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Cannot install igraph package

5 messages · Tom Callaway, Pai, Paul Smith

Original
Paul Smith
# 
Dear All,

I am trying to install

igraph package

but getting the following error:

------------------
make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1
ERROR: compilation failed for package ?igraph?
* removing ?/usr/lib64/R/library/igraph?
------------------

Any ideas?

Thanks in advance,

Paul
Tom Callaway
#
On 10/09/2017 11:16 AM, Paul Smith wrote:
Need to see a lot more logs, specifically, the items before that Error
occurs.

~tom
Paul Smith
#
On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com> wrote:
Thanks, Tom. Below, you can find more logs:

---------------------
 #  define strdup igraph_i_strdup

In file included from /usr/include/string.h:634:0,
                 from src/foreign-gml-parser.y:54:
/usr/include/bits/string2.h:208:0: note: this is the location of the
previous definition
 #   define strdup(s) __strdup (s)

gcc -m64 -I/usr/include/R -DNDEBUG   -I/usr/local/include  -DUSING_R
-I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include
-ICOLAMD/Include -ISuiteSparse_config -I/usr/local/include -O2 -g
-pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
-m64 -mtune=generic -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT
-DPACKAGE_VERSION=\"1.1.1\" -DINTERNAL_ARPACK
-DIGRAPH_THREAD_LOCAL=/**/ -fpic  -O2 -g -pipe -Wall
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
-m64 -mtune=generic  -c foreign-graphml.c -o foreign-graphml.o
foreign-graphml.c: In function ?igraph_write_graph_graphml?:
foreign-graphml.c:1408:46: error: expected ?)? before ?GRAPHML_NAMESPACE_URI?
   ret=fprintf(outstream, "<graphml xmlns=\"" GRAPHML_NAMESPACE_URI "\"\n");
                                              ^~~~~~~~~~~~~~~~~~~~~
foreign-graphml.c:1412:59: error: expected ?)? before ?GRAPHML_NAMESPACE_URI?
   ret=fprintf(outstream, "         xsi:schemaLocation=\""
GRAPHML_NAMESPACE_URI "\n");
                                                           ^~~~~~~~~~~~~~~~~~~~~
foreign-graphml.c:1414:38: error: expected ?)? before ?GRAPHML_NAMESPACE_URI?
   ret=fprintf(outstream, "         " GRAPHML_NAMESPACE_URI
"/1.0/graphml.xsd\">\n");
                                      ^~~~~~~~~~~~~~~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:159: foreign-graphml.o] Error 1
ERROR: compilation failed for package ?igraph?
* removing ?/usr/lib64/R/library/igraph?

The downloaded source packages are in
    ?/tmp/Rtmpq4eKlz/downloaded_packages?
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("igraph") :
  installation of package ?igraph? had non-zero exit status
---------------------

Are they enough logs?

Paul
1 day later
Pai
# 
Hello,

Could you please test the solution at 
https://stackoverflow.com/questions/45318188/getting-error-in-function-igraph-write-graph-graphml-while-installing-igrap

Specifically -

install.packages("devtools")
library(devtools)
install_github("igraph/rigraph")

Please let us know if this works

Regards,
-- Saint Pai
On Tue, Oct 10, 2017 at 01:40:53AM +0100, Paul Smith wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Smith
    

    

      
      #
    

  


  

      
Thanks, Saint Pai, that did the trick!

Paul

        
On Wed, Oct 11, 2017 at 12:33 PM, Pai <mkpai at redhat.com> wrote: