Re: [igraph] building igraph in R using a local copy of the C library

[Gábor Csárdi]

Hi, sorry for the delay.

You need a gfortran version that is compatible with R:
https://cran.rstudio.com/bin/macosx/tools/

Gabor

On Thu, Jan 7, 2016 at 2:35 PM, Jason Cory Brunson <address@hidden> wrote:
> I'd thought i'd run make in the rigraph directory, but perhaps i hadn't; i
> did it and indeed it created the NAMESPACE file. Thanks!
>
> I continued on from there. Turns out i also didn't have gfortran installed,
> so i used homebrew to install gcc. But then, running document() again from
> the rigraph directory, i got an error that has me (and my friend) stuck:
>
> ld: warning: directory not found for option
> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
> ld: warning: directory not found for option
> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [igraph.so] Error 1
> ERROR: compilation failed for package ‘igraph’
> * removing
> ‘/private/var/folders/pg/fjg8r4fj5v33zqmwptf9mfg80000gn/T/RtmpO9W90V/devtools_install_1646c2db26e0f/igraph’
> Error: Command failed (1)
>
> For reference, here's my gfortran version info:
>
> GNU Fortran (Homebrew gcc 4.8.3_1) 4.8.3
> Copyright (C) 2013 Free Software Foundation, Inc.
>
> Thanks yet again for your guidance,
>
> Cory
>
>
> On 12/29/15 5:07 AM, Gábor Csárdi wrote:
>>
>> Perhaps you ran make in the igraph directory? You need to run make in
>> rigraph, and it should create a NAMESPACE file, AFAIR.
>>
>> Gabor
>>
>> On Wed, Dec 23, 2015 at 6:57 PM, Jason Cory Brunson <address@hidden>
>> wrote:
>>>
>>> Thanks, Gábor.
>>>
>>> I've reached my first hangup. Here's what i've done so far (Mac OS X
>>> 10.9):
>>>
>>> 1. Fork both igraph and rigraph repositories.
>>> 2. Clone both to local directories.
>>> 3. Edit the .gitmodules file in the rigraph directory to point to the
>>> adjacent igraph directory ("../igraph"), and update ("git submodule
>>> update
>>> --init").
>>> 4. (After installing Automake) make ("make").
>>>
>>> So far (as i can tell), so good. Here's what threw an error:
>>>
>>> 5. In R, with devtools, in the rigraph directory, document the package
>>> (which is necessary to then load it into the session, e.g. via load_all):
>>> "document()". Here's the error, with the few output lines preceding it:
>>>
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars.tmp
>>> config.status: creating src/Makevars
>>> config.status: src/Makevars is unchanged
>>> config.status: creating src/config.h
>>> config.status: src/config.h is unchanged
>>> ERROR: a 'NAMESPACE' file is required
>>> * removing
>>>
>>> ‘/private/var/folders/pg/fjg8r4fj5v33zqmwptf9mfg80000gn/T/Rtmpm4Uw4x/devtools_install_d9511fcb3c02/igraph’
>>> Error: Command failed (1)
>>>
>>> The rigraph directory has no NAMESPACE file—and my understanding is that
>>> the
>>> NAMESPACE file should be created, not required, by document(). As an
>>> experiment, i copied the NAMESPACE file from the current release of
>>> igraph
>>> into the rigraph directory and tried "document()", but received "ERROR:
>>> compilation failed for package ‘igraph’".
>>>
>>> Thanks again,
>>>
>>> Cory
>>>
>>>
>>> On 12/13/15 6:25 PM, Gábor Csárdi wrote:
>>>>
>>>> Hi,
>>>>
>>>> the C igraph library is a submodule in the dev tree of the R package.
>>>> So one thing you could do is forking both repos, and point the
>>>> submodule in the forked R repo to the forked C repo.
>>>>
>>>> The build process is far from trivial, unfortunately, but we can help
>>>> if you get stuck. You can start it by just issuing 'make' in the R
>>>> package repo root.
>>>>
>>>> Gabor
>>>>
>>>> On Fri, Dec 11, 2015 at 8:27 PM, Jason Cory Brunson <address@hidden>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to be able to build the igraph package in R using a local
>>>>> copy
>>>>> of the C library in a sandbox directory (i.e. not where libraries are
>>>>> installed by default), for the purpose of writing additional functions
>>>>> in
>>>>> the C library to call in R (python would be OK too).
>>>>>
>>>>> A friend with more programming experience tried to help me, but ran
>>>>> into
>>>>> trouble early on. So i wonder if there's a straightforward sequence of
>>>>> steps
>>>>> i should take, or if a walkthrough is posted somewhere—or if this is
>>>>> simply
>>>>> not something someone not fluent in C should be doing.
>>>>>
>>>>> I did not see anything in the list archives. Thanks for any help.
>>>>>
>>>>> Cory
>>>>>
>>>>> _______________________________________________
>>>>> igraph-help mailing list
>>>>> address@hidden
>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>
>>>> _______________________________________________
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>>>> address@hidden
>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>>
>>>
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>>
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