* bug#49314: Stan package broken
@ 2021-07-01 11:06 Kyle Andrews
2021-07-23 5:25 ` Sarah Morgensen
2022-07-12 13:14 ` Maxim Cournoyer
0 siblings, 2 replies; 3+ messages in thread
From: Kyle Andrews @ 2021-07-01 11:06 UTC (permalink / raw)
To: 49314
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
^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#49314: Stan package broken
2021-07-01 11:06 bug#49314: Stan package broken Kyle Andrews
@ 2021-07-23 5:25 ` Sarah Morgensen
2022-07-12 13:14 ` Maxim Cournoyer
1 sibling, 0 replies; 3+ messages in thread
From: Sarah Morgensen @ 2021-07-23 5:25 UTC (permalink / raw)
To: Kyle Andrews; +Cc: 49314
Hello,
Thanks for the bug report.
Kyle Andrews <kyle.c.andrews@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
^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#49314: Stan package broken
2021-07-01 11:06 bug#49314: Stan package broken Kyle Andrews
2021-07-23 5:25 ` Sarah Morgensen
@ 2022-07-12 13:14 ` Maxim Cournoyer
1 sibling, 0 replies; 3+ messages in thread
From: Maxim Cournoyer @ 2022-07-12 13:14 UTC (permalink / raw)
To: Kyle Andrews; +Cc: 49314-done
Hi,
Kyle Andrews <kyle.c.andrews@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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2021-07-01 11:06 bug#49314: Stan package broken Kyle Andrews
2021-07-23 5:25 ` Sarah Morgensen
2022-07-12 13:14 ` Maxim Cournoyer
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