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