stan-dev / stan-dev/rstan

Rstan does not compile on Ubuntu 16.04; truncated g++ command

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Description

Summary:

install.packages("rstan") does not compile.

Description:

Call to g++ appears to be truncated during compilation, resulting in a "-o ....{targets}..." call without the necessary "g++ ..." prefix.

Reproducible Steps:

I am running R 3.6.1 on a Ubuntu 16.04 system. My ~/.R/Makevars looks like this:

CXX14FLAGS=-O3 -march=native -mtune=native
CXX14 = g++ -std=c++1y -Wno-unused-variable -Wno-unused-function -fPIC

I start R and execute "install.packages('rstan')" . I don't have steps to reproduce the entire state of my system.

Current Output:

template class auto_ptr;
^
-o rstan.so chains.o pointer-tools.o init.o stanc.o misc.o sparse_extractors.o stan/lang/ast_def.o stan/lang/grammars/program_grammar_inst.o stan/lang/grammars/expression_grammar_inst.o stan/lang/grammars/statement_grammar_inst.o stan/lang/grammars/expression07_grammar_inst.o stan/lang/grammars/statement_2_grammar_inst.o stan/lang/grammars/block_var_decls_grammar_inst.o stan/lang/grammars/term_grammar_inst.o stan/lang/grammars/indexes_grammar_inst.o stan/lang/grammars/semantic_actions_def.o stan/lang/grammars/whitespace_grammar_inst.o stan/lang/grammars/bare_type_grammar_inst.o stan/lang/grammars/local_var_decls_grammar_inst.o stan/lang/grammars/functions_grammar_inst.o -L/usr/lib/R/lib -lR
/bin/bash: line 2: -o: command not found
/usr/share/R/share/make/shlib.mk:6: recipe for target 'rstan.so' failed

Previous steps in the compilation process look fine and work, e.g.:

g++ -std=c++1y -Wno-unused-variable -Wno-unused-function -fPIC -std=c++1y -I/usr/share/R/include -DNDEBUG -I"../inst/include" [truncated]

Expected Output:

I'd expect the call to begin with "g++" along with the supplied arguments.

RStan Version:

Attempting to install 2.19.2.

R Version:

3.6.1

Operating System:

Ubuntu 16.04

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the reported ~/.R/Makevars settings and the R package installation entry point, install.packages("rstan"). Compare the truncated command with the make rule in /usr/share/R/share/make/shlib.mk:6 and determine why the compiler prefix is missing. Done means the Ubuntu 16.04 installation invokes g++ with the supplied arguments instead of treating -o as a command.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, r, ubuntu
Domain
build-system
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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