[Phylobase-devl] various build questions
Brian O'Meara
omeara.brian at gmail.com
Thu Jul 22 19:10:13 CEST 2010
Thanks, Mark. One way to look at CRAN's checks for its release of
phylobase is http://cran.r-project.org/web/checks/check_results_phylobase.html
And R-forge's info on builds for the latest version is at https://r-forge.r-project.org/R/?group_id=111
(but you have to look into each daily build/daily check log).
CRAN shows v 0.5 builds on everything but Solaris, but R-forge shows v
0.6 has errors on Windows 32 bit and Mac 32 bit.
There may be better ways of checking all this.
Brian
On Jul 22, 2010, at 12:29 PM, Mark Holder wrote:
> Hi again,
> http://win-builder.r-project.org/aJTkLv5eh3pA/00install.out
>
> is now returning a 404.
>
>
> Do we know that the phylobase windows build is still broken?
>
>
> (sorry for the newbie question, I don't normally use R so I'm
> pretty unfamiliar with the R community and the basics for where I
> should look for such info).
>
>
> Mark
>
>
>
> On Jul 22, 2010, at 11:24 AM, Mark Holder wrote:
>
>> Hi Ben,
>> Just a status report.
>>
>>
>> As it turns out, it is not so easy to build R on windows
>> (particularly for those of us who had previous CygWin installations).
>>
>> The link labelled
>> mingw-w64-1.0-bin_i686-mingw_20100322.zip
>> was in fact just a link to the MinGW-64 sourceforge site. That
>> particularly version of the mingw-w64-1.0-bin_i686-mingw tools does
>> not seem to be available anymore.
>>
>> I notice that today the link has been changed to say "R 2.11.0 used http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Automated%20Builds/mingw-w64-1.0-bin_i686-mingw_20100322.zip
>> , but this is apparently no longer available for download." I
>> guess that it was just bad luck that I tried to do this the for the
>> first time when they are just discovering that the toolkit they
>> require is no longer available for download.
>>
>> The more recent version of mingw-w64-1.0-bin_i686-mingw_.... from http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Automated%20Builds/
>> include gcc 4.5 This does not appear to be compatible with R-2.11.x
>>
>> I'm currently investigating use the snapshots found at http://www.stats.ox.ac.uk/pub/Rtools/
>> to build.
>>
>> But it is all a bit complicated because that page mixes and matches
>> build tools for the eight windows build variant. 8 comes from 2^3
>> where the 3 are the three binary choices for:
>> - gcc 4.5 vs earlier
>> - R2.11. vs R2.12
>> - 32 bit vs 64 bit
>>
>> Based on http://win-builder.r-project.org I think I just need
>> R-2.11.1 on 64bit. I think that means that I have to use gcc 4.2.
>>
>>
>>
>>
>> For what it is worth:
>>
>> The reason that the newest gcc breaks R build (for me) is similar
>> to what is described at http://tolstoy.newcastle.edu.au/R/e11/devel/10/07/0032.html
>> except that I see the problems during linking not at the make
>> check stage. When deciding what symbols to include in a DLL, R's
>> builds have rules that used nm to list all symbols, then they use
>> sed to remove underscores from the names (assuming that g++ will
>> mangle names in that way exactly). I guess that g++ changed their
>> name mangling.
>>
>> I confess that I do not understand R's make configuration system.
>> I've never seen one like it. I don't want to sound hypercritical,
>> but doing things like piping nm to sed to figure out what symbols
>> you want to include is not a path to long term happiness in life ;-)
>>
>>
>>
>> I'll let you know if I make any progress.
>>
>>
>> Mark
>>
>>
>>
>> On Jul 18, 2010, at 10:25 AM, Ben Bolker wrote:
>>
>>> thanks Mark.
>>>
>>> Mark Holder wrote:
>>>> Hi,
>>>> I'll give it another shot. It'll probably be Wednesday before I
>>>> even have a chance to try.
>>>>
>>>> all the best,
>>>> mark
>>>>
>>>>
>>>> On Jul 15, 2010, at 9:19 AM, Ben Bolker wrote:
>>>>
>>>>> About 64-bit toolchain:
>>>>> http://www.murdoch-sutherland.com/Rtools/ says:
>>>>>
>>>>>
>>>>> Tools for 64 bit Windows builds
>>>>>
>>>>> Most of the tools used for 32 bit builds work fine as well for
>>>>> 64 bit
>>>>> builds, but the gcc version is necessarily different. We use the
>>>>> MinGW-w64 version, available from SourceForge.net.
>>>>> R 2.11.0 used mingw-w64-1.0-bin_i686-mingw_20100322.zip.
>>>>> Current snapshot builds are currently using the same version,
>>>>> but we may
>>>>> update before the next release of R.
>>>>>
>>>>> To install, simply unzip the whole file into a directory such as
>>>>> Rtools/MinGW-w64, and add Rools/MinGW-w64/bin to your PATH ahead
>>>>> of the
>>>>> Rtools/MinGW/bin directory. Then follow the instructions in the "R
>>>>> Administration and Installation" manual, section "Building R for
>>>>> 64-bit
>>>>> Windows" to build R. Building packages proceeds as on other
>>>>> platforms
>>>>> provided 64 bit R and the 64 bit gcc are found on the PATH
>>>>> before 32 bit
>>>>> versions. Note that these instructions are currently evolving
>>>>> rapidly;
>>>>> plans are for a single combined build by the time 2.12.0 is
>>>>> released.
>>>>>
>>>>> That seems fairly unambiguous?
>>>>> Are you willing to take a stab at installing those tools and see
>>>>> if
>>>>> it helps replicate the problem?
>>>>>
>>>>> cheers
>>>>> Ben
>>>>>
>>>>>
>>>>>
>>>>> Mark Holder wrote:
>>>>>> Hi,
>>>>>> 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:
>>>>>> https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.1
>>>>>> 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.
>>>>>>
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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
>>>>>>> *** NEW E-MAIL ADDRESSES:
>>>>>>> *** 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
>>>>>
>>>>> --
>>>>> Ben Bolker
>>>>> *** NEW E-MAIL ADDRESSES:
>>>>> *** 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
>>>>>
>>>>
>>>
>>>
>>> --
>>> Ben Bolker
>>> *** NEW E-MAIL ADDRESSES:
>>> *** 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
>>>
>>
>
> Mark Holder
>
> mtholder at ku.edu
> http://phylo.bio.ku.edu/mark-holder
>
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>
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>
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------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
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