installation of package ‘igraph’ had non-zero exit status

[liuyifang]

Hi
The igraph r package has the same bug as igraph in igraph/igraph@0ddc772

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: *** [foreign-graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’

[gaborcsardi]

This is unfortunately a bug in igraph. To work around it you need a newer compiler, or wait for the next igraph release.

[liuyifang]

Thanks for your information.
Could you tell the next igraph release date, if it will be soon, I can wait.

[gaborcsardi]

I would do it today if I could, but CRAN does not like that. But surely within two weeks I would say.

Btw. I think you can also apply this patch: https://github.com/igraph/igraph/pull/1020/files if you don't want to wait.

[liuyifang]

Thanks for your advice, I manually update the source code and solved this bug. But I meet another issue:

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/liuyf/R/R_LIBS/igraph/libs/igraph.so':
libiconv.so.2: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

My R Environment:

CentOS Linux release 7.3.1611 (Core)
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)
R 3.4.1

[liuyifang]

Problem solved.
This is because my CentOS system does not contain libiconv.so.2 shared library.
To solve this:

wget https://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.15.tar.gz
tar -zxvf libiconv-1.15.tar.gz
cd libiconv-1.15
./configure --prefix=/usr/local
make
make install

Then

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

[arpitghiya-zz]

Hello

I have followed your suggestion and applied the patch in the source code. Although, this time I am getting a different error while installing igraph. Can you please help.

src/foreign-gml-lexer.l:102: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
gcc -m64 -std=gnu99 -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 -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION="1.1.1" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=// -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c foreign-gml-parser.c -o foreign-gml-parser.o
In file included from src/foreign-gml-parser.y:59:
igraph_hacks_internal.h:42:1: warning: "strdup" redefined
In file included from /usr/include/string.h:637,
from src/foreign-gml-parser.y:54:
/usr/include/bits/string2.h:1316:1: warning: this is the location of the previous definition
gcc -m64 -std=gnu99 -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 -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION="1.1.1" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=// -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c foreign-graphml.c -o foreign-graphml.o
foreign-graphml.c: In function ‘igraph_write_graph_graphml’:
foreign-graphml.c:1408: error: ‘GRAPHML_NAMESPACE_URI’ undeclared (first use in this function)
foreign-graphml.c:1408: error: (Each undeclared identifier is reported only once
foreign-graphml.c:1408: error: for each function it appears in.)
make: *** [foreign-graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’

• removing ‘/usr/lib64/R/library/igraph’

[liuyifang]

Hi
You need also update src/foreign-graphml.c following this link: igraph/igraph@9acfa54
Then it will be ok.

[arpitghiya-zz]

Thanks! This helped

[SKrPl]

@gaborcsardi I am still facing the same problem while installing.

[Norali81]

Hi, is there anywhere I can find instructions on how to apply the patch? Thanks a lot!