# Dealing with Catalina

**URL:** <https://discourse.mc-stan.org/t/dealing-with-catalina/11285>\
**Category:** Developers\
**Tags:** rstan\
**Created:** [October 7, 2019, 8:16pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285 "2019-10-07T20:16:31Z")\
**Posts on this page:** 20\
**Page:** 7

<div class="post-metadata">

**Author:** ![kevinushey](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kevinushey/32/6132_2.png) [@kevinushey](https://discourse.mc-stan.org/u/kevinushey)\
**Post date:** [October 17, 2019, 10:38pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/122 "2019-10-17T22:38:00Z")

</div>

Can you confirm whether the object compiled by `Rcpp::sourceCpp()` is using the system C++ standard library or the one provided by R? Try running this after compiling the C++ object:

```

dlls <- getLoadedDLLs()
paths <- vapply(dlls, `[[`, "path", FUN.VALUE = character(1))
invisible(lapply(paths, function(path) {
  
  if (!file.exists(path))
    return(FALSE)
  
  output <- system(paste("otool -L", shQuote(path), "| grep libc++ || true"), intern = TRUE)
  if (length(output) == 0)
    return(FALSE)
  
  writeLines(paste0(path, ":"))
  writeLines(output)
  
}))

```

I wonder if you’ll see something like this:

```
/private/var/folders/b4/2422hswx71z8mgwtv4rhxchr0000gn/T/RtmpuZz5kZ/sourceCpp-x86_64-apple-darwin15.6.0-1.0.2/sourcecpp_47b76cd81e72/sourceCpp_2.so:
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 800.6.0)

```

If you still see the issue even with everyone using R’s libc++, I will be surprised!

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<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 17, 2019, 10:58pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/123 "2019-10-17T22:58:58Z")

</div>

@ssp3nc3r says that he got

> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so:  
> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)  
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/readr/libs/readr.so:  
> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)  
> /private/var/folders/lc/h55t9rqs08df0y000pnp61d40000gn/T/Rtmp0GWy17/sourceCpp-x86\_64-apple-darwin15.6.0-1.0.2/sourcecpp\_ced87afdaccc/sourceCpp\_2.so:  
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 800.6.0)

which seems to confirm your haunch. So, do we need to make `Rcpp::sourceCpp` and `inline::cxxfunction` use R’s libc++.1.dylib somehow? Or is the only option to do the `install_name_tool` thing?

---

<div class="post-metadata">

**Author:** ![kevinushey](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kevinushey/32/6132_2.png) [@kevinushey](https://discourse.mc-stan.org/u/kevinushey)\
**Post date:** [October 17, 2019, 11:13pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/124 "2019-10-17T23:13:23Z")

</div>

There _should_ be a way to do this with some special flags in `~/.R/Makevars`, but I’m not sure exactly how this could be accomplished yet. Overriding which standard library gets used by the compiler is a bit tricky, and requires some orchestration of flags both during compilation and linking.

`install_name_tool` is normally a simpler workaround, but I’m not sure if there’s a clear space for it to fit during `Rcpp::sourceCpp()`.

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<div class="post-metadata">

**Author:** ![bigmanj](https://avatars.discourse-cdn.com/v4/letter/b/aeb1de/32.png) [@bigmanj](https://discourse.mc-stan.org/u/bigmanj)\
**Post date:** [October 18, 2019, 1:35am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/125 "2019-10-18T01:35:31Z")

</div>

Hi, sorry–as a new used I could not post more until 24hrs.

I think I figured out where to look (silly me, just needed verbose = TRUE).

I think it is here:

In file included from /usr/local/clang7/include/c++/v1/cstdlib:86:  
/usr/local/clang7/include/c++/v1/stdlib.h:94:15: fatal error: ‘stdlib.h’ file not found  
#include\_next \<stdlib.h\>

Thank you!

---

<div class="post-metadata">

**Author:** ![janhannig](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/janhannig/32/6050_2.png) [@janhannig](https://discourse.mc-stan.org/u/janhannig)\
**Post date:** [October 18, 2019, 10:35am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/126 "2019-10-18T10:35:27Z")

</div>

> [@kevinushey](#):
>
> dlls ← getLoadedDLLs() paths ← vapply(dlls, `[[`, “path”, FUN.VALUE = character(1)) invisible(lapply(paths, function(path) { if (!file.exists(path)) return(FALSE) output ← system(paste(“otool -L”, shQuote(path), “| grep libc++ || true”), intern = TRUE) if (length(output) == 0) return(FALSE) writeLines(paste0(path, “:”)) writeLines(output) }))

I ran this and got:

```no-highlight
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/libs/Rcpp.so:
	/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)

```

I am intermediate computer user and I am not sure what I am supposed to do to fix this issue.

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 18, 2019, 6:45pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/127 "2019-10-18T18:45:40Z")

</div>

@kevinushey Have you seen a Mac with Catalina where the `install_name_tool` makes exceptions work? On @ssp3nc3r’s Mac, I get the attached log where `install_name_tool` seems to work but exceptions continue to not work.

[exceptions.txt](https://discourse.mc-stan.org/uploads/short-url/bRl1UeM4FSeB0Qj3QL5RoDGavGu.txt) (5.5 KB)

---

<div class="post-metadata">

**Author:** ![kevinushey](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/kevinushey/32/6132_2.png) [@kevinushey](https://discourse.mc-stan.org/u/kevinushey)\
**Post date:** [October 18, 2019, 7:03pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/128 "2019-10-18T19:03:31Z")

</div>

I believe install\_name\_tool would need to be called before the compiled shared object is loaded.

An easier way to verify and test would be with an installed package that does the same thing, fixing up the .so before load.

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<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 18, 2019, 7:13pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/129 "2019-10-18T19:13:11Z")

</div>

Maybe. But `Rcpp::sourceCpp` and `inline::cxxfunction` are loading the DLLs automatically, so I don’t see how those would ever work on a Catalina machine. Prior to Catalina, rstan was working with essentially

1. `inline::cxxfunction`
2. `install_name_tool ...`
3. `dyn.unload(path)`
4. `dyn.load(path)`

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<div class="post-metadata">

**Author:** ![mattwilliamson13](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mattwilliamson13/32/773_2.png) [@mattwilliamson13](https://discourse.mc-stan.org/u/mattwilliamson13)\
**Post date:** [October 21, 2019, 2:37am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/130 "2019-10-21T02:37:17Z")

</div>

Does the new Stan release solve this issue or is Catalina still causing problems?

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<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 21, 2019, 3:31am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/131 "2019-10-21T03:31:40Z")

</div>

Unlikely

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<div class="post-metadata">

**Author:** ![bensilver95](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bensilver95/32/6185_2.png) [@bensilver95](https://discourse.mc-stan.org/u/bensilver95)\
**Post date:** [October 21, 2019, 4:32pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/132 "2019-10-21T16:32:42Z")

</div>

Hello, I am a new Stan user and just want to echo that I am having the exact same issue as other people here. It seems like conversation on this thread has fallen off in the past few days - was a permanent, consistent solution ever found? Thanks.

---

<div class="post-metadata">

**Author:** ![bgoodri](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bgoodri/32/4451_2.png) [@bgoodri](https://discourse.mc-stan.org/u/bgoodri)\
**Post date:** [October 21, 2019, 6:21pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/133 "2019-10-21T18:21:27Z")

</div>

No.

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<div class="post-metadata">

**Author:** ![jonah](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/jonah/32/200_2.png) [@jonah](https://discourse.mc-stan.org/u/jonah)\
**Post date:** [October 21, 2019, 6:29pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/134 "2019-10-21T18:29:31Z")

</div>

> [@bensilver95](#):
>
> Hello, I am a new Stan user and just want to echo that I am having the exact same issue as other people here. It seems like conversation on this thread has fallen off in the past few days - was a permanent, consistent solution ever found? Thanks.

Not yet but @bgoodri and others are working on it!

If you want to try running Stan from R a different way in the meantime this might work:

> [@Error in rstan](https://discourse.mc-stan.org/t/error-in-rstan/11368/10):
>
> As a last resort, if CmdStan doesn’t have problems with Catalina (I would think more it’s likely to be ok than RStan) then you could try out the new (unreleased, and unannounced until now, and subject to change) CmdStanR interface, which can be installed from GitHub devtools::install\_github("stan-dev/cmdstanr") There’s a brief intro vignette showing how to install cmdstan (there’s an install\_cmdstan function) and then use cmdstanr to fit models from R (and obtain a stanfit object from the resu…

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<div class="post-metadata">

**Author:** ![torkar](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/torkar/32/1355_2.png) [@torkar](https://discourse.mc-stan.org/u/torkar)\
**Post date:** [October 21, 2019, 7:39pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/135 "2019-10-21T19:39:01Z")

</div>

I use `Docker` for now, and it works nicely :)

[https://cloud.docker.com/repository/docker/torkar/rstan](https://cloud.docker.com/repository/docker/torkar/rstan)

Install via the terminal by writing (on one line):

`docker run -e PASSWORD=YOURPASSWORD -p 8787:8787 -v /PATH/TO/YOUR/HOMEDIR:/home/rstudio torkar/rstan:latest`

Change `YOURPASSWORD` and `/PATH/TO/YOUR/HOMEDIR`. Point your browser to `localhost:8787`.

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<div class="post-metadata">

**Author:** ![cesmithjr](https://avatars.discourse-cdn.com/v4/letter/c/a4c791/32.png) [@cesmithjr](https://discourse.mc-stan.org/u/cesmithjr)\
**Post date:** [October 22, 2019, 1:15am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/136 "2019-10-22T01:15:09Z")

</div>

Docker is the only way I can work right now on the machines I “upgraded” to Catalina. It’s just amazing that Apple has bricked so many people. I have several friends who just can’t work until there is a simple solution.

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<div class="post-metadata">

**Author:** ![mansillo](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mansillo/32/4308_2.png) [@mansillo](https://discourse.mc-stan.org/u/mansillo)\
**Post date:** [October 22, 2019, 8:21am UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/137 "2019-10-22T08:21:18Z")

</div>

I tried to load blavaan earlier today and got an error - adding it in case it points to a solution

> library(blavaan)  
> Loading required package: Rcpp  
> Error: package or namespace load failed for ‘blavaan’ in dyn.load(file, DLLpath = DLLpath, …):  
> unable to load shared object ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so’:  
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so, 6): Library not loaded: /usr/local/gfortran/lib/libgfortran.5.dylib  
> Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so  
> Reason: image not found  
> install.packages(“blavaan”)  
> Installing package into ‘/Users/lukemansillo/Library/R/3.6/library’  
> (as ‘lib’ is unspecified)  
> trying URL ‘[http://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/blavaan\_0.3-7.tgz](http://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/blavaan_0.3-7.tgz)’  
> Content type ‘application/x-gzip’ length 10100210 bytes (9.6 MB)  
> ==================================================  
> downloaded 9.6 MB  
> The downloaded binary packages are in  
> /var/folders/bx/8ltnl1nd13b3k8vjzl8m7ffw0000gn/T//RtmpEpxFYL/downloaded\_packages  
> library(blavaan)  
> Error: package or namespace load failed for ‘blavaan’ in dyn.load(file, DLLpath = DLLpath, …):  
> unable to load shared object ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so’:  
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so, 6): Library not loaded: /usr/local/gfortran/lib/libgfortran.5.dylib  
> Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg/libs/quantreg.so  
> Reason: image not found

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<div class="post-metadata">

**Author:** ![martinmodrak](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/martinmodrak/32/133_2.png) [@martinmodrak](https://discourse.mc-stan.org/u/martinmodrak)\
**Post date:** [October 23, 2019, 1:43pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/138 "2019-10-23T13:43:16Z")

</div>

For transparency: I posted about the issues with Catalina on [official Stan Twitter](https://twitter.com/mcmc_stan/status/1186923309662953472) so that users are warned. If you think I’ve mischaracterized the situation, let me know and I will update the info there (people with access to official Twitter can obviously do it themselves).

Wish you good luck with hunting this down.

---

<div class="post-metadata">

**Author:** ![mansillo](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mansillo/32/4308_2.png) [@mansillo](https://discourse.mc-stan.org/u/mansillo)\
**Post date:** [October 23, 2019, 2:43pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/139 "2019-10-23T14:43:48Z")

</div>

@torkar I just installed `Docker` ran a brms job with it but the error emerged for one of the chains:

> m\_demos\_secular\_age ← brm(auth\_theta\_st |weights(weight)~ s(age,by=religion\_sample),family=gaussian(),  
> data=survey\_data,  
> cores = 4,chains=4, iter = 5000,  
> file=“models/m\_demos\_secular\_age”)  
> Compiling the C++ model  
> recompiling to avoid crashing R session  
> Start sampling  
> starting worker pid=1162 on localhost:11460 at 01:37:30.530  
> starting worker pid=1176 on localhost:11460 at 01:37:30.722  
> starting worker pid=1190 on localhost:11460 at 01:37:30.911  
> starting worker pid=1204 on localhost:11460 at 01:37:31.099  
> SAMPLING FOR MODEL ‘0c266c38e0747884b21cf03aad6cbcc2’ NOW (CHAIN 1).  
> Chain 1:  
> Chain 1: Gradient evaluation took 0.00253 seconds  
> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 25.3 seconds.  
> Chain 1: Adjust your expectations accordingly!  
> Chain 1:  
> Chain 1:  
> Chain 1: Iteration: 1 / 5000 [0%] (Warmup)  
> SAMPLING FOR MODEL ‘0c266c38e0747884b21cf03aad6cbcc2’ NOW (CHAIN 2).  
> Chain 2:  
> Chain 2: Gradient evaluation took 0.002729 seconds  
> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 27.29 seconds.  
> Chain 2: Adjust your expectations accordingly!  
> Chain 2:  
> Chain 2:  
> Chain 2: Iteration: 1 / 5000 [0%] (Warmup)  
> SAMPLING FOR MODEL ‘0c266c38e0747884b21cf03aad6cbcc2’ NOW (CHAIN 3).  
> Chain 3:  
> Chain 3: Gradient evaluation took 0.003116 seconds  
> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 31.16 seconds.  
> Chain 3: Adjust your expectations accordingly!  
> Chain 3:  
> Chain 3:  
> [1] “Error in sampler$call\_sampler(args\_list[[i]]) : "  
> [2] " c++ exception (unknown reason)”  
> error occurred during calling the sampler; sampling not done  
> SAMPLING FOR MODEL ‘0c266c38e0747884b21cf03aad6cbcc2’ NOW (CHAIN 4).  
> Chain 4:  
> Chain 4: Gradient evaluation took 0.002956 seconds  
> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 29.56 seconds.  
> Chain 4: Adjust your expectations accordingly!  
> Chain 4:  
> Chain 4:  
> Chain 4: Iteration: 1 / 5000 [0%] (Warmup)

Am I possibly doing/done something wrong? Have you had success sampling with each implementation of rstan? Does this extend to brms or any other package such as blavaan that acts as a wrapper for RStan?

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<div class="post-metadata">

**Author:** ![torkar](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/torkar/32/1355_2.png) [@torkar](https://discourse.mc-stan.org/u/torkar)\
**Post date:** [October 23, 2019, 2:50pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/140 "2019-10-23T14:50:23Z")

</div>

You are running this on `localhost:8787`?!? I, and others, have used the `Docker` image now for a number of days and I haven’t seen that error on `Docker` :( Can you send a MWE (incl. data) that I can try to run to see what happens?

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<div class="post-metadata">

**Author:** ![mansillo](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/mansillo/32/4308_2.png) [@mansillo](https://discourse.mc-stan.org/u/mansillo)\
**Post date:** [October 23, 2019, 2:54pm UTC](https://discourse.mc-stan.org/t/dealing-with-catalina/11285/141 "2019-10-23T14:54:15Z")

</div>

I was _hoping_ it could be that I was doing something wrong since I’m unfamiliar with much computer science. What do you mean by running it on `localhost:8787` exactly?

[Previous page](https://discourse.mc-stan.org/t/dealing-with-catalina/11285.md?page=6)

[Next page](https://discourse.mc-stan.org/t/dealing-with-catalina/11285.md?page=8)