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 <[email protected]> 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 <[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 >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ > 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
