the reply and the research. The relevant file is > >> > >>[djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron > >>-rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42 > >>/home/djisgitt/R-2.3.0/etc/Renviron > >> > >>so I don't see that as the problem. > >> > > > >Have you checked the permissions on all of the directories in the > >file's path? Have you verified that PostgreSQL is using the same > >$R_HOME? You can check the environment with plr_environ(): > > > > > Yes. At least world read all the way. The best way to make sure this is the case I've found is su - postgres stat /home/djisgitt/R-2.3.0/etc/Renviron (or ls, whatever) I've seen people swearing they have world access all the way and then noticing they are missing a little bit somewhere. -- Alvaro Herrera http://www.CommandPrompt.com/ PostgreSQL Replication, Consulting, Custom Development, 24x7 support
On Wed, Aug 23, 2006 at 09:37:17AM -0500, Don Isgitt wrote: > Michael Fuhr wrote: > >Have you checked the permissions on all of the directories in the > >file's path? Have you verified that PostgreSQL is using the same > >$R_HOME? You can check the environment with plr_environ(): > > > Yes. At least world read all the way. Just readable or also executable? What's the output of the following? ls -ld /home/djisgitt/R-2.3.0/etc /home/djisgitt/R-2.3.0 /home/djisgitt /home -- Michael Fuhr
Alvaro Herrera wrote: > Don Isgitt wrote: > >> Michael Fuhr wrote: >> >>> On Wed, Aug 23, 2006 at 08:38:01AM -0500, Don Isgitt wrote: >>> >>> >>>> Thanks for the reply and the research. The relevant file is >>>> >>>> [djisgitt@prs1 R-2.3.0]$ ls -l $R_HOME/etc/Renviron >>>> -rw-rw-r-- 1 djisgitt djisgitt 1151 Jun 1 11:42 >>>> /home/djisgitt/R-2.3.0/etc/Renviron >>>> >>>> so I don't see that as the problem. >>>> >>>> >>> Have you checked the permissions on all of the directories in the >>> file's path? Have you verified that PostgreSQL is using the same >>> $R_HOME? You can check the environment with plr_environ(): >>> >>> >>> >> Yes. At least world read all the way. >> > > The best way to make sure this is the case I've found is > > su - postgres > stat /home/djisgitt/R-2.3.0/etc/Renviron > (or ls, whatever) > > I've seen people swearing they have world access all the way and then > noticing they are missing a little bit somewhere. > > Quite so, Alvaro & Michael. Yes, world read as I said, but missing execute at one level. Sorry for my carelessness. It works as expected now. Thank you, Don
Don Isgitt wrote: > Quite so, Alvaro & Michael. Yes, world read as I said, but missing > execute at one level. Sorry for my carelessness. It works as expected now. > Ah, good to know. I'll add myself a todo to eliminate the crash in this scenario. I will include a fix in the next release, which will probably be sometime after postgres 8.2 beta starts. Joe