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 <[email protected]> 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
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https://lists.nongnu.org/mailman/listinfo/igraph-help
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