GNU bug report logs - #49314
Stan package broken

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Kyle Andrews <kyle.c.andrews <at> gmail.com>
To: bug-guix <at> gnu.org
Subject: Stan package broken
Date: Thu, 01 Jul 2021 07:06:39 -0400

Hello,

I tried to run a "Hello World" stan model using the r-rstan package.

#+BEGIN_SRC R
stancode="data {
  int<lower=0> N;
  vector[N] x;
  vector[N] y;
}
parameters {
  real alpha;
  real beta;
  real<lower=0> sigma;
}
model {
  y ~ normal(alpha + beta * x, sigma);
}
"
stan_lm = stan(model_code = stancode)
#+END_SRC

Running that code I get the error:

#+BEGIN_EXAMPLE
Error in dyn.load(libLFile) : 
  unable to load shared object '/tmp/Rtmp1AXXXr/file1ffd36a95fa3.so':
  /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/Rtmp1AXXXr/file1ffd36a95fa3.so)
Error in sink(type = "output") : invalid connection
#+END_EXAMPLE

I setup my environment with:

: guix environment --ad-hoc r-rstan r-rstanarm r

Message #8 received at 49314 <at> debbugs.gnu.org (full text, mbox):

From: Sarah Morgensen <iskarian <at> mgsn.dev>
To: Kyle Andrews <kyle.c.andrews <at> gmail.com>
Cc: 49314 <at> debbugs.gnu.org
Subject: Re: bug#49314: Stan package broken
Date: Thu, 22 Jul 2021 22:25:37 -0700

Hello,

Thanks for the bug report.

Kyle Andrews <kyle.c.andrews <at> gmail.com> writes:

[...]

> #+BEGIN_EXAMPLE
> Error in dyn.load(libLFile) : 
>   unable to load shared object '/tmp/Rtmp1AXXXr/file1ffd36a95fa3.so':
>   /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/Rtmp1AXXXr/file1ffd36a95fa3.so)

This kind of error typically occurs when something is compiled with a
newer version of GCC/glibc and then linked with an older version. Do you
happen to have a gcc or gcc-toolchain installed in your profile (and
does removing it solve this issue)?

> Error in sink(type = "output") : invalid connection
> #+END_EXAMPLE
>
> I setup my environment with:
>
> : guix environment --ad-hoc r-rstan r-rstanarm r

Alternatively, you could try

  guix environment --pure --ad-hoc r-rstan r-rstanarm r bash coreutils

(Using --pure prevents packages from your profile being used.)

--
Sarah

Message #13 received at 49314-done <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: Kyle Andrews <kyle.c.andrews <at> gmail.com>
Cc: 49314-done <at> debbugs.gnu.org
Subject: Re: bug#49314: Stan package broken
Date: Tue, 12 Jul 2022 09:14:29 -0400

Hi,

Kyle Andrews <kyle.c.andrews <at> gmail.com> writes:

> Hello,
>
> I tried to run a "Hello World" stan model using the r-rstan package.
>
> #+BEGIN_SRC R
> stancode="data {
>   int<lower=0> N;
>   vector[N] x;
>   vector[N] y;
> }
> parameters {
>   real alpha;
>   real beta;
>   real<lower=0> sigma;
> }
> model {
>   y ~ normal(alpha + beta * x, sigma);
> }
> "
> stan_lm = stan(model_code = stancode)
> #+END_SRC
>
>
> Running that code I get the error:
>
> #+BEGIN_EXAMPLE
> Error in dyn.load(libLFile) : 
>   unable to load shared object '/tmp/Rtmp1AXXXr/file1ffd36a95fa3.so':
>   /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/Rtmp1AXXXr/file1ffd36a95fa3.so)
> Error in sink(type = "output") : invalid connection
> #+END_EXAMPLE
>
> I setup my environment with:
>
> : guix environment --ad-hoc r-rstan r-rstanarm r

I've tried exercising some of the things shown at
https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started in 'guix
shell r-rstan r-rstanarm r-minimal' and it seems to work.  I'm on Guix
commit 17892c5.

Closing.

Thanks for the report!

Maxim

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