How to add flags to compiler flags

[Thomas Nyberg]

I'm trying to use load_all() to get some code running, but the error messages seem to indicate that I need the "-std=c++11" set for the code to compile correctly. But looking through devtools/searching the internet, I see no way to add flags to the compiler. Here is the error output:

> library(devtools)

Attaching package: ‘devtools’

The following objects are masked from ‘package:utils’:

    ?, help

The following object is masked from ‘package:base’:

    system.file

> load_all()
Loading CCD
Re-compiling CCD
'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/home/twn/Projects/ohdsi/OHDSI/CCD'  \
  --library='/tmp/RtmpfjJYpm' --no-R --no-data --no-help --no-demo --no-inst  \
  --no-docs --no-exec --no-multiarch --no-test-load --preclean

OpenBLAS : Your OS does not support AVX instructions. OpenBLAS is using Nehalem kernels as a fallback, which may give poorer performance.
* installing *source* package 'CCD' ...
** libs
g++ -I/usr/share/R/include -DNDEBUG -I. -Iccd -DR_BUILD -DDOUBLE_PRECISION  -I"/home/twn/R/x86_64-pc-linux-gnu-library/3.0/Rcpp/include" -I"/home/twn/R/x86_64-pc-linux-gnu-library/3.0/BH/include" -I"/home/twn/R/x86_64-pc-linux-gnu-library/3.0/RcppEigen/include"  -UNDEBUG -Wall -pedantic -g -O0 -fpic  -O3 -pipe  -g  -c RcppCcdInterface.cpp -o RcppCcdInterface.o
In file included from /usr/include/c++/4.8/cstdint:35:0,
                 from ccd/Types.h:11,
                 from ccd/CcdInterface.h:23,
                 from RcppCcdInterface.h:10,
                 from RcppCcdInterface.cpp:10:
/usr/include/c++/4.8/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
RcppCcdInterface.cpp:452:2: warning: identifier 'nullptr' is a keyword in C++11 [-Wc++0x-compat]
  if (*model == nullptr) {
  ^
In file included from ccd/CcdInterface.h:23:0,
                 from RcppCcdInterface.h:10,
                 from RcppCcdInterface.cpp:10:
ccd/Types.h:100:1: warning: scoped enums only available with -std=c++11 or -std=gnu++11 [enabled by default]
 enum class ModelType {
 ^
ccd/Types.h: In function 'bool bsccs::Models::requiresStratumID(bsccs::ModelType)':
ccd/Types.h:114:23: error: 'ModelType' is not a class or namespace
  return (modelType == ModelType::CONDITIONAL_LOGISTIC ||
                       ^
ccd/Types.h:115:26: error: 'ModelType' is not a class or namespace
             modelType == ModelType::CONDITIONAL_POISSON ||
                          ^
ccd/Types.h:116:26: error: 'ModelType' is not a class or namespace
             modelType == ModelType::SELF_CONTROLLED_MODEL);
                          ^
ccd/Types.h: In function 'bool bsccs::Models::requiresCensoredData(bsccs::ModelType)':
ccd/Types.h:120:23: error: 'ModelType' is not a class or namespace
  return (modelType == ModelType::COX);
                       ^
ccd/Types.h: In function 'bool bsccs::Models::requiresOffset(bsccs::ModelType)':
ccd/Types.h:124:23: error: 'ModelType' is not a class or namespace
  return (modelType == ModelType::SELF_CONTROLLED_MODEL);
                       ^
In file included from RcppCcdInterface.h:11:0,
                 from RcppCcdInterface.cpp:10:
ccd/priors/JointPrior.h: In member function 'virtual const string bsccs::priors::MixtureJointPrior::getDescription() const':
ccd/priors/JointPrior.h:56:28: error: range-based 'for' loops are not allowed in C++98 mode
      for (PriorPtr prior : uniquePriors) {
                            ^
In file included from ccd/CyclicCoordinateDescent.h:13:0,
                 from RcppCcdInterface.cpp:14:
ccd/engine/AbstractModelSpecifics.h: At global scope:
ccd/engine/AbstractModelSpecifics.h:23:1: warning: scoped enums only available with -std=c++11 or -std=gnu++11 [enabled by default]
 enum class ModelType; // forward declaration
 ^
ccd/engine/AbstractModelSpecifics.h:23:1: warning: elaborated-type-specifier for a scoped enum must not use the 'class' keyword [enabled by default]
RcppCcdInterface.cpp: In function 'Eigen::MatrixXd ccdGetFisherInformation(SEXP, SEXP)':
RcppCcdInterface.cpp:76:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
      for (auto it = covariates.begin(); it != covariates.end(); ++it) {
           ^
RcppCcdInterface.cpp:76:16: error: 'it' does not name a type
      for (auto it = covariates.begin(); it != covariates.end(); ++it) {
                ^
RcppCcdInterface.cpp:76:41: error: expected ';' before 'it'
      for (auto it = covariates.begin(); it != covariates.end(); ++it) {
                                         ^
RcppCcdInterface.cpp:76:41: error: 'it' was not declared in this scope
RcppCcdInterface.cpp: In static member function 'static bsccs::ModelType bsccs::RcppCcdInterface::parseModelType(const string&)':
RcppCcdInterface.cpp:332:40: error: 'bsccs::ModelType' is not a class or namespace
   bsccs::ModelType modelType =  bsccs::ModelType::LOGISTIC;
                                        ^
RcppCcdInterface.cpp:334:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::SELF_CONTROLLED_MODEL;
                       ^
RcppCcdInterface.cpp:336:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::CONDITIONAL_POISSON;
                       ^
RcppCcdInterface.cpp:338:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::CONDITIONAL_LOGISTIC;
                       ^
RcppCcdInterface.cpp:340:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::LOGISTIC;
                       ^
RcppCcdInterface.cpp:342:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::NORMAL;
                       ^
RcppCcdInterface.cpp:344:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::POISSON;
                       ^
RcppCcdInterface.cpp:346:23: error: 'bsccs::ModelType' is not a class or namespace
    modelType = bsccs::ModelType::COX;
                       ^
RcppCcdInterface.cpp: In member function 'virtual void bsccs::RcppCcdInterface::initializeModelImpl(bsccs::ModelData**, bsccs::CyclicCoordinateDescent**, bsccs::AbstractModelSpecifics**)':
RcppCcdInterface.cpp:452:16: error: 'nullptr' was not declared in this scope
  if (*model == nullptr) {
                ^
make: *** [RcppCcdInterface.o] Error 1
ERROR: compilation failed for package 'CCD'
* removing '/tmp/RtmpfjJYpm/CCD'
Error: Command failed (1)
Execution halted

Thanks for any help!

[Thomas Nyberg]

It appears that adding an environment variable of 'PKG_CXXFLAGS=-std=c++11' fixes this problem. I'm not sure why I didn't try this earlier...

ccd/Types.h: In function<span style="color: #000;" class="

...

[Winston Chang]

Have you tried using a Makevars file? For example:

  https://github.com/hadley/dplyr/blob/master/src/Makevars

It's also documented (confusingly) in Writing R extensions:

  http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars

-Winston

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[Thomas Nyberg]

Yes the project I was trying to compile apparently does have a Makevars file and adding the line

'PKG_CXXFLAGS = -std=c++11'

seems also to solve the problem. The Makevars file already had the following line '

CXX_STD = CXX11

It's pretty clear that the author meant for that flag to do what I wanted. Is that not the correct flag to use?

P.S. After reading that link, I see the following about Makevars:

"Also, do not set variables such as CPPFLAGS, CFLAGS etc.: these should be settable by users (sites) through appropriate personal (site-wide) Makevars files. See Customizing package compilation in R Installation and Administration,"

So I guess maybe the point is that I'm expected to have my own Makevars file which I keep updated myself...

Thanks for all the information! I should definitely now have enough info to figure out all the build stuff from here!

Cheers,
Thomas

RcppCcdInterface.<span style="co

...

[Thomas Nyberg]

I'm coming back to this because I never fully resolved this issue. In a redhat box I have running gcc 4.8.3 20140911 (Red Hat 4.8.3-7), only using the variable 'CXX_STD = CXX11' works fine, but on a newly setup Linux Mint system with gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2, that flag alone doesn't seem to work. In that case I need to use 'PKG_CXXFLAGS = -std=c++11'. Of course, it could be some other issue other than just redhat vs. linux mint, but that's really the only difference in the setup. In both cases, I've compiled R myself, installed devtools (and hence Rcpp) from cran, etc. Why isn't the 'CXX_STD = CXX11' flag being accepted?

...