Need to re-Port a C++ source code to OSX10.7

Question

Level 1

4 points

Need to re-Port a C++ source code to OSX10.7

Hi,

I am trying to port a C++ Genetics program called PHASE on behalf of the Author to OSX10.7 as the last time I did it was in PowerPC architecture. Unsurprisingly just running $ make doesn't work. I get the following error message:

$ make

g++ -O2 -DBIGDATASETS -I. -I.. -c phase.cpp

In file included from /usr/include/c++/4.2.1/backward/strstream:51,

from ./tnt/vec.h:35,

from tnt/cmat.h:42,

from classpop.hpp:19,

from phase.cpp:5:

/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.

In file included from classpop.hpp:15,

from phase.cpp:5:

HapList2.hpp:59: error: extra qualification ‘HapList::’ on member ‘Add’

HapList2.hpp:60: error: extra qualification ‘HapList::’ on member ‘Add’

make: *** [phase.o] Error 1

I have no idea how to try and fix this problem. Is there anyone out there familiar with porting C++ source code to OSX10.7 that may be able to help.

many thanks

Matt

iMac, Mac OS X (10.7.3), 27" i7

Posted on Mar 22, 2012 11:01 AM

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Answer 1

g_wolfman

Level 4

3,472 points

Mar 22, 2012 12:52 PM in response to mattnev

Well, it's rather difficult to know without actually seeing hte source code...but at a guess, the HapList2.hpp includes a class declaration for a class called HapList (or maybe even a class definition...who knows). In the declaration is a member attribute or function called Add. I'll assume it's a function. And it's been declared something like this:

class HapList
{
public:
  HapList::Add();
};

That is wrong. It should be declared like this:

class HapList

{

public:

Add();

};

Old versions of g++ (and Visual C++) allow member declarations to use qualified names, but it's a syntax error in standard C++. Member declarations must use unqualified names for the members themselves.

I wouldn't be surprised if you need to go through and clean up a lot of badly written code.

For the warning, you can either find all the old header includes and fix them (like the message told you) or suppress the warning using -Wno-deprecated as a command line flag to teh compiler.

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Answer 2

etresoft

Level 9

56,662 points

Mar 22, 2012 7:16 PM in response to mattnev

Actually, this isn't a problem of porting C++ to Lion. It is just a problem of porting to C++. The source code uses the old pre-standard headers like "string.h". Modern C++ headers don't have any extension. The bad part is that this "modern" style of C++ is from 1993. Your source code was obsolete twenty years ago.

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Answer 3

mattnev Author

Level 1

4 points

Mar 23, 2012 3:06 AM in response to etresoft

Hi etresoft,

Many thanks for your reply.

The problem is I had nothing to do with the writing of the source code I just need the program for my work and upgrading to Lion means the PowerPC ported version doesn't work. I have ported a number of different incarnations this program a few times and each time there is a different problem and the source code that worked with my last port (including a fix) doesn't work under Lion. I am hoping that someone like me who is a lab scientist who knows next to nothing about C++ can fix this problem.

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Answer 4

mattnev Author

Level 1

4 points

Mar 23, 2012 3:41 AM in response to g_wolfman

Hi g_wolfmanand many thanks for replying,

In the header file HapList2.hpp there is the following that seems to fit your description:

------------------------------------------------------------------

class HapList {

public:

ListType haplist; // list of haplotypes and frequencies

vector<ListType::iterator> PositiveHaps; // pointers to haps with positive frequency

public:

HapList ();

HapList (const HapList &);

HapList (istream & istr);

HapList (const HapList &, int firstlocus, int lastlocus); // extract

//list from first up to (but not including) last

HapList (const HapList &, const HapList &, double minfreq=0.0); // concatenate two haplists

HapList (const HapList &, const HapList &, vector<CIndividual> & pop, double minfreq=0.0); // concatenate two haplists, but only include haps that can exist in pop

const HapList & operator = (const HapList &);

~HapList();

// the next two functions respectively

// add a record whose Freq, PseudoCounts, and Prob are

// the product, or minimum, of 2 other records

// (used in concatenating two haplists)

void AddMultiple(const Haplotype &, const HapRecord &, const HapRecord &);

void AddMin(const Haplotype &, const HapRecord &, const HapRecord &);

void Add (const HapList & h1, double minfreq);

void Add(const Haplotype &, const HapRecord &);

void Add(const Haplotype &, double freq = 1.0);

void Add(CIndividual &,int,bool,double freq = 1.0);

void Add(CIndividual &,double freq = 1.0,bool = false);

void Add(vector<CIndividual> & pop,int, bool = false);

// Add routines that return pointers to the added haplotype

ListType::iterator HapList::Add (CIndividual & ind, int chr, double freq, bool & isnewhap, bool usebestguess = false);

ListType::iterator HapList::Add (const Haplotype & h, double freq, bool & isnewhap);

ListType::iterator Find(const Haplotype & h, const vector<int> & uselist);

------------------------------------------------------------------

How would you suggest I modify this?.

regards

Matt

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Answer 5

mattnev Author

Level 1

4 points

Mar 23, 2012 5:28 AM in response to g_wolfman

Update:

Following my previous message I have had a go and it seems to have worked so many thanks. I had to do simmilar in a few header files but the make has now completed sucessfully. I am just testing that it runs the same.

As to the warnings about the depreciated headers, at the moment I have just ignored them as it hasn't stopped the porting and I wasn't sure where to put the -Wno-deprecated command. Is this likely to cause problems with my ported app?.

thanks again

Matt

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Answer 6

etresoft

Level 9

56,662 points

Mar 23, 2012 6:10 AM in response to mattnev

C++ is problematic. It takes many, many years of experience to use it well. Sometimes, once someone gets to the point where they really understand C++, they may realize it was all waste of time. Instead of re-porting it to whatever version of C++ is current, they just re-do it in Perl or Python and be done with it.

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