Installation clang error

[JackStat]

I am unable to install the current master branch because of a clang error

The downloaded binary packages are in
    /var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T//RtmpStAaCt/downloaded_packages
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T/RtmpStAaCt/devtools6c036871f8b7/gbm-developers-gbm-7b0e3ce'  \
  --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library'  \
  --install-tests 

* installing *source* package ‘gbm’ ...
** libs
clang-omp++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -fopenmp -fPIC  -Wall -mtune=core2 -g -O2  -c adaboost.cpp -o adaboost.o
Assertion failed: (CXXThisValue && "no 'this' value for this function"), function LoadCXXThis, file /tmp/clang-omp20150923-62433-20jwzc/llvm-2015-04-01/tools/clang/lib/CodeGen/CodeGenFunction.h, line 1782.
0  clang-3.5                0x0000000105c2043f llvm::sys::PrintStackTrace(__sFILE*) + 40
1  clang-3.5                0x0000000105c2080c SignalHandler(int) + 227
2  libsystem_platform.dylib 0x00007fff98bb4eaa _sigtramp + 26
3  clang-3.5                0x0000000107212710 guard variable for isAllowedInitiallyIDChar(unsigned int, clang::LangOptions const&)::C99DisallowedInitialIDChars + 77768
4  clang-3.5                0x0000000105c20691 abort + 22
5  clang-3.5                0x0000000105c2067b abort + 0
6  clang-3.5                0x0000000105ffc76e clang::StmtVisitorBase<clang::make_ptr, (anonymous namespace)::ScalarExprEmitter, llvm::Value*>::Visit(clang::Stmt*) + 4286
7  clang-3.5                0x0000000106001b0b (anonymous namespace)::ScalarExprEmitter::VisitCastExpr(clang::CastExpr*) + 787
8  clang-3.5                0x0000000105ff68ba clang::CodeGen::CodeGenFunction::EmitScalarExpr(clang::Expr const*, bool) + 102
9  clang-3.5                0x0000000105fe69df clang::CodeGen::CodeGenFunction::EmitCXXMemberCallExpr(clang::CXXMemberCallExpr const*, clang::CodeGen::ReturnValueSlot) + 745
10 clang-3.5                0x0000000105fde7e0 clang::CodeGen::CodeGenFunction::EmitCallExpr(clang::CallExpr const*, clang::CodeGen::ReturnValueSlot) + 230
11 clang-3.5                0x0000000106000317 (anonymous namespace)::ScalarExprEmitter::VisitCallExpr(clang::CallExpr const*) + 75
12 clang-3.5                0x0000000105ff68ba clang::CodeGen::CodeGenFunction::EmitScalarExpr(clang::Expr const*, bool) + 102
13 clang-3.5                0x000000010605c807 clang::CodeGen::CodeGenFunction::EmitOMPDirectiveWithLoop(clang::OpenMPDirectiveKind, clang::OpenMPDirectiveKind, clang::OMPExecutableDirective const&) + 1405
14 clang-3.5                0x000000010605a2a0 clang::CodeGen::CodeGenFunction::EmitOMPDirectiveWithParallelMicrotask(clang::OpenMPDirectiveKind, llvm::ArrayRef<clang::OpenMPDirectiveKind>, clang::OMPExecutableDirective const&) + 2510
15 clang-3.5                0x000000010605ee18 clang::CodeGen::CodeGenFunction::EmitOMPParallelForDirective(clang::OMPParallelForDirective const&) + 40
16 clang-3.5                0x0000000106053060 clang::CodeGen::CodeGenFunction::EmitCompoundStmtWithoutScope(clang::CompoundStmt const&, bool, clang::CodeGen::AggValueSlot) + 72
17 clang-3.5                0x000000010607fd93 clang::CodeGen::CodeGenFunction::EmitFunctionBody(clang::CodeGen::FunctionArgList&, clang::Stmt const*) + 95
18 clang-3.5                0x0000000106080332 clang::CodeGen::CodeGenFunction::GenerateCode(clang::GlobalDecl, llvm::Function*, clang::CodeGen::CGFunctionInfo const&) + 1170
19 clang-3.5                0x000000010608a2d4 clang::CodeGen::CodeGenModule::EmitGlobalFunctionDefinition(clang::GlobalDecl, llvm::GlobalValue*) + 1322
20 clang-3.5                0x0000000106088055 clang::CodeGen::CodeGenModule::EmitGlobalDefinition(clang::GlobalDecl, llvm::GlobalValue*) + 505
21 clang-3.5                0x00000001060cc192 (anonymous namespace)::CodeGeneratorImpl::HandleTopLevelDecl(clang::DeclGroupRef) + 80
22 clang-3.5                0x000000010607c224 clang::BackendConsumer::HandleTopLevelDecl(clang::DeclGroupRef) + 132
23 clang-3.5                0x00000001062cd9c1 clang::ParseAST(clang::Sema&, bool, bool) + 316
24 clang-3.5                0x0000000105dac1c9 clang::FrontendAction::Execute() + 67
25 clang-3.5                0x0000000105d8a0de clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) + 528
26 clang-3.5                0x0000000105dd52db clang::ExecuteCompilerInvocation(clang::CompilerInstance*) + 3995
27 clang-3.5                0x0000000105212ce9 cc1_main(char const**, char const**, char const*, void*) + 1059
28 clang-3.5                0x00000001052122c0 main + 7805
29 libdyld.dylib            0x00007fff91b6c5ad start + 1
Stack dump:
0.  Program arguments: /usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/clang-3.5 -cc1 -fopenmp -omp-main-file-path adaboost.cpp -triple x86_64-apple-macosx10.11.0 -emit-obj -disable-free -main-file-name adaboost.cpp -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -gdwarf-2 -dwarf-column-info -coverage-file /private/var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T/RtmpStAaCt/devtools6c036871f8b7/gbm-developers-gbm-7b0e3ce/src/adaboost.o -resource-dir /usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../lib/clang/3.5.0 -D NDEBUG -I /Library/Frameworks/R.framework/Resources/include -I /usr/local/include -I /usr/local/include/freetype2 -I /opt/X11/include -I /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include -stdlib=libc++ -O2 -Wall -fdeprecated-macro -fdebug-compilation-dir /private/var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T/RtmpStAaCt/devtools6c036871f8b7/gbm-developers-gbm-7b0e3ce/src -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.11.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fdiagnostics-show-option -vectorize-loops -vectorize-slp -o adaboost.o -x c++ adaboost.cpp 
1.  adaboost.cpp:42:1: current parser token 'double'
2.  adaboost.cpp:30:17: LLVM IR generation of declaration 'CAdaBoost::ComputeWorkingResponse'
3.  adaboost.cpp:30:17: Generating code for declaration 'CAdaBoost::ComputeWorkingResponse'
clang-3.5: error: unable to execute command: Illegal instruction: 4
clang-3.5: error: clang frontend command failed due to signal (use -v to see invocation)
clang version 3.5.0 
Target: x86_64-apple-darwin15.3.0
Thread model: posix
clang-3.5: note: diagnostic msg: PLEASE submit a bug report to http://llvm.org/bugs/ and include the crash backtrace, preprocessed source, and associated run script.
clang-3.5: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang-3.5: note: diagnostic msg: /var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T/adaboost-bd29ef.cpp
clang-3.5: note: diagnostic msg: /var/folders/0x/p_3gmzmj7990ymlmtn0d5j580000gn/T/adaboost-bd29ef.sh
clang-3.5: note: diagnostic msg: 

********************
make: *** [adaboost.o] Error 254
ERROR: compilation failed for package ‘gbm’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gbm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gbm’
Error: Command failed (1)

[pdmetcalfe]

Ooh, we've broken clang.

Anyone with a Mac want to solve this (or buy me one)? 😃

[patr1ckm]

I can confirm this. I have a mac, but not sure how to fix.

[pdmetcalfe]

Oh. Super. Thanks!

It builds on the travis OS X environment, if that helps at all?

[patr1ckm]

It looks like the error has changed, I now get the following:

* installing *source* package ‘gbm’ ...
** libs
clang-omp++ -I/Library/Frameworks/R.framework/Resources/include     -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -fopenmp -fPIC  -Wall -mtune=core2 -O3    -c adaboost.cpp -o adaboost.o
In file included from adaboost.cpp:12:
In file included from ./adaboost.h:18:
In file included from ./distribution.h:24:
In file included from ./dataset.h:21:
In file included from ./datadistparams.h:19:
In file included from ./gbm_exception.h:4:
In file included from /usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../include/c++/v1/string:435:
/usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../include/c++/v1/iosfwd:90:10: fatal error: 'wchar.h' file not found
#include <wchar.h>  // for mbstate_t
         ^
1 error generated.
make: *** [adaboost.o] Error 1
ERROR: compilation failed for package ‘gbm’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gbm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gbm’
Error: Command failed (1)

[patr1ckm]

I was able to compile the new gbm under OSX 10.12.1 using g++/gcc-6.

Here are the steps:

0. Install homebrew
1. brew install homebrew/versions/gcc6 (this takes 45+ minutes)
2. brew install clang-omp (I actually don't think this matters since I'm compiling with g++-6 instead of clang)
3. xcode-select --install (In case you just updated OSX)
4. The contents of my ~/.R/Makevars is

CC=gcc-6
CXX=g++-6
CXX1X = g++-6
SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp

5. Install from github

devtools::install_github("gbm-developers/gbm")

The compile commands look like:

g++-6 -I/Library/Frameworks/R.framework/Resources/include     -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"  -fopenmp -fPIC  -Wall -mtune=core2 -O3    -c tweedie.cpp -o tweedie.o

And there are a lot of warnings/deprecations. Here are a sample of them:

node.h:107:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<CNode> left_node_ptr_;
        ^~~~~~~~
In file included from /usr/local/Cellar/gcc/6.2.0/include/c++/6.2.0/bits/locale_conv.h:41:0,
                 from /usr/local/Cellar/gcc/6.2.0/include/c++/6.2.0/locale:43,
                 from /usr/local/Cellar/gcc/6.2.0/include/c++/6.2.0/iomanip:43,
                 from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/RcppCommon.h:52,
                 from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include/Rcpp.h:27,
                 from datadistparams.h:22,
                 from dataset.h:21,
                 from node.h:26,
                 from varsplitter.h:15,
                 from varsplitter.cpp:12:
/usr/local/Cellar/gcc/6.2.0/include/c++/6.2.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;

/var/folders/w5/869dx88d64v2409q78xqhsw00000gp/T//ccXGLXHj.s:3193:11: warning: section "__const_coal" is deprecated
        .section __DATA,__const_coal,coalesced
                 ^      ~~~~~~~~~~~~
/var/folders/w5/869dx88d64v2409q78xqhsw00000gp/T//ccXGLXHj.s:3193:11: note: change section name to "__const"
        .section __DATA,__const_coal,coalesced
                 ^      ~~~~~~~~~~~~
/var/folders/w5/869dx88d64v2409q78xqhsw00000gp/T//ccXGLXHj.s:563:11: warning: section "__textcoal_nt" is deprecated
        .section __TEXT,__textcoal_nt,coalesced,pure_instructions
                 ^      ~~~~~~~~~~~~~
/var/folders/w5/869dx88d64v2409q78xqhsw00000gp/T//ccXGLXHj.s:563:11: note: change section name to "__text"
        .section __TEXT,__textcoal_nt,coalesced,pure_instructions
                 ^      ~~~~~~~~~~~~~
/var/folders/w5/869dx88d64v2409q78xqhsw00000gp/T//cceCcXN4.s:3059:11: warning: section "__datacoal_nt" is deprecated
        .section __DATA,__datacoal_nt,coalesced

Here are some benchmarks

set.seed(104)
n <- 10000
p <- 500
x <- matrix(rnorm(n*p), n, p)
b <- rep(.5, ncol(x))
y <- x %*% b

library(microbenchmark)
microbenchmark(gbm::gbm(y~., data=data.frame(y, x), distribution="Gaussian", 
                           n.trees=100, par.details = gbmParallel(num_threads=8)),
               gbm::gbm(y~., data=data.frame(y, x), distribution="Gaussian", 
                           n.trees=100, par.details = gbmParallel(num_threads=1)), 
               times=5)
Unit: seconds
                                                                                                                                expr
 gbm::gbm(y ~ ., data = data.frame(y, x), distribution = "Gaussian",      n.trees = 100, par.details = gbmParallel(num_threads = 8))
 gbm::gbm(y ~ ., data = data.frame(y, x), distribution = "Gaussian",      n.trees = 100, par.details = gbmParallel(num_threads = 1))
      min        lq      mean    median        uq       max neval cld
  6.93019  7.052409  7.225445  7.205979  7.401769  7.536879     5  a 
 15.36158 15.467243 15.649213 15.672217 15.869813 15.875209     5   b

[patr1ckm]

@pdmetcalfe Update: It should work on MacOS or OS X out of the box without any of the above steps, even without XCode.