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tools for automatically recording and saving the history of various t…
…uning variables
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| R version 4.3.1 (2023-06-16) -- "Beagle Scouts" | ||
| Copyright (C) 2023 The R Foundation for Statistical Computing | ||
| Platform: x86_64-apple-darwin20 (64-bit) | ||
|
|
||
| R is free software and comes with ABSOLUTELY NO WARRANTY. | ||
| You are welcome to redistribute it under certain conditions. | ||
| Type 'license()' or 'licence()' for distribution details. | ||
|
|
||
| Natural language support but running in an English locale | ||
|
|
||
| R is a collaborative project with many contributors. | ||
| Type 'contributors()' for more information and | ||
| 'citation()' on how to cite R or R packages in publications. | ||
|
|
||
| Type 'demo()' for some demos, 'help()' for on-line help, or | ||
| 'help.start()' for an HTML browser interface to help. | ||
| Type 'q()' to quit R. | ||
|
|
||
| > setwd('/Users/perry/Projects/GitHub/nimble-dev/nimbleHMC/') | ||
| > code <- nimbleCode({ | ||
| + a[1] ~ dnorm(0, 1) | ||
| + a[2] ~ dnorm(a[1]+1, 1) | ||
| + a[3] ~ dnorm(a[2]+1, 1) | ||
| + d ~ dnorm(a[3], sd=2) | ||
| + }) | ||
| + constants <- list() | ||
| + data <- list(d = 5) | ||
| + inits <- list(a = rep(0, 3)) | ||
| Error in nimbleCode({ : could not find function "nimbleCode" | ||
| > > > > library(nimble) | ||
| nimble version 1.2.0 is loaded. | ||
| For more information on NIMBLE and a User Manual, | ||
| please visit https://R-nimble.org. | ||
|
|
||
| Note for advanced users who have written their own MCMC samplers: | ||
| As of version 0.13.0, NIMBLE's protocol for handling posterior | ||
| predictive nodes has changed in a way that could affect user-defined | ||
| samplers in some situations. Please see Section 15.5.1 of the User Manual. | ||
|
|
||
| Attaching package: ‘nimble’ | ||
|
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||
| The following object is masked from ‘package:stats’: | ||
|
|
||
| simulate | ||
|
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||
| Warning message: | ||
| package ‘nimble’ was built under R version 4.3.3 | ||
| > code <- nimbleCode({ | ||
| + a[1] ~ dnorm(0, 1) | ||
| + a[2] ~ dnorm(a[1]+1, 1) | ||
| + a[3] ~ dnorm(a[2]+1, 1) | ||
| + d ~ dnorm(a[3], sd=2) | ||
| + }) | ||
| + constants <- list() | ||
| + data <- list(d = 5) | ||
| + inits <- list(a = rep(0, 3)) | ||
| > type <- 'NUTS' | ||
| > cat(paste0('testing ', type, ' sampler\n')) | ||
| testing NUTS sampler | ||
| > Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE) | ||
| Defining model | ||
| Building model | ||
| Setting data and initial values | ||
| Running calculate on model | ||
| [Note] Any error reports that follow may simply reflect missing values in model variables. | ||
| Checking model sizes and dimensions | ||
| > Rmodel$calculate() | ||
| [1] -8.493901 | ||
| > conf <- configureMCMC(Rmodel, nodes = NULL) | ||
| ===== Monitors ===== | ||
| thin = 1: a | ||
| ===== Samplers ===== | ||
| (no samplers assigned) | ||
| ===== Comments ===== | ||
| [Warning] No samplers assigned for 3 nodes, use conf$getUnsampledNodes() for node names. | ||
| > conf$addSampler('a', type, control = list(nwarmup = 1000)) | ||
| Error in conf$addSampler("a", type, control = list(nwarmup = 1000)) : | ||
| cannot find sampler type 'NUTS' | ||
| > library(nimbleHMC) | ||
| > conf$addSampler('a', type, control = list(nwarmup = 1000)) | ||
| > Rmcmc <- buildMCMC(conf) | ||
| > Cmodel <- compileNimble(Rmodel) | ||
| Compiling | ||
| [Note] This may take a minute. | ||
| [Note] Use 'showCompilerOutput = TRUE' to see C++ compilation details. | ||
| > Cmcmc <- compileNimble(Rmcmc, project = Rmodel) | ||
| Compiling | ||
| [Note] This may take a minute. | ||
| [Note] Use 'showCompilerOutput = TRUE' to see C++ compilation details. | ||
| Error: Error, wrong number of indices provided for adaptWindow_counter[timesRan]. | ||
| This occurred for: adaptWindow_counter[timesRan] | ||
| This was part of the call: adaptWindow_counter[timesRan] <<- adaptWindow_counter | ||
| > q('no') | ||
|
|
||
| Process R finished at Thu Jun 20 20:07:01 2024 | ||
|
|
||
|
|
||
| R version 4.3.1 (2023-06-16) -- "Beagle Scouts" | ||
| Copyright (C) 2023 The R Foundation for Statistical Computing | ||
| Platform: x86_64-apple-darwin20 (64-bit) | ||
|
|
||
| R is free software and comes with ABSOLUTELY NO WARRANTY. | ||
| You are welcome to redistribute it under certain conditions. | ||
| Type 'license()' or 'licence()' for distribution details. | ||
|
|
||
| Natural language support but running in an English locale | ||
|
|
||
| R is a collaborative project with many contributors. | ||
| Type 'contributors()' for more information and | ||
| 'citation()' on how to cite R or R packages in publications. | ||
|
|
||
| Type 'demo()' for some demos, 'help()' for on-line help, or | ||
| 'help.start()' for an HTML browser interface to help. | ||
| Type 'q()' to quit R. | ||
|
|
||
| > setwd('/Users/perry/Projects/GitHub/nimble-dev/nimbleHMC/') | ||
| > library(nimble) | ||
| nimble version 1.2.0 is loaded. | ||
| For more information on NIMBLE and a User Manual, | ||
| please visit https://R-nimble.org. | ||
|
|
||
| Note for advanced users who have written their own MCMC samplers: | ||
| As of version 0.13.0, NIMBLE's protocol for handling posterior | ||
| predictive nodes has changed in a way that could affect user-defined | ||
| samplers in some situations. Please see Section 15.5.1 of the User Manual. | ||
|
|
||
| Attaching package: ‘nimble’ | ||
|
|
||
| The following object is masked from ‘package:stats’: | ||
|
|
||
| simulate | ||
|
|
||
| Warning message: | ||
| package ‘nimble’ was built under R version 4.3.3 | ||
| > library(nimbleHMC) | ||
| > code <- nimbleCode({ | ||
| + a[1] ~ dnorm(0, 1) | ||
| + a[2] ~ dnorm(a[1]+1, 1) | ||
| + a[3] ~ dnorm(a[2]+1, 1) | ||
| + d ~ dnorm(a[3], sd=2) | ||
| + }) | ||
| + constants <- list() | ||
| + data <- list(d = 5) | ||
| + inits <- list(a = rep(0, 3)) | ||
| > type <- 'NUTS' | ||
| > cat(paste0('testing ', type, ' sampler\n')) | ||
| testing NUTS sampler | ||
| > Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE) | ||
| Defining model | ||
| Building model | ||
| Setting data and initial values | ||
| Running calculate on model | ||
| [Note] Any error reports that follow may simply reflect missing values in model variables. | ||
| Checking model sizes and dimensions | ||
| > Rmodel$calculate() | ||
| [1] -8.493901 | ||
| > conf <- configureMCMC(Rmodel, nodes = NULL) | ||
| ===== Monitors ===== | ||
| thin = 1: a | ||
| ===== Samplers ===== | ||
| (no samplers assigned) | ||
| ===== Comments ===== | ||
| [Warning] No samplers assigned for 3 nodes, use conf$getUnsampledNodes() for node names. | ||
| > conf$addSampler('a', type, control = list(nwarmup = 1000)) | ||
| > Rmcmc <- buildMCMC(conf) | ||
| > Cmodel <- compileNimble(Rmodel) | ||
| Compiling | ||
| [Note] This may take a minute. | ||
| [Note] Use 'showCompilerOutput = TRUE' to see C++ compilation details. | ||
| > Cmcmc <- compileNimble(Rmcmc, project = Rmodel) | ||
| Compiling | ||
| [Note] This may take a minute. | ||
| [Note] Use 'showCompilerOutput = TRUE' to see C++ compilation details. | ||
| Error: Failed to create the shared library. Run 'printErrors()' to see the compilation errors. | ||
| > printErrors() | ||
| using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’ | ||
| using SDK: ‘MacOSX14.4.sdk’ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:1: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Core:382: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:2: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/LU:45: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:3: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Cholesky:12: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Jacobi:29: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:3: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Cholesky:43: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:4: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/QR:15: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Householder:27: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:4: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/QR:48: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:5: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/SVD:48: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:6: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Geometry:57: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| In file included from P_1_MCMC.cpp:8: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/nimble/EigenTypedefs.h:24: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Dense:7: | ||
| In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/Eigenvalues:58: | ||
| /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nimble/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] | ||
| #pragma clang diagnostic pop | ||
| ^ | ||
| P_1_MCMC.cpp:2350:1: error: use of undeclared identifier 'save_histories' | ||
| save_histories(epsilon_history, Hbar_history, logEpsilonBar_history, sum_metropolis_prob_history, n_leapfrog_history, depth_history, logProb_history, adaptWindow_iter_history, adaptWindow_counter_history); | ||
| ^ | ||
| 9 warnings and 1 error generated. | ||
| make: *** [P_1_MCMC.o] Error 1 | ||
| > q('no') | ||
|
|
||
| Process R finished at Thu Jun 20 20:08:58 2024 | ||
|
|
||
|
|
||
| R version 4.3.1 (2023-06-16) -- "Beagle Scouts" | ||
| Copyright (C) 2023 The R Foundation for Statistical Computing | ||
| Platform: x86_64-apple-darwin20 (64-bit) | ||
|
|
||
| R is free software and comes with ABSOLUTELY NO WARRANTY. | ||
| You are welcome to redistribute it under certain conditions. | ||
| Type 'license()' or 'licence()' for distribution details. | ||
|
|
||
| Natural language support but running in an English locale | ||
|
|
||
| R is a collaborative project with many contributors. | ||
| Type 'contributors()' for more information and | ||
| 'citation()' on how to cite R or R packages in publications. | ||
|
|
||
| Type 'demo()' for some demos, 'help()' for on-line help, or | ||
| 'help.start()' for an HTML browser interface to help. | ||
| Type 'q()' to quit R. | ||
|
|
||
| > setwd('/Users/perry/Projects/GitHub/nimble-dev/nimbleHMC/') | ||
| > library(nimble) | ||
| nimble version 1.2.0 is loaded. | ||
| For more information on NIMBLE and a User Manual, | ||
| please visit https://R-nimble.org. | ||
|
|
||
| Note for advanced users who have written their own MCMC samplers: | ||
| As of version 0.13.0, NIMBLE's protocol for handling posterior | ||
| predictive nodes has changed in a way that could affect user-defined | ||
| samplers in some situations. Please see Section 15.5.1 of the User Manual. | ||
|
|
||
| Attaching package: ‘nimble’ | ||
|
|
||
| The following object is masked from ‘package:stats’: | ||
|
|
||
| simulate | ||
|
|
||
| Warning message: | ||
| package ‘nimble’ was built under R version 4.3.3 | ||
| > library(nimbleHMC) | ||
| > code <- nimbleCode({ | ||
| + a[1] ~ dnorm(0, 1) | ||
| + a[2] ~ dnorm(a[1]+1, 1) | ||
| + a[3] ~ dnorm(a[2]+1, 1) | ||
| + d ~ dnorm(a[3], sd=2) | ||
| + }) | ||
| + constants <- list() | ||
| + data <- list(d = 5) | ||
| + inits <- list(a = rep(0, 3)) | ||
| > type <- 'NUTS' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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