Wow, thanks so much for digging into this Tamas! I'm traveling at a
conference and away from my desktop but will try these and report back when
I get home!
On Wed, May 27, 2015 at 4:48 PM Tamas Nepusz <[email protected]> wrote:
> Hi Nick,
>
> I have researched this problem a bit tonight and here's what I found out.
> These
> are very technical details and might not help a lot at this stage, but
> I thought I'd send them to the mailing list anyway in case someone else is
> struggling with the same problem and finds this thread.
>
> The core of the problem is as follows. igraph needs to link to libxml2 to
> support reading GraphML files. When you install Anaconda Python, it brings
> its
> own copy of libxml2 in ~/anaconda/lib. Now, when igraph tries to figure
> out how
> to link to libxml2, it invokes an executable named xml2-config, which is
> supposed to print out the compiler and linker flags necessary to link to
> libxml2.
>
> OS X does not ship xml2-config by default, so in case of OS X, we fall
> back to
> an "educated guess" during the compilation phase, and this seems to work
> nicely. However, Anaconda Python ships its *own* copy of xml2-config, so
> igraph
> invokes Anaconda's xml2-config and uses the compiler and linker flags from
> there. For sake of comparison, these are the linker flags proposed by
> xml2-config in Anaconda Python:
>
> -L${HOME}/anaconda/lib -lxml2 -lz -liconv -lm
>
> and this is our "educated guess" that we would have used in case of a
> missing
> xml2-config:
>
> -lxml2
>
> Now, when the linker sees the flags suggested by Anaconda's
> libxml2-config, it
> tries to use the libxml2 library from Anaconda Python (since Anaconda's lib
> directory is inserted at the front of the library path), and subsequently
> it
> reads ${HOME}/anaconda/lib/libxml2.la to figure out libxml2's
> dependencies.
> libxml2.la references /usr/lib/libiconv.la, which does not exist on OS X,
> and
> the compilation fails.
>
> On my machine, the compilation worked even with Anaconda Python installed
> because I did _not_ have Anaconda's bin directory (i.e.
> ${HOME}/anaconda/bin)
> on my path (deliberately), so the compilation phase of igraph did _not_
> find
> Anaconda's xml2-config executable and used the "educated guess" instead.
> This
> made igraph link to the copy of libxml2 provided by OS X instead of libxml2
> provided by Anaconda Python, and I'm a bit unsure whether this could lead
> to
> further problems down the road (probably not), but the bottom line is that
> the
> compilation succeeded.
>
> At the moment, there are three workarounds:
>
> #1) Temporarily rename Anaconda's xml2-config to something else before
> installing igraph using "pip install python-igraph" so it is not found
> during
> the compilation phase. igraph will then link to libxml2 provided by OS X.
>
> #2) Patch ~/anaconda/lib/libxml2.la so it does not refer to
> /usr/lib/libiconv.la. I haven't tried this, but it would probably work.
>
> #3) Compile igraph's C core independently from Homebrew (http://brew.sh,
> using
> "brew install igraph"), and then try "pip install python-igraph". In this
> case,
> "pip install python-igraph" will find the copy of igraph's core C library
> from
> Homebrew and does not try to compile it on its own.
>
> All the best,
> Tamas
>
> > But I should add: it's a completely clean OS and conda install, so I
> > imagine whatever problem I'm running into isn't unique to me.
> >
> > On Sun, May 24, 2015 at 1:51 PM Nick Eubank <[email protected]>
> wrote:
> >
> > > (I'm on 10.10 if that matters)
> > >
> > > On Sun, May 24, 2015 at 1:51 PM Nick Eubank <[email protected]>
> wrote:
> > >
> > >> Thanks -- silly question, but any suggestions on how to trace that?
> Seems
> > >> like a lot goes on in this install, and it's not explicitly in any
> > >> options...
> > >>
> > >> Also interestingly, I seem to have the library, and even reinstalled
> it
> > >> to no avail...
> > >>
> > >> On Sun, May 24, 2015 at 4:35 AM Tamas Nepusz <[email protected]>
> wrote:
> > >>
> > >>> Hi Nick,
> > >>>
> > >>> > Tried doing a new python-igraph install on a new computer with
> clean
> > >>> > anaconda 2.7.3 install. Got:
> > >>> > [...]
> > >>> > grep: /usr/lib/libiconv.la: No such file or directory
> > >>> > sed: /usr/lib/libiconv.la: No such file or directory
> > >>> I have seen it a few times before -- it's quite common and not
> specific
> > >>> to
> > >>> igraph. (Googling for "missing libiconv.la" reveals quite a lot of
> > >>> hits). Some
> > >>> other .la file on your system (probably in /usr/lib, but maybe not)
> lists
> > >>> /usr/lib/libiconv.la as a dependency even though it should not be
> > >>> required. Try
> > >>> to find out which other .la file refers to libiconv.la and then
> either
> > >>> move
> > >>> that file aside temporarily or remove libiconv.la temporarily from
> the
> > >>> list of
> > >>> dependencies in that other file.
> > >>>
> > >>> T.
> > >>>
> > >>> _______________________________________________
> > >>> igraph-help mailing list
> > >>> [email protected]
> > >>> https://lists.nongnu.org/mailman/listinfo/igraph-help
> > >>>
> > >>
>
> > _______________________________________________
> > igraph-help mailing list
> > [email protected]
> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
> --
> T.
>
> _______________________________________________
> igraph-help mailing list
> [email protected]
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
_______________________________________________
igraph-help mailing list
[email protected]
https://lists.nongnu.org/mailman/listinfo/igraph-help
