Re: [igraph] igraph_1.0.1.tar.gz compile problem

[Tamas Nepusz]

Hi John,

It seems like R is still picking up the include files of the _old_
libxml2 when compiling igraph and not the new one. I'm not that
familiar with the R interface so I cannot help you more here (but
maybe Gabor can), but it seems like the lib=... option only defines
where to _install_ the new packages but dos not influence where R will
search for the library dependencies.

Is it possible to upgrade the system-wide libxml2 to a newer version
instead of compiling and installing one locally?

T.

T.


On Fri, Oct 2, 2015 at 12:26 AM, John Nyhuis <address@hidden> wrote:
> Following the advice here (Thanks!), I compiled a custom libxml2 (ver 2.9.2)
> in /net/lebowski/vol1/sw/R/3.2.2/lib64/lib/
>
> I fed this ld path to R using the following command:
>> install.packages("igraph", lib =
>> "/net/lebowski/vol1/sw/R/3.2.2/lib64/lib/")
>
> and ended up with the same error, included below:
>
> foreign-graphml.c:65: warning: excess elements in struct initializer
> foreign-graphml.c:65: warning: (near initialization for ‘blankEntityStruct’)
> foreign-graphml.c: In function ‘igraph_read_graph_graphml’:
> foreign-graphml.c:1330: error: ‘XML_PARSE_HUGE’ undeclared (first use in
> this function)
> foreign-graphml.c:1330: error: (Each undeclared identifier is reported only
> once
> foreign-graphml.c:1330: error: for each function it appears in.)
> make: *** [foreign-graphml.o] Error 1
> ERROR: compilation failed for package ‘igraph’
> * removing ‘/net/lebowski/vol1/sw/R/3.2.2/lib64/lib/igraph’
>
> The downloaded source packages are in
>         ‘/tmp/RtmpnVIhWA/downloaded_packages’
> Warning message:
> In install.packages("igraph", lib =
> "/net/lebowski/vol1/sw/R/3.2.2/lib64/lib/") :
>   installation of package ‘igraph’ had non-zero exit status
>
>
> Could it be something else?  Changing out libxml2 did not seem to make any
> difference in my compile error...
> Any help would be appreciated.  Thanks in advance!
>
>
> Thanks,
> John Nyhuis
> IT Manager, Stam Lab
> 2211 Elliott Avenue
> 6th Floor, 6S139
> Seattle, WA 98121
> O: (206)-267-1097 ext 220
> F: (206)-441-3033
>
> On 10/01/2015 05:02 AM, Gábor Csárdi wrote:
>>
>> You need a fairly recent version of the libxml2 library, including the
>> development headers.
>>
>> Gabor
>>
>> On Wed, Sep 30, 2015 at 10:38 PM, John Nyhuis <address@hidden> wrote:
>>>
>>> When I try to install igraph_1.0.1.tar.gz in R 3.2.2, I fail with the
>>> following compile error:
>>>
>>> foreign-graphml.c:65: warning: excess elements in struct initializer
>>> foreign-graphml.c:65: warning: (near initialization for
>>> ‘blankEntityStruct’)
>>> foreign-graphml.c: In function ‘igraph_read_graph_graphml’:
>>> foreign-graphml.c:1330: error: ‘XML_PARSE_HUGE’ undeclared (first use in
>>> this function)
>>> foreign-graphml.c:1330: error: (Each undeclared identifier is reported
>>> only
>>> once
>>> foreign-graphml.c:1330: error: for each function it appears in.)
>>> make: *** [foreign-graphml.o] Error 1
>>> ERROR: compilation failed for package ‘igraph’
>>>
>>> This is with gcc version 4.1.2 20080704
>>> on a RHEL 5.11 cluster running R 3.2.2
>>>
>>> Can anyone point me in the correct direction?
>>>
>>>
>>>
>>> --
>>> Thanks,
>>> John Nyhuis
>>> IT Manager, Stam Lab
>>> 2211 Elliott Avenue
>>> 6th Floor, 6S139
>>> Seattle, WA 98121
>>> O: (206)-267-1097 ext 220
>>> F: (206)-441-3033
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help