remove tensorflow support (#882)

* excising tf support * fix typo * update travis in light of tf removal * fix typo in run_tests.R * additional removal of tf-related code * fix syntax in test-benchmarks and lingering tf ref in install_requirements * remove base/64
nimble-dev · May 23, 2019 · 599ff8e · 599ff8e
1 parent 9cdf5c7
commit 599ff8e
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Showing 22 changed files with 41 additions and 2,865 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -14,7 +14,7 @@ cache:
 matrix:
   include:
     - os: osx
-      env: NIMBLE_TEST_BATCH=1 NIMBLE_USE_TENSORFLOW=0
+      env: NIMBLE_TEST_BATCH=1
     - os: linux
       env: NIMBLE_TEST_BATCH=1
     - os: linux
@@ -56,8 +56,6 @@ install:
   - R CMD INSTALL packages/nimble
 
 script:
-  - source /home/travis/.virtualenvs/r-tensorflow/bin/activate \
-    || echo 'Missing tensorflow'
   # - pip freeze
   - ./run_tests.R
 

diff --git a/install_requirements.R b/install_requirements.R
@@ -18,16 +18,3 @@ for (package in requirements) {
     }
 }
 
-## Tensorflow requires custom installation.
-if (Sys.getenv('NIMBLE_USE_TENSORFLOW') %in% c('', '1')) {
-    if (!require(tensorflow)) {
-        install.packages('tensorflow', repos = 'http://cran.us.r-project.org')
-        library(tensorflow)
-    }
-    tryCatch({
-        ## Calling tf$ triggers loading of the python tensorflow library. 
-        cat('Found Tensorflow version', tf$`__version__`, '\n')
-    }, error = function(e) {
-        install_tensorflow()
-    })
-}
diff --git a/packages/Makefile b/packages/Makefile
@@ -68,7 +68,6 @@ clang-format: FORCE
 	  nimble/inst/include/nimble/NimArrBase.h \
 	  nimble/inst/include/nimble/NimArr.h \
 	  nimble/inst/include/nimble/predefinedNimbleLists.h \
-	  nimble/inst/include/nimble/tensorflow.h \
 	  nimble/inst/CppCode/predefinedNimbleLists.cpp \
 	  nimble/inst/CppCode/tensorflow.cpp \
 	  -i

diff --git a/packages/nimble/DESCRIPTION b/packages/nimble/DESCRIPTION
@@ -22,7 +22,7 @@ Depends:
 Imports:
     methods,igraph,coda,R6
 Suggests:
-    testthat,R2WinBUGS,rjags,rstan,xtable,abind,ggplot2,tensorflow,reticulate
+    testthat,R2WinBUGS,rjags,rstan,xtable,abind,ggplot2
 URL: https://r-nimble.org
 SystemRequirements: GNU make
 License: BSD_3_clause + file LICENSE | GPL (>= 2)
@@ -66,7 +66,6 @@ Collate:
     genCpp_maps.R
     genCpp_liftMaps.R
     genCpp_eigenization.R
-    genCpp_TFize.R
     genCpp_addDebugMarks.R
     genCpp_generateCpp.R
     RCfunction_core.R

diff --git a/packages/nimble/R/RCfunction_compile.R b/packages/nimble/R/RCfunction_compile.R
@@ -419,24 +419,17 @@ RCfunProcessing <- setRefClass(
                 writeLines('***** READY FOR eigenize *****')
                 browser()
             }
-
-            if(nimbleOptions('experimentalUseTensorflow')) {
-                exprClasses_TFize(compileInfo$nimExpr,
-                                  compileInfo$newLocalSymTab,
-                                  compileInfo$typeEnv)
-            } else {
-                tryResult <- try(
-                    exprClasses_eigenize(compileInfo$nimExpr,
-                                         compileInfo$newLocalSymTab,
-                                         compileInfo$typeEnv))
-                if(inherits(tryResult, 'try-error')) {
-                    stop(
-                        paste('There is some problem at the Eigen processing step for this code:\n',
-                              paste(deparse(compileInfo$origRcode),
-                                    collapse = '\n'),
-                              collapse = '\n'),
-                        call. = FALSE)
-                }
+            tryResult <- try(
+                exprClasses_eigenize(compileInfo$nimExpr,
+                                     compileInfo$newLocalSymTab,
+                                     compileInfo$typeEnv))
+            if(inherits(tryResult, 'try-error')) {
+                stop(
+                    paste('There is some problem at the Eigen processing step for this code:\n',
+                          paste(deparse(compileInfo$origRcode),
+                                collapse = '\n'),
+                          collapse = '\n'),
+                    call. = FALSE)
             }
             if(debug) {
                 print('nimDeparse(compileInfo$nimExpr)')

diff --git a/packages/nimble/R/cppDefs_RCfunction.R b/packages/nimble/R/cppDefs_RCfunction.R
@@ -19,8 +19,7 @@ RCfunctionDef <- setRefClass('RCfunctionDef',
                                                        '<math.h>',
                                                        nimbleIncludeFile("EigenTypedefs.h"),
                                                        nimbleIncludeFile("Utils.h"),
-                                                       nimbleIncludeFile("accessorClasses.h"),
-                                                       if(nimbleOptions('experimentalUseTensorflow')) nimbleIncludeFile("tensorflow.h") else character())
+                                                       nimbleIncludeFile("accessorClasses.h"))
                                      CPPusings <<- c(CPPusings) 
                                      callSuper(...)
                                  },

diff --git a/packages/nimble/R/cppDefs_cppProject.R b/packages/nimble/R/cppDefs_cppProject.R
@@ -226,18 +226,6 @@ cppProjectClass <- setRefClass('cppProjectClass',
                                        writeDynamicRegistrationsDotCpp(cppName, dllName)
                                        nimbleUserNamespace$sessionSpecificDll <- compileStaticCode(dllName, cppName, showCompilerOutput)
                                    },
-                                   compileTensorflowWrapper = function(showCompilerOutput = nimbleOptions('showCompilerOutput')) {
-                                       # Load prerequisite DLLs.
-                                       if(!requireNamespace('tensorflow')) stop('tensorflow package must be installed. Try "install.packages(\"tensorflow\")"')
-                                       tfPath <- tensorflow::tf$`__path__`  # This line triggers loading of _pywrap_tensorflow_internal.so.
-                                       tensorflowDllPath <- file.path(tfPath, 'python', '_pywrap_tensorflow_internal.so')
-                                       if(!file.exists(tensorflowDllPath))  stop(paste('Missing shared library', tensorflowDllPath))
-
-                                       timeStamp <- format(Sys.time(), "%m_%d_%H_%M_%S")
-                                       dllName <- paste0("nimble-tensorflow_", timeStamp)
-                                       cppName <- file.path(system.file(package = 'nimble'), 'CppCode', 'tensorflow.cpp')
-                                       nimbleUserNamespace$tensorflowWrapperDll <- compileStaticCode(dllName, cppName, showCompilerOutput)
-                                   },
                                    compileFile = function(names, showCompilerOutput = nimbleOptions('showCompilerOutput'),
                                                           .useLib = UseLibraryMakevars) {
                                        names <- Rname2CppName(names)
@@ -267,23 +255,6 @@ cppProjectClass <- setRefClass('cppProjectClass',
                                        if(is.null(nimbleUserNamespace$sessionSpecificDll)) {
                                            compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
                                        }
-                                       if(nimbleOptions('experimentalUseTensorflow')) {
-                                           if (is.null(nimbleUserNamespace$tensorflowWrapperDll)) {
-                                               compileTensorflowWrapper(showCompilerOutput = showCompilerOutput)
-                                           }
-                                           compileOnce <- FALSE  # TODO Compile tensorflow.cpp once and link against the .so file.
-                                           if (compileOnce) {
-                                               # This passes the the tensorflow wrapper .so as a compiler flag to R CMD SHLIB.
-                                               # This fails on travis because passing this linker flag overrides PKG_LIBS from Makevars.
-                                               # For more details, see http://www.hep.by/gnu/r-patched/r-exts/R-exts_96.html
-                                               # "Supplying linker commands as arguments to R CMD SHLIB will take precedence over PKG_LIBS in `Makevars'."
-                                               SHLIBcmd <- paste(SHLIBcmd, nimbleUserNamespace$tensorflowWrapperDll[['path']])
-                                           } else {
-                                               # This recompiles the tensorflow.cpp wrapper each time it is needed.
-                                               # This is inefficient, but works for now.
-                                               SHLIBcmd <- paste(SHLIBcmd, file.path(system.file(package = 'nimble'), 'CppCode', 'tensorflow.cpp'))
-                                           }
-                                       }
 
                                        origSHLIBcmd <- SHLIBcmd
                                        if(isTRUE(nimbleOptions('stopCompilationBeforeLinking'))) {## used only for testing, when we want to go quickly and skip linking and bail out