E C++/Mavericks Best Practices

This guide mostly addresses how to adapt C/C++ code in Bioconductor packages to build on Mac OS X 10.9 (Mavericks). If your package does not use C or C++ code, you can assume this document is not relevant to you.

E.1 Table of Contents

This document is written to be read from beginning to end, except for the last section.

Orientation: how to approach developing for Mavericks.
C++11: important info about C++11 and clang’s standard library implementation.
Issues specific to the Mavericks environment: special considerations for tools available for Mavericks.
C++ Best Practices: generally applicable best practices for C++ in Bioconductor packages.
Issues with code from external sources: tips for using code not written by the package contributor.
Lessons learned from specific issues: a repository of knowledge about specific problems.

You might skip to the lessons-learned section to check if your issue has already been explored.

E.2 Orientation

Note: For simplicity, this guide uses ‘GCC’ (GNU Compiler Collection) and ‘clang’ to refer to each respective collection of tools (including C++ compilers), rather than simply the ‘GCC C compiler’ or ‘clang C compiler’. ‘Mavericks environment’ refers to the combination of clang and Xcode versions available by default for Mavericks.

With the release of the Mavericks build of R, CRAN and Bioconductor have adopted Apple’s preferred toolchain for building packages for the Mavericks platform. Bioconductor packages are built on the Mavericks platform using the OS X default combination of clang and Xcode.

The introduction of the Mavericks environment has revealed a number of issues with building packages, most of which are due to C/C++ code that relies too heavily on the GCC way of doing things. Most problems revealed by the transition to Mavericks are caused by C++ coding practices that are universally recognized as problematic, and are addressed by adhering to established best practices.

Here are some common sources of problems, posed as how the Mavericks environment contrasts with GCC:

Undefined behavior. Under GCC the undefined behavior might fail silently without affecting program execution, whereas the same code in the Mavericks environment leads to a segfault (“segmentation fault”).
Issues related to naming, particularly in circumventing the protections offered by C++ namespaces. GCC header organization seems to be more forgiving of loose naming, whereas the Mavericks environment is more exacting.
C++11 as the default language specification, and clang’s libc++. libc++ is an implementation of the C++11 standard library written from scratch. At the time of this writing the libc++ implementation is only available for Mac OS X.
Code not written directly by the package contributor(s). Many Bioconductor packages that do not transition well to the Mavericks environment include third-party (e.g., Boost) or generated (e.g., SWIG) code. Many external code sources make assumptions that are not valid for the Mavericks environment. The compounded difficulty of diagnosing problems in code not written by the package author limits the Bioconductor team’s ability to help with your package.

E.2.1 What is different about developing for the Mavericks environment?

The biggest change is the introduction of clang’s libc++ implementation of the C++11 standard library and the library headers associated with Xcode. clang is gaining market share for several reasons, helped by the fact that clang is intended only as a compiler for C-based languages. Advocates of clang hold that clang:

offers better diagnostic information for errors and warnings
has quicker compilation times
sometimes yields smaller binaries
in some cases yields faster execution speeds (disputed)

For guidance on compiler flags to use while developing, see the relevant section of the Package Guidelines page.

E.2.1.1 Differences in unspecified behavior, memory addressing policies

Some errors encountered during the transition seem to be attributable to reliance on non-portable unspecified behaviors. See the section of this guide about unspecified behavior for more information.

For example, many aspects of C/C++ memory addressing are implementation-dependent, which means expected behavior is not prescribed by the C/C++ standard (“unspecified”) and is therefore up to compiler writers to decide.

The foremost difference regarding memory is clang seems to be more restrictive about out-of-bounds memory addressing.

E.2.1.2 How to find bugs

With GCC the preferred debugger is gdb, but many prefer lldb for debugging in the Mavericks environment.

Because a number of bugs in packages are related to memory addressing or layout errors, relying on a debugger alone might not be sufficient to track down memory errors. Valgrind is the premier tool for detecting memory errors.

See the Bioconductor guide on debugging C/C++ code for examples of using a debugger and Valgrind.

E.2.1.3 What if I cannot access a Mavericks machine?

There is no substitute for using a Mavericks machine to troubleshoot packages that fail on Mavericks. Many of the errors seen are only reproducible with the combination of clang, Xcode, and OS X 10.9.

But there are several options short of procuring a Mavericks machine:

As an exploratory measure, install a more recent version of GCC and compile your package with -std=c++11 or -std=gnu++11 compiler arguments; as of version 4.8.1, GCC implements all major features of the 2011 ISO C++ standard. Diagnostics for errors and warnings have also greatly improved with recent GCC versions. Using a C++11 implementation might reveal warnings or errors that point to the same issues encountered on Mavericks.
Install clang; this is of limited value because many errors are unique to the Mavericks environment.
Use Valgrind for memory addressing problems; because so many errors on the Mavericks platform are related to memory addressing problems, many errors should be equally discoverable using Valgrind on Linux.
If you are unable to diagnose your problem using the combination of build system output and Valgrind, feel free to contact the bioc-devel mailing list.

E.3 C++11

Although the default version of clang on Mavericks includes support for all C++11 features, Bioconductor support for C++11 is dependent on the platform with the oldest toolchain. Because the current Snow Leopard (Mac OS X 10.6.8) toolchain does not support any C++11 features, Bioconductor packages generally should not use C++11 features. Eventually, when Mavericks is more widely adopted, support for Snow Leopard will be dropped.

C++11 is not completely backward-compatible with older standards.

It is possible to tell clang to use older versions of the standard library (the default is libc++), but relying on OS version-specific compilation settings is not a workable long-term solution. This approach greatly increases the maintenance burden for package authors and limits the Bioconductor team’s ability to offer support.

An insidious and more catastrophic consequence of using non-default standard libraries is the issue of binary incompatibility. Packages linked against one standard library are liable to crash (mysteriously) when interfacing with packages linked against a different standard library. This is also true for programs at the OS level: any program compiled and linked against libstdc++ on the Mavericks platform is, by default, assumed to be incompatible with programs compiled and linked against libc++.

Code should be adapted to avoid constructs that are backward- or forward-incompatible. See the forward-incompatibility problems section for examples.

E.4 Issues specific to Mavericks environment

E.4.1 C Linkage

C++ uses extern "C" to give declarations C linkage, and hence make the declarations accessible to C code. Some R headers when #included in C++ will include C++ system headers that should not have C linkage. According to the relevant Writing R Extensions Manual section, R header files should not be included within extern "C" blocks.

A typical symptom of bad linkage is at package load time (not compilation or link time) an error says a particular symbol cannot be found.

C++ mangles names, so the symbol name R says it cannot find will often be unrecognizable. Use the c++filt program installed on your system or an online name demangler to produce a human-readable version of the symbol name. Note that mangled names are environment-specific so a demangler meant for GCC symbol names on Linux will not demangle clang symbol names from a Mac.

Solution: All R headers should be #included outside extern "C" blocks.

Example of correct #include of R headers:

#include <R.h>
extern "C" {
  void foo(); // function 'foo' and other code in this block has C linkage
  ...
}
extern "C" void bar(); // function 'bar' has C linkage

E.4.2 OpenMP

As of this writing the Mavericks environment does not support OpenMP, and it is unknown if the tools released by Apple ever will.

Code should not rely on the availability of OpenMP. Independent of concerns over OpenMP support, code should be written from the start to degrade nicely in a single-threaded environment.

See the Writing R Extensions Manual section for information about OpenMP code in R packages, and detecting support.

Solution: use preprocessor if-else directives so code degrades gracefully if OpenMP support is not available:

#ifdef SUPPORT_OPENMP
    // multithreaded OpenMP version of code
#else
    // single-threaded version of code
#endif

See the ShortRead package for an example of good practices around support for OpenMP.

E.5 C++ Best Practices

These C++ practices are applicable for most C++ projects, but have been identified by the Bioconductor community as particularly helpful in avoiding issues in the Mavericks environment.

E.5.1 Use Rcpp

The Rcpp CRAN package allows seamless integration of C++ with R, and is cross-platform. The package affords many of the same benefits for the R C interface that make C++ so appealing as a language, while eliminating many of the pitfalls of programming to the R interface.

The package is well documented, and has an extensive repository of working examples for many tasks: the Rcpp Gallery.

E.5.2 Avoid name resolution errors

A name resolution error occurs when the compiler encounters an identifier (e.g., variable or function name) that is ambiguous (that is, there is a “collision” between two or more identifiers), or name lookup rules lead the compiler to resolve a name incorrectly. clang is more exacting about identifiers.

A typical symptom of a name resolution error is the compiler complains that the type or number of arguments a function got is different from what it expects, and the compiler points to a C++ header file in the standard library.

There are two primary issues with name resolution when writing R packages:

E.5.2.1 Re-mapping of identifiers from R headers

For convenience, R aliases common identifiers from R headers. E.g., Rf_length(SEXP) becomes length(SEXP). While this may be convenient for C, the organization of headers in the Mavericks environment seems to lead to more collisions than with GCC. See relevant section of the Writing R Extensions Manual

Solution: prevent re-mapping of R identifiers for C++ code by defining the R_NO_REMAP symbol. This can be done at the package level with a -DR_NO_REMAP preprocessor flag, or on a file-by-file basis with #define R_NO_REMAP. Use fully-qualified versions of R identifiers, usually by prepending Rf_.

Example excerpt from header file that prevents re-mapping:

file CxxCode.h
------------------

#ifndef CXX_CODE_H
#define CXX_CODE_H
#ifdef __cplusplus
#define R_NO_REMAP
#endif

...

void foo(SEXP s) {
    if(Rf_length(s) > 1) // fully qualified: 'Rf_length'
        ...
}

#endif

Note Rf_length is just one example of the many R identifiers that might conflict with names in C++ standard library headers.

E.5.2.2 Namespace hygiene

Namespaces were introduced in C++ to limit the incidence of name collisions. Many authors new to C++, however, use using-directives (particularly the ‘using namespace std’ directive) unnecessarily, thereby reintroducing the very problems namespaces are meant to solve.

As pointed out in the cppreference Notes section the use of the using namespace std directive introduces the entire std namespace for name resolution. There is a high likelihood that among all the headers in the standard library there is an identifier that conflicts with the identifiers in your package.

Solution: avoid the ‘using namespace std’ directive completely if possible, especially in header files. Prefer using-declarations over using-directives or simply use fully-qualified versions of standard library identifiers. New C++ authors overestimate how much including the scope resolution operator (namely ‘std::’) affects readability.

Example of introducing std namespace identifiers:

#include <map>
#include <utility>
// Suppose we want to access the std::map and std::make_pair identifiers

Many new C++ authors will use a using-directive to introduce the identifiers they need. Avoid if possible:

using namespace std; // introduces entire std namespace for resolution

One alternative is using-declarations (e.g., ‘using std::map;’, which allow hand-picking of identifiers to introduce (as opposed to the entire std namespace); here we just want std::map and std::make_pair. Even if the list of identifiers we want is quite long we just need a single using-declaration for each one:

using std::map; // 'map' and 'make_pair' introduced at declaration scope
using std::make_pair;

Using-declarations can also be block-scoped. This is preferred over using-declarations at global scope, as it prevents the unnecessary introduction of names at the global scope, a tenet of good namespace hygiene:

void foo() {
     using std::map;
     using std::make_pair;
     map<int, int> m;
     m.insert(make_pair(5, 7));
     ...
}

A perfectly good alternative is to simply precede standard library identifiers with ‘std::’, which most C++ programmers are accustomed to reading:

void foo() {
     std::map<int, int> m;
     m.insert(std::make_pair(5, 7));
}

E.5.3 Avoid undefined behavior and non-portable unspecified behavior

There are two major categories of behavior that is not prescribed by the C or C++ standards:

undefined behavior is specified to be arbitrary; code that produces the behavior might cause the program to crash, or it might execute without complaint (“silently”). The effect can also differ from one program execution to the next. Well-known examples include division by zero, indexing outside of array bounds, and dereferencing a null pointer.
unspecified behavior is consistent and documented, but decided by an implementation. These are behaviors that are either not mentioned at all by the respective standard, or are mentioned to say that they are implementation-dependent. Well-known examples include the size of the int type and the size of pointers.

A typical symptom of problematic undefined or unspecified behaviors is a segfault that only appears in the Mavericks environment. The reason the problem was not discovered before might be that GCC silently allows the code to execute instead of crashing the program.

Solution: code defensively to avoid problematic constructs and use debuggers to find the code that leads to errors.

E.6 Issues with code from external sources

Some packages need to use code not written directly by the contributor(s). The most common scenario is to include the source code of a library written by a third party. Some packages also use code produced by code generation tools, e.g., SWIG. First, see the relevant [Package Guidelines section][third-party-libraries] for guidance on code from external sources.

See the lessons learned section of this guide for suggestions about specific code sources.

E.6.1 Generated Code

Some packages use code that is generated by third-party tools, i.e., code written by machines. SWIG is a common example.

A problem with code written by machines is that the code is meant to be read by machines. The top of each code file produced by SWIG, for example, states that the code is not meant to be read or edited by hand.

Because many code generation tools make assumptions that are invalid for the Mavericks environment, the code needs human attention to fix errors; but because of the inscrutable nature of machine-written code it is very difficult to isolate the errors.

Solution: re-generate problem code if possible, otherwise fix by hand. Fixing by hand is strongly discouraged.

E.6.2 Third-party libraries

Some packages include third-party libraries that were not written in a compiler-independent way, and so do not build out-of-the-box in the Mavericks environment.

Solutions in approximate order of preference:

Check if an existing CRAN or Bioconductor package provides the same functionality, while meeting the performance needs of your use case. Eliminating third-party code from your package greatly reduces the maintenance burden.
Check if the library has been updated. Some libraries with an active user community undergo updates that add support for more compilers/environments.
Check if the maintainers are aware the library does not work for the Mavericks environment, and find out if support is forthcoming. It is usually easy to directly contact authors of libraries maintained by an individual or a small group.
Use an actively maintained alternate library that provides equivalent functionality. Sometimes if a library is no longer maintained, it is because the library has been abandoned for an alternative project that provides the same functionality.
Update the library code included in your package by hand. Strongly discouraged. Maintainer assumes responsibility for keeping code up-to-date with mainline source project. If undertaken, record descriptions of changes that are needed so when the codebase is updated the changes can be easily reproduced.

E.7 Lessons learned from specific issues

This section serves as a loosely organized repository for knowledge gained about specific problems and their solutions. It is not expected to be comprehensive. Items will be added as the knowledge base grows. Bioconductor is eager for suggestions; please write the bioc-devel mailing list if you have any!

If you have no idea where to start for diagnosing your broken package it might be worthwhile to skim over all of this section.

Where relevant, the issue is marked as being discoverable at compile time or runtime.

Where applicable, a link to a live code demo is provided.

E.7.1 Forward-incompatibility problems with C++11

C++11 is not completely backward-compatible. In particular, the API for some parts of the standard library has changed slightly, in perhaps subtle ways. Most issues require minimal tweaking to fix.

E.7.1.1 Container iterator const-ness

Type: compile time

A number of operations on standard library containers now require iterators to be const. Two ready examples are the insert and erase methods that take iterator parameters.

E.7.2 Iterating standard library containers

Type: runtime

Generally, using the special past-the-end iterator value other than for equality checks (i.e., == or !=) results in undefined behavior. Particularly, in the Mavericks environment:

Dereferencing an iterator with the past-the-end value results in a segfault
Incrementing an iterator beyond the past-the-end value results in a segfault

E.7.3 External code sources

Common examples of external code sources are SWIG, Boost, and numerous file format libraries. Code from external sources is sometimes written in non-compiler-independent way. Check the documentation to see if the Mavericks environment is supported.

E.7.3.1 Boost

Boost is a source of free, peer-reviewed C++ libraries that enhance the language. Many parts of Boost are “header-only”, which means they do not need to be separately compiled and the headers merely need to appear in the search path in order for client code to use them.

Many Boost libraries are platform-independent, but not all. Some Boost libraries are either in the process of adding Mavericks environment support, or the library authors have announced Mavericks environment support will not be added.

Solutions in approximate order of preference:

Use the BH package on CRAN, if possible. The BH package provides several Boost header-only libraries. Using the BH package means the maintenance cost of using Boost in your package is virtually nothing.
Update the Boost libraries you include with your package. Boost libraries sometimes contain bugs, or are later updated to add support for other platforms. It is the Bioconductor package maintainer’s responsibility to keep all code in the package updated.
Contact the authors of the specific Boost library. If you cannot find an announcement regarding support for the Mavericks environment, it might be worth contacting the library authors to inquire.

E.7.3.2 SWIG

SWIG generates code to interface between code written in C/C++ and other languages. At the time of this writing, SWIG support for clang is limited, and SWIG particularly has problems with clang’s libc++ version of the (C++11) standard library. Some of the problems are limited to issues that can be addressed by tweaking function signatures. Other problems are deeply embedded in the way SWIG produces code.

At the time of this writing, this thread on the SWIG-devel mailing list seems to have the most in-depth discussion about working with SWIG on Mavericks.

Solutions in approximate order of preference:

Eliminate SWIG code, if possible. This will probably do the most for reducing maintenance burden.
Re-generate SWIG code with the newest version of SWIG. At the time of this writing SWIG was recently updated to include partial support for C++11, which might alleviate problems with clang’s libc++. See the SWIG document about C++11 support. It is possible the new version will not produce the problematic code. Note code must be valid for all supported compilers.
Troubleshoot and fix errors by hand. Strongly discouraged. If undertaken, record descriptions of the changes that were needed so if the code is regenerated the changes can be easily reproduced.

Read SWIG documentation to find guidance about troubleshooting. (For example, the SWIG -E switch outputs results after the preprocessor has run.) Perhaps start by removing all SWIG functionality and gradually adding features. Find information on the web about how to fix the errors for your package.

E.7.3.3 f2c

f2c is a tool that converts Fortran77 code to C/C++ code. The maintenance burden required to make f2c code cross-platform is substantial. Since a fortran compiler (or emulator) is required to install R, f2c is usually unnecessary. Several packages use native fortran code without a problem.

Solution: If at all possible, remove the need for f2c. The only recourse is to finesse makefiles to the point that each supported platform more or less has a targeted makefile. Please write the bioc-devel mailing list if you have trouble.

D C and Fortran code

F Debug: Links in Rd files