On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com> wrote:> > On 10/09/2017 11:16 AM, Paul Smith wrote: >> >> 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? > > Need to see a lot more logs, specifically, the items before that Error > occurs.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
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:> On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com>
wrote:
> >
> > On 10/09/2017 11:16 AM, Paul Smith wrote:
> >>
> >> 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?
> >
> > Need to see a lot more logs, specifically, the items before that Error
> > occurs.
>
> 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
>
> _______________________________________________
> R-SIG-Fedora mailing list
> R-SIG-Fedora at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
--
Regards,
M K Pai
Data Scientist
Red Hat
Thanks, Saint Pai, that did the trick! Paul On Wed, Oct 11, 2017 at 12:33 PM, Pai <mkpai at redhat.com> wrote:> 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: >> On Mon, Oct 9, 2017 at 4:42 PM, Tom Callaway <tcallawa at redhat.com> wrote: >> > >> > On 10/09/2017 11:16 AM, Paul Smith wrote: >> >> >> >> 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? >> > >> > Need to see a lot more logs, specifically, the items before that Error >> > occurs. >> >> 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 >> >> _______________________________________________ >> R-SIG-Fedora mailing list >> R-SIG-Fedora at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > -- > Regards, > M K Pai > Data Scientist > Red Hat