[Phylobase-devl] various build questions

Mark Holder mtholder at gmail.com
Fri Jul 9 20:32:09 CEST 2010

	I've just been playing around with the Windows builds. I'm afraid that I have very little to report.

	It is hard for me to figure out exactly what version MinGW I should be using to replicate this (and there are issues with the MinGW version that I selected, making it pretty useless right now).  Does anyone know the procedure for getting a 64bit machine up and building C-extensions to R?

	I just committed a change to:
	that allows it to build on a 64 bit machine using visual studio 2010.  But that change seems to be totally unrelated to the g++ issues that show up on http://win-builder.r-project.org/

	I'll see if I can install a bleeding edge g++ on one of my linux boxes.  Perhaps that will reveal the same complaints and I can diagnose.

	NCL's "nxsstring" class uses some hacky operator overloading which seems to be the source of the problem, but I'm not sure of the exact cause.  That code has been compiling for years... the joys of working with C++.

	I'll let you know if I can figure out anything.  If anyone wants an account on my windows machine to work on this remotely, I can set up ssh on it and get you an account set up.


On Jul 8, 2010, at 4:58 PM, Ben Bolker wrote:

>  hi folks ...
>  current version of phylobase is building/checking on my machine
> (32-bit Linux: it was choking on R CMD check, but re-installing seems to
> have fixed that).
> * R-forge shows that builds on R-devel (2.12.0) are not working because
> "Rscript" can't be found (this applies both to linux and windows 32 bit).
> https://r-forge.r-project.org/R/?group_id=111&log=build_win32&pkg=phylobase&flavor=devel
>  I'm having some trouble building R-devel on my machine but will
> hopefully succeed soon.
>  * Furthermore, 64-bit windows builds on win-builder.r-project.org are
> failing, with a variety of errors, listed in:
> http://win-builder.r-project.org/aJTkLv5eh3pA/00install.out
>  Any thoughts?  Anyone have a 64-bit windows machine for testing
> purposes ... ?  (I will see if I can get access to one here, but it
> could take a little while ...)
>  cheers
>    Ben
>  the first few errors in the 64-bit windows build are:
> nxsmultiformat.cpp: In member function 'bool
> MultiFormatReader::readFastaSequences(FileToCharBuffer&, const
> NxsDiscreteDatatypeMapper&, std::list<std::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::allocator<std::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > >&, std::list<std::vector<int,
> std::allocator<int> >, std::allocator<std::vector<int,
> std::allocator<int> > > >&, size_t&)':
> nxsmultiformat.cpp:334: error: ambiguous overload for 'operator<<' in
> '((NxsString*)((NxsString*)err.NxsString::operator<<(((const
> char*)"Illegal state code
> \"")))->NxsString::operator<<(((int)c)))->NxsString::operator<<(((const
> char*)"\" found when reading character ")) <<
> ((NxsDiscreteStateRow*)row)->std::vector<_Tp, _Alloc>::size [with _Tp =
> int, _Alloc = std::allocator<int>]()'
> ./ncl/nxsstring.h:582: note: candidates are: NxsString&
> NxsString::operator<<(int)
> ./ncl/nxsstring.h:591: note:                 NxsString&
> NxsString::operator<<(unsigned int)
> ./ncl/nxsstring.h:600: note:                 NxsString&
> NxsString::operator<<(long int)
> ./ncl/nxsstring.h:609: note:                 NxsString&
> NxsString::operator<<(long unsigned int)
> ./ncl/nxsstring.h:618: note:                 NxsString&
> NxsString::operator<<(double)
> ./ncl/nxsstring.h:627: note:                 NxsString&
> NxsString::operator<<(const char*) <near match>
> ./ncl/nxsstring.h:636: note:                 NxsString&
> NxsString::operator<<(char)
> ./ncl/nxsstring.h:645: note:                 NxsString&
> NxsString::operator<<(const std::string&) <near match>
> ./ncl/nxsstring.h:544: note:                 NxsString&
> NxsString::operator<<(NxsString& (*)(NxsString&)) <near match>
> -- 
> Ben Bolker
> ***   bbolker at gmail.com , bolker at math.mcmaster.ca
> bolker at ufl.edu / people.biology.ufl.edu/bolker
> GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl

More information about the Phylobase-devl mailing list