Building R package with integrate_ode_bdf() results in `Symbol not found: _CVode`

seananderson commented 4 years ago

Summary:

If I try to build an R package that uses rstan and includes the BDF ODE solver (integrate_ode_bdf), I receive the error Symbol not found: _CVode.

Description:

I am unable to build R packages that use the integrate_ode_bdf ODE solver using the set up as built by rstantools.
The integrate_ode_rk45 ODE solver works.
I can also build rstan models that use integrate_ode_bdf through rstan::stan_model or rstan::stan outside of an R package structure.
I have posted a minimal R package in a GitHub repo below as an example.
I'm not sure if this is an rstan or rstantools issue. If this should be an rstantools issue this could be moved there or this can be closed and I will repost.

Reproducible Steps:

Try to install this minimal package I put together using rstantools::rstan_create_package() and an example from the Stan manual:

remotes::install_github("seananderson/testBDF")

Current Output:

Error: package or namespace load failed for ‘testBDF’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so, 6): Symbol not found: _CVode
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so
Error: loading failed
Execution halted

I assume the important error is Symbol not found: _CVode

The above was on OS X as described below. On Windows R 3.6.2 I've been told the error is:

undefined reference to `CVodeFree' collect2.exe: error: ld returned 1 exit status

Expected Output:

The package to build and install. The package will build and install if integrate_ode_bdf is replaced with integrate_ode_rk45.

RStan Version:

rstan: 2.21.2 StanHeaders: 2.21.0.5 rstantools: 2.1.1 or 2.1.1.9000

R Version:

R version 4.0.2 (2020-06-22)

(Also tested on Windows R 3.6.2)

Operating System:

OS X 10.15.6

(Also tested on Windows 10 1909)

jgabry commented 4 years ago

I assume the important error is Symbol not found: _CVode

The above was on OS X as described below. On Windows R 3.6.2 I've been told the error is:
undefined reference to `CVodeFree' collect2.exe: error: ld returned 1 exit status

Sorry you're getting an error. Thanks for reporting this. @bgoodri Any idea what's going here?

bgoodri commented 4 years ago

I can replicate the installation error on Linux, but I don't know why it is occurring. Perhaps the shared library of StanHeaders is not built correctly, but after a quick look it seems to include the right headers for that CVodeUserData thing.

On Fri, Jul 31, 2020 at 1:24 PM Sean Anderson notifications@github.com wrote:

Summary:

If I try to build an R package that uses rstan and includes the BDF ODE solver (integrate_ode_bdf), I receive the error Symbol not found: _CVode. Description:

I am unable to build R packages that use the integrate_ode_bdf ODE solver using the set up as built by rstantools.

The integrate_ode_rk45 ODE solver works.

I can also build rstan models that use integrate_ode_bdf through rstan::stan_model or rstan::stan outside of an R package structure.

I have posted a minimal R package in a GitHub repo below as an example.

I'm not sure if this is an rstan or rstantools issue. If this should be an rstantools issue this could be moved there or this can be closed and I will repost.

Reproducible Steps:

Try to install this minimal package https://github.com/seananderson/testBDF I put together using rstantools::rstan_create_package() and an example from the Stan manual:

remotes::install_github("seananderson/testBDF")

Current Output:

Error: package or namespace load failed for ‘testBDF’ in dyn.load(file, DLLpath = DLLpath, ...):

unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so':

dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so, 6): Symbol not found: _CVode

Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so

Expected in: flat namespace

in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-testBDF/00new/testBDF/libs/testBDF.so

Error: loading failed

Execution halted

I assume the important error is Symbol not found: _CVode

The above was on OS X as described below. On Windows R 3.6.2 I've been told the error is:

undefined reference to `CVodeFree' collect2.exe: error: ld returned 1 exit status

Expected Output:

The package to build and install. The package will build and install if integrate_ode_bdf is replaced with integrate_ode_rk45. RStan Version:

rstan: 2.21.2 StanHeaders: 2.21.0.5 rstantools: 2.1.1 or 2.1.1.9000 R Version:

R version 4.0.2 (2020-06-22)

(Also tested on Windows R 3.6.2) Operating System:

OS X 10.15.6

(Also tested on Windows 10 1909)

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bgoodri commented 4 years ago

OK, this is not as bad as I feared. Basically, rstantools does not do the right thing when the package wants to utilize CVODES. To fix it on Linux / Mac

Open Makevars
Delete the line that says "# Generated by rstantools. Do not edit by hand."
At the end of the line that starts with PKG_LIBS, add the text -L"$(STANHEADERS_SRC)/../../lib/" -lStanHeaders

To fix it on Windows,

Open Makevars.win
Delete the line that says "# Generated by rstantools. Do not edit by hand."
At the end of the line that starts with PKG_LIBS, add the text -L"$(STANHEADERS_SRC)/../../libs/" -lStanHeaders

Note that the added line refers to the lib subdirectory on Linux / Mac and the libs subdirectory on Windows.

jgabry commented 4 years ago

@bgoodri Thanks for figuring this out. Can this be fixed in rstantools to avoid people having to manually edit Makevars?

bgoodri commented 4 years ago

Yes

On Fri, Aug 7, 2020, 12:04 PM Jonah Gabry notifications@github.com wrote:

@bgoodri https://github.com/bgoodri Thanks for figuring this out. Can this be fixed in rstantools to avoid people having to manually edit Makevars?

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jgabry commented 4 years ago

Ok, we might as well submit a new rstantools. If you fix it in rstantools let me know and I can submit a new version of rstantools to CRAN.

bgoodri commented 4 years ago

We need to somehow detect when the Stan programs are calling a function that utilizes CVODES. I guess grepl() on the Stan programs could work.

On Sat, Aug 8, 2020 at 3:57 PM Jonah Gabry notifications@github.com wrote:

Ok, we might as well submit a new rstantools. If you fix it in rstantools let me know and I can submit a new version of rstantools to CRAN.

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stan-dev / rstan