[Phylobase-devl] Compilation woes

David Orme d.orme at imperial.ac.uk
Mon Aug 4 14:30:48 CEST 2008

Hi everyone,

Just to show that I am following the development - even if my  
contributions have been negligible!

I think there is a great demand (extrapolating from Silwood,  
admittedly) for a more comprehensive function for reading nexus. The  
ape version has recently seen some changes that have cause no end of  
woes here, particularly problems with node labels. NCL is a killer  
feature and, recognising that these aren't trivial problems to solve,   
it would be a shame to see it branched. The package would get  
immediate uptake by code developers if it included a robust and stable  
nexus reader.


On 4 Aug 2008, at 07:07, Peter Cowan wrote:

> Hi all,
> I can't say that I have any special insight into the current
> compilation issues.  Last time we went through this Stephan eventually
> emailed me the R code that runs the package building.  So I do know
> that a fresh copy of the SVN directory is made into a temporary
> directory.  So I would be very surprised if the issue was related to
> build products remaining.
> There seem to be a lot of configuration files under version control in
> the top NCL folder.  A quick look at the SourceForge version shows
> that they have fewer files.  I do think that at least some of these
> configure files are auto created.  Perhaps we should pare down to only
> the necessary files.
> As for the immediate future of NCL, I think it's going to be a killer
> feature of the package.  However, so far it has consumed a lot of
> developer time just trying to get it to build properly.  At least on
> my part that is due to a lack of expertise with makefiles and C++ in
> generally, perhaps this could be solved by contacting the NCL
> developers?  I have also had frustrating experiences using the NCL
> commands.  I sent an email regarding this experience previously to the
> list.  I suspect that the performance issues will easily overcome.  My
> vote would be, if NCL is preventing successful building and thus
> adoption of the package we should consider separating it, perhaps into
> a branch.  I think there is a way for us to build multiple version of
> the package see the "distr - S4 classes for distributions" package.
> My 2 cents
> Peter
> On Sun, Aug 3, 2008 at 9:49 PM, Steve Kembel <skembel at berkeley.edu>  
> wrote:
>> Hi Brian,
>>> Thanks for looking into this, Steve and Ben. If it is just a matter
>>> of old files not being rewritten properly, this should be able to be
>>> taken care of in the Makefile (effectively, make clean first). I'll
>>> check it out some more.
>> I'm not 100% sure about this. The install errors I get in Linux are
>> not very reproducible, but that's my guess. For example I got a very
>> similar error to the R-Forge linux build errors the first time I  
>> tried
>> to build, but then slightly different errors on subsequent attempts,
>> and no errors with a fresh copy of the code.
>> A few more things about this:
>> -make clean doesn't actually seem to work properly, there isn't a
>> clean action defined in the ncl makefile, maybe this is part of the
>> problem.
>> -there is a script pkg/cleanup that gets rid of a lot of the
>> accumulated files. I don't know if this could be incorporated into  
>> the
>> make clean action. I missed this until now but I think this is
>> something that Thibaut wrote to get phylobase to compile on linux_x64
>> a long while back. The message in which he describes it was pre-R-
>> Forge so I'm including a copy of the text below. Sounds like part of
>> the problem is indeed files not being deleted and messing up
>> subsequent builds.
>> -if i build the package from a clean copy of the code, the following
>> files are left behind.
>> steve at pundit:~/code/phylobase$ svn status
>> ?      pkg.Rcheck
>> ?      phylobase.Rcheck
>> ?      phylobase_0.3-1.tar.gz
>> ?      pkg/config.log
>> ?      pkg/config.status
>> ?      pkg/src/phylobase.so
>> ?      pkg/src/Makevars
>> ?      pkg/src/RcppSrc/libRcpp.a
>> ?      pkg/src/ncl/config.log
>> ?      pkg/src/ncl/config.status
>> ?      pkg/src/ncl/stamp-h1
>> ?      pkg/src/ncl/libtool
>> ?      pkg/src/ncl/configure.lineno
>> ?      pkg/src/ncl/Makefile
>> ?      pkg/src/ncl/ncl/.deps
>> ?      pkg/src/ncl/ncl/Makefile
>> ?      pkg/src/ncl/ncl/.libs
>> -if I then run the cleanup script, the following files are still  
>> left:
>> steve at pundit:~/code/phylobase/pkg$ svn status
>> ?      src/ncl/config.log
>> ?      src/ncl/config.status
>> ?      src/ncl/stamp-h1
>> ?      src/ncl/libtool
>> ?      src/ncl/configure.lineno
>> ?      src/ncl/Makefile
>> ?      src/ncl/ncl/.deps
>> ?      src/ncl/ncl/Makefile
>> Hope this helps. I definitely agree about the value of having NCL in
>> phylobase, let's see if we can sort out these issues.
>> Steve
>> Begin forwarded message:
>>> From: Thibaut Jombart
>>> Date: February 13, 2008 9:16:53 AM PST
>>> To: phylobase-devel at nescent.org
>>> Subject: Re: [phylobase-devel] 64bits compilation troubles: IT WORKS
>>> Ben Bolker wrote:
>>>> OK, but ...
>>>> I thought your last e-mail said that even hacking -fPIC into
>>>> the Makefile didn't work.  I think "we" should first figure out
>>>> if we can get it to build with a hacked Makefile, then figure
>>>> out how to make the Makefile get constructed properly.
>>>> (At worst, that might allow us to make a 64-bit binary
>>>> to post on the web page, although fixing this properly
>>>> would certainly be better.)
>>>> I was guessing that ./configure --with-pics would
>>>> work, but you tried that ...
>>>> I think we might also be able to shove it into the
>>>> automake flags somewhere ...
>>>> Ben
>>> Hi people,
>>> So I now have phylobase installed on my 64bits laptop. Yet, it does
>>> not answer how we will generally fix the problem.
>>> In fact, hacking the src/ncl/configure file indeed works, but didn't
>>> for the following reason. It seems that .o objects are compiled only
>>> when they do not already exist. If then do, then all what is done is
>>> linking, and so the hack was not effective. So, this works for me:
>>> 1) first run the cleanup script to override stuff like .o files.
>>> 2) modify the configure script like follows:
>>> (starting from line 20560)
>>>          CXXFLAGS_OPTIM_SPEED="-O3 -ffast-math"
>>>          CXXFLAGS_OPTIM_SPEED="-O3 -ffast-math"
>>>          CXXFLAGS_OPTIM_SIZE="-Os -ffast-math"
>>>          # modif by Thibaut
>>>          CXXFLAGS_USE_FPIC="-fPIC"
>>>      fi
>>>      case "$build_os" in
>>>          darwin*) CXXFLAGS_WARNINGS="$CXXFLAGS_WARNINGS -Wno-long-
>>> double";;
>>>          *);;
>>>      esac
>>>  fi
>>>  if test "x$CXXFLAGS_OPTIM_SIZE" = "x"; then
>>>  fi
>>> 3) run R CMD INSTALL (only warnings)
>>> Cheers,
>>> Thibaut.
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