getline on MacOSX 10.6 crashing C compiler? - macos

Question

I'm having a really hard time getting an R library installed that requires some compilation in C. I'm using a Mac OSX Snow Leopard machine and trying to install this R package (here).
I've looked at the thread talking about getline on macs and have tried a few of these fixes, but nothing is working! I'm a newbie and don't know any C, so that may be why! Can anyone give me some tips on how I could modify files in this package to get it to install?? Anyhelp would be pathetically appreciated! Here's the error I'm getting:
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -D_FASTMAP -DMAQ_LONGREADS -fPIC -g -O2 -c bed2vector.C -o bed2vector.o
In file included from /usr/include/c++/4.2.1/backward/strstream:51,
from bed2vector.C:8:
/usr/include/c++/4.2.1/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
bed2vector.C: In function ‘int get_a_line(FILE*, BZFILE*, int, std::string&)’:
bed2vector.C:74: error: no matching function for call to ‘getline(char**, size_t*, FILE*&)’
make: *** [bed2vector.o] Error 1
chmod: /Library/Frameworks/R.framework/Resources/library/spp/libs/i386/*: No such file or directory
ERROR: compilation failed for package 'spp'

Answer 1

The easiest solution is probably to add a static definition for getline() to bed2vector.c. This might be good enough:
/* PASTE AT TOP OF FILE */
#include <stdio.h> /* flockfile, getc_unlocked, funlockfile */
#include <stdlib.h> /* malloc, realloc */
#include <errno.h> /* errno */
#include <unistd.h> /* ssize_t */
extern "C" ssize_t getline(char **lineptr, size_t *n, FILE *stream);
/* PASTE REMAINDER AT BOTTOM OF FILE */
ssize_t
getline(char **linep, size_t *np, FILE *stream)
{
char *p = NULL;
size_t i = 0;
if (!linep || !np) {
errno = EINVAL;
return -1;
}
if (!(*linep) || !(*np)) {
*np = 120;
*linep = (char *)malloc(*np);
if (!(*linep)) {
return -1;
}
}
flockfile(stream);
p = *linep;
for (int ch = 0; (ch = getc_unlocked(stream)) != EOF;) {
if (i > *np) {
/* Grow *linep. */
size_t m = *np * 2;
char *s = (char *)realloc(*linep, m);
if (!s) {
int error = errno;
funlockfile(stream);
errno = error;
return -1;
}
*linep = s;
*np = m;
}
p[i] = ch;
if ('\n' == ch) break;
i += 1;
}
funlockfile(stream);
/* Null-terminate the string. */
if (i > *np) {
/* Grow *linep. */
size_t m = *np * 2;
char *s = (char *)realloc(*linep, m);
if (!s) {
return -1;
}
*linep = s;
*np = m;
}
p[i + 1] = '\0';
return ((i > 0)? i : -1);
}
This doesn't handle the case where the line is longer than the maximum value that ssize_t can represent. If you run into that case, you've likely got other problems.

Answer 2

Zeroth question: Have you considered using a package manager like fink or MacPorts rather than compiling yourself? I know that fink has an R package.
First question: How is the R build managed? Is there a ./configure? If so have you looked at the options to it? Does it use make? Scons? Some other dependency manager?
Second question: Have you told the build system that you are working on a Mac? Can you specify that you don't have a libc with native getline?
If the build system doesn't support Mac OS---but I image that R's does---you are probably going to have to download the standalone version, and hack the build to include it. How exactly you do that depends on the build system. And you may need to hack the source some.