Re: [R-SIG-Mac] Can't make odbc FreeTDS connections in R.app, can with RStudio, /usr/local/bin/R, Rscript

[Simon Urbanek]

Joey,

it is hard to say - it could be a bug in the driver. I would recommend using 
lldb to find the trace so you know where it happens - it would be anywhere from 
the odbc package, odbc library or the driver. If there is a difference, also 
check if you are loading the same versions of packages in each (cf .libPaths()) 
and which libraries are used. You could use JDBC with jTDS instead to see if 
that works better (or a native driver if it exists).

Cheers,
Simon



> On 12/08/2021, at 5:31 AM, Joey Reid via R-SIG-Mac  
> wrote:
> 
> I’m experiencing some weirdness with database connections using R 4.1 on 
> macOS 11.5.1 and the `odbc` package with the FreeTDS driver. I can replicate 
> the problem on my coworker’s Mac with R 4.0 (macOS 11, not sure which 
> version). 
> 
> Running this code works fine on the command line (or with RStudio, 
> /usr/local/bin/R), /usr/local/bin/Rscript -e “library(odbc); con = 
> dbConnect(odbc(), 'GISLibrary'); dbGetQuery(con, ‘select 1 num’); 
> dbDisconnect(con)”
> 
> But the connection fails with the exact same code in R.app (I’ve tried R.app 
> rev 7976 and 7982). I often get a segfault, like "address 0x7f975f481cb0, 
> cause 'memory not mapped’”. The connection works fine with the ODBC Driver 17 
> for SQL Server in all execution environments.
> 
> The connection also fails in some environments (rmarkdown::render, Rscript 
> -e) if I load the package sf before making the first connection attempt, 
> e.g., Rscript -e "library(odbc); library(sf);  con = dbConnect(odbc(), 
> 'GISLibrary'); dbGetQuery(con, 'select 1 num'); dbDisconnect(con);". If I 
> delay loading sf until after I’ve successfully made a connection with the 
> FreeTDS driver I can continue to make connections.
> 
> I saw the recent post about breaking ABI changes in the Rcpp package, so I 
> followed the instructions to re-install all packages that depend on Rcpp. 
> That did not solve the problem.
> 
> Thanks,
> 
> Joey Reid
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[R-SIG-Mac] Can't make odbc FreeTDS connections in R.app, can with RStudio, /usr/local/bin/R, Rscript

[Joey Reid via R-SIG-Mac]

I’m experiencing some weirdness with database connections using R 4.1 on macOS 
11.5.1 and the `odbc` package with the FreeTDS driver. I can replicate the 
problem on my coworker’s Mac with R 4.0 (macOS 11, not sure which version). 

Running this code works fine on the command line (or with RStudio, 
/usr/local/bin/R), /usr/local/bin/Rscript -e “library(odbc); con = 
dbConnect(odbc(), 'GISLibrary'); dbGetQuery(con, ‘select 1 num’); 
dbDisconnect(con)”

But the connection fails with the exact same code in R.app (I’ve tried R.app 
rev 7976 and 7982). I often get a segfault, like "address 0x7f975f481cb0, cause 
'memory not mapped’”. The connection works fine with the ODBC Driver 17 for SQL 
Server in all execution environments.

The connection also fails in some environments (rmarkdown::render, Rscript -e) 
if I load the package sf before making the first connection attempt, e.g., 
Rscript -e "library(odbc); library(sf);  con = dbConnect(odbc(), 'GISLibrary'); 
dbGetQuery(con, 'select 1 num'); dbDisconnect(con);". If I delay loading sf 
until after I’ve successfully made a connection with the FreeTDS driver I can 
continue to make connections.

I saw the recent post about breaking ABI changes in the Rcpp package, so I 
followed the instructions to re-install all packages that depend on Rcpp. That 
did not solve the problem.

Thanks,

Joey Reid
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