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steve-the-bayesian / BOOM

A C++ library for Bayesian modeling, mainly through Markov chain Monte Carlo, but with a few other methods supported. BOOM = "Bayesian Object Oriented Modeling". It is also the sound your computer makes when it crashes.
GNU Lesser General Public License v2.1
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Current CRAN version of Boom (0.9.14) does not seem to be compatible with the current version of bsts (0.9.9) #76

Open jimhester opened 8 months ago

jimhester commented 8 months ago

We see the following when trying to compile bsts (0.9.9) with the current version of Boom (0.9.14) installed.

create_shared_state_model.cpp: In member function ‘BOOM::Ptr<BOOM::SharedStateModel> BOOM::bsts::ConditionallyIndependentSharedStateModelFactory::CreateSharedLocalLevel(SEXP, BOOM::CIMSSMB*, const string&)’:
create_shared_state_model.cpp:164:64: error: no matching function for call to ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, std::vector<BOOM::Ptr<BOOM::MvnBase> >&, std::vector<BOOM::Ptr<BOOM::VariableSelectionPrior> >&)’
           state_model_sampler)(state_model.get(), slabs, spikes);
                                                                ^
In file included from create_shared_state_model.cpp:34:0:
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, const std::vector<BOOM::Ptr<BOOM::MvnBase> >&, const std::vector<BOOM::Ptr<BOOM::VariableSelectionPrior> >&, const std::vector<BOOM::Ptr<BOOM::UnivParams> >&, BOOM::RNG&)
     ConditionallyIndependentSharedLocalLevelPosteriorSampler(
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note:   candidate expects 5 arguments, 3 provided
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&)
   class ConditionallyIndependentSharedLocalLevelPosteriorSampler
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note:   candidate expects 1 argument, 3 provided
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&)
/root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note:   candidate expects 1 argument, 3 provided

After installing a previous version of Boom (0.9.11) installation of bsts (0.9.9) succeeded.

Appreciate your time and hopefully it will be a quick fix!

steve-the-bayesian commented 8 months ago

Hi Jim. bsts is currently broken on CRAN but the fix is in flight. Hold tight for a couple days. If you're doing something mission critical I can send you the tarballs directly. Steve

On Mon, Dec 18, 2023 at 11:17 AM Jim Hester @.***> wrote:

We see the following when trying to compile bsts (0.9.9) with the current version of Boom (0.9.14) installed.

create_shared_state_model.cpp: In member function ‘BOOM::Ptr BOOM::bsts::ConditionallyIndependentSharedStateModelFactory::CreateSharedLocalLevel(SEXP, BOOM::CIMSSMB, const string&)’: create_shared_state_model.cpp:164:64: error: no matching function for call to ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel, std::vector<BOOM::Ptr >&, std::vector<BOOM::Ptr >&)’ state_model_sampler)(state_model.get(), slabs, spikes); ^ In file included from create_shared_state_model.cpp:34:0: /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, const std::vector<BOOM::Ptr >&, const std::vector<BOOM::Ptr >&, const std::vector<BOOM::Ptr >&, BOOM::RNG&) ConditionallyIndependentSharedLocalLevelPosteriorSampler( ^~~~~~~~~~~~ /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate expects 5 arguments, 3 provided /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&) class ConditionallyIndependentSharedLocalLevelPosteriorSampler ^~~~~~~~~~~~ /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&) /root/R/x86_64-pc-linux-gnu-library/4.1/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided

After installing a previous version of Boom (0.9.11) installation of bsts (0.9.9) succeeded.

Appreciate your time and hopefully it will be a quick fix!

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jimhester commented 8 months ago

Sounds good, thanks for the prompt reply, and good luck getting the new bsts through CRAN.

barracuda156 commented 8 months ago

Same here:

* installing *source* package ‘bsts’ ...
** using staged installation
** libs
using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlib_flag) 13.2.0’
using C++11
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
  running command ''xcrun' --show-sdk-path 2>&1' had status 64
using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’
/opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I`/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c aggregate_time_series.cc -o aggregate_time_series.o
/opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I`/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c bsts.cc -o bsts.o
/opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I`/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c bsts_init.cc -o bsts_init.o
/opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I`/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c create_dynamic_intercept_state_model.cpp -o create_dynamic_intercept_state_model.o
/opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I`/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c create_shared_state_model.cpp -o create_shared_state_model.o
create_shared_state_model.cpp: In member function 'BOOM::Ptr<BOOM::SharedStateModel> BOOM::bsts::ConditionallyIndependentSharedStateModelFactory::CreateSharedLocalLevel(SEXP, BOOM::CIMSSMB*, const std::string&)':
create_shared_state_model.cpp:164:64: error: no matching function for call to 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, std::vector<BOOM::Ptr<BOOM::MvnBase> >&, std::vector<BOOM::Ptr<BOOM::VariableSelectionPrior> >&)'
  164 |           state_model_sampler)(state_model.get(), slabs, spikes);
      |                                                                ^
In file included from create_shared_state_model.cpp:34:
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, const std::vector<BOOM::Ptr<BOOM::MvnBase> >&, const std::vector<BOOM::Ptr<BOOM::VariableSelectionPrior> >&, const std::vector<BOOM::Ptr<BOOM::UnivParams> >&, BOOM::RNG&)'
  125 |     ConditionallyIndependentSharedLocalLevelPosteriorSampler(
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note:   candidate expects 5 arguments, 3 provided
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&)'
  106 |   class ConditionallyIndependentSharedLocalLevelPosteriorSampler
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note:   candidate expects 1 argument, 3 provided
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&)'
/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note:   candidate expects 1 argument, 3 provided
make: *** [create_shared_state_model.o] Error 1
ERROR: compilation failed for package ‘bsts’
steve-the-bayesian commented 8 months ago

Fix for bsts is in flight. Sadly, CRAN does not accept packages in batches. Apologies for the interruption. If you need them and can't wait for CRAN I can send you the matching set of tarballs.

On Mon, Dec 18, 2023 at 12:49 PM Sergey Fedorov @.***> wrote:

Same here:

  • installing source package ‘bsts’ ... using staged installation libs using C++ compiler: ‘g++-mp-13 (MacPorts gcc13 13.2.0_4+stdlibflag) 13.2.0’ using C++11 Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) : running command ''xcrun' --show-sdk-path 2>&1' had status 64 using SDK: ‘NA’‘NA’‘NA’‘NA’‘NA’‘NA’ /opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc -c aggregate_time_series.cc -o aggregate_timeseries.o /opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD -DR_NOREMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc -c bsts.cc -o bsts.o /opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc -c bsts_init.cc -o bstsinit.o /opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc -c create_dynamic_intercept_state_model.cpp -o create_dynamic_intercept_statemodel.o /opt/local/bin/g++-mp-13 -std=gnu++11 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/local/Library/Frameworks/R.framework/Resources/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD -DR_NO_REMAP -DRLANGUAGE -I'/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include' -isystem/opt/local/include/LegacySupport -I/opt/local/include -fPIC -pipe -Os -arch ppc -c create_shared_state_model.cpp -o create_shared_state_model.o create_shared_state_model.cpp: In member function 'BOOM::Ptr BOOM::bsts::ConditionallyIndependentSharedStateModelFactory::CreateSharedLocalLevel(SEXP, BOOM::CIMSSMB, const std::string&)': create_shared_state_model.cpp:164:64: error: no matching function for call to 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel, std::vector<BOOM::Ptr >&, std::vector<BOOM::Ptr >&)' 164 | state_model_sampler)(state_model.get(), slabs, spikes); | ^ In file included from create_shared_state_model.cpp:34: /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelStateModel*, const std::vector<BOOM::Ptr >&, const std::vector<BOOM::Ptr >&, const std::vector<BOOM::Ptr >&, BOOM::RNG&)' 125 | ConditionallyIndependentSharedLocalLevelPosteriorSampler( | ^~~~~~~~~~~~ /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate expects 5 arguments, 3 provided /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&)' 106 | class ConditionallyIndependentSharedLocalLevelPosteriorSampler | ^~~~~~~~~~~~ /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: 'BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&)' /opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided make: *** [create_shared_state_model.o] Error 1 ERROR: compilation failed for package ‘bsts’

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barracuda156 commented 8 months ago

@steve-the-bayesian Thank you, not worth the trouble, we can wait for the fixed version. (I wanted to add bsts to Macports, and I will need some publicly available upstream source or CRAN tarball for that anyway.)

steve-the-bayesian commented 8 months ago

That’s awesome! Thanks for the macports support.

On Mon, Dec 18, 2023 at 1:36 PM Sergey Fedorov @.***> wrote:

@steve-the-bayesian https://github.com/steve-the-bayesian Thank you, not worth the trouble, we can wait for the fixed version. (I wanted to add bsts to Macports, and I will need some publicly available upstream source or CRAN tarball for that anyway.)

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barracuda156 commented 8 months ago

That’s awesome! Thanks for the macports support.

https://ports.macports.org/port/R-Boom https://ports.macports.org/port/R-BoomSpikeSlab

marc-mabe commented 8 months ago

Is there any new on this? I have the same issue trying to upgrade Alpine needing the new BOOM version related to https://github.com/steve-the-bayesian/BOOM/pull/72

steve-the-bayesian commented 8 months ago

I'm fighting with CRAN over a warning produced by ASAN. Things got held up by the Christmas holiday.

On Mon, Jan 8, 2024 at 3:41 AM Marc Bennewitz @.***> wrote:

Is there any new on this? I have the same issue trying to upgrade Alpine needing the new BOOM version related to #72 https://github.com/steve-the-bayesian/BOOM/pull/72

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marc-mabe commented 5 months ago

As far as I can see it's working now with bsts 0.9.10 and boom 0.9.15 :tada: