[igraph] igraph 1.1.2 compile error with R

[Panner]

Hello. I was trying to install R-package DESeq2 and it failed to install
apparently due to error in igraph update.

I have also tried to manually install it from a file with

install.packages("./igraph_1.1.2.tar.gz", type = "SOURCE", repos=NULL)

command, but the error remains. Older versions like 1.0.1 and even 1.1.1
worked, but they're not enough for DESeq2.

Might this be an error on my side or a bug in igraph?

The end part of the output while tryin to install igraph_1.1.2.tar.gz:





In file included from src/foreign-gml-parser.y:59:0:
igraph_hacks_internal.h:42:0: warning: "strdup" redefined
# define strdup igraph_i_strdup
^
In file included from /usr/include/string.h:630:0,
from src/foreign-gml-parser.y:54:
/usr/include/x86_64-linux-gnu/bits/string2.h:1291:0: note: this is the
location of the previous definition
# define strdup(s) __strdup (s)
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DUSING_R -I. -Iinclude
-Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include
-ISuiteSparse_config -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DNDEBUG
-DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.1\"
-DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -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");
^
/usr/lib/R/etc/Makeconf:159: recipe for target 'foreign-graphml.o' failed
make: *** [foreign-graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/home/pp/R/x86_64-pc-linux-gnu-library/3.4/igraph’
* restoring previous ‘/home/pp/R/x86_64-pc-linux-gnu-library/3.4/igraph’
Warning in install.packages :
installation of package ‘./Downloads/igraph_1.1.2.tar.gz’ had non-zero
exit status

[Jannick]

Post by Panner
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DUSING_R -I.
-Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -
ICOLAMD/Include -ISuiteSparse_config -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -
DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -
DPACKAGE_VERSION=\"1.1.1\" -DINTERNAL_ARPACK -
DIGRAPH_THREAD_LOCAL=/**/ -fpic -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
foreign-graphml.c -o foreign-graphml.o
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");

You could try to replace the file foreign-graphml.c with the latest version at
https://github.com/igraph/igraph/blob/master/src/foreign-graphml.c (click
'Raw' to see the plain file for easy download) which contains an amendment
regarding this kind of compilation error.

Thanks,
J.

[Panner]

Thank you! That did solve the problem!

Post by Jannick

Post by Panner
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DUSING_R -I.
-Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -
ICOLAMD/Include -ISuiteSparse_config -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -
DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -
DPACKAGE_VERSION=\"1.1.1\" -DINTERNAL_ARPACK -
DIGRAPH_THREAD_LOCAL=/**/ -fpic -g -O2 -fstack-protector-strong -
Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
foreign-graphml.c -o foreign-graphml.o
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");

You could try to replace the file foreign-graphml.c with the latest version at
https://github.com/igraph/igraph/blob/master/src/foreign-graphml.c (click
'Raw' to see the plain file for easy download) which contains an amendment
regarding this kind of compilation error.
Thanks,
J.
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