Uncategorized

Error installing R/igraph unable to load shared object ‘../igraph.so’: libgfortran.so.4: cannot open shared object file: No such file or directory

Ashok Ragavendran5 Comments

#+BLOG

I ran into this tiny error that could have consumed my whole day. I had set up an AWS ubuntu 16.04 (Xenial) image and installed R. I think I followed some random web page and ended up installing the latest version of R v3.4.2

I was trying to install this package “`phangorn“` which has igraph as it’s dependency and lo behold, i could not install it kept failing with this error:

igraph-error.png

Google turned up a few links that seemed to be helpful including installing libxml2-dev

The link below helped me first trouble shoot the foreign-graphml error

 igraph_hacks_internal.h:42:0: warning: "strdup" redefined
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

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, "\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/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/igraph’

ERROR: dependency ‘igraph’ is not available for package ‘phangorn’

removing ‘/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4/phangorn’

The downloaded source packages are in ‘/tmp/Rtmp7mCd4h/downloaded_packages’
Warning messages: 
1: In install.packages("phangorn", repos = "http://cran.mtu.edu") : installation of package ‘igraph’ had non-zero exit status 
2: In install.packages("phangorn", repos = "http://cran.mtu.edu") : installation of package ‘phangorn’ had non-zero exit status

However, they all did not seem to be address the second round of errors where ever after compiling, the igraph.so failed to load.

Turns out it was a simple thing to fix. The key is to recognize that the second line of the error message was the culprit, even though it does not actually throw an error

libgfortran.so.4: cannot open shared object file: No such file or directory

There was no libgfortran.so.4 installed on my machine and this is not available by default on Xenial.

ubuntu@ip-172-31-93-178:/usr/local/lib$ find /usr -name "libgfortran*"
/usr/share/doc/libgfortran3
/usr/share/doc/libgfortran-5-dev
/usr/lib/gcc/x86_64-linux-gnu/5/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/5/libgfortranbegin.a
/usr/lib/gcc/x86_64-linux-gnu/5/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/5/libgfortran.spec
/usr/lib/x86_64-linux-gnu/libgfortran.so.3
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0

However, the R version I had installed was somehow compiled with this version and further investigation reveraled that this was basically part of the gcc-7 toolchain. So, for my purposes I installed gcc-7 and gfortran-7 from a ‘ppa’ on ubuntu based on this SO post and this post. So I added the ppa:jonathonf/gcc-7.1 as specified in one of the comments and then installed as follows

sudo apt-get install gcc-7 g++-7 gfortran-7

the gfortran-7 is key as that is what installs the gfortran command and Voila!!! now I can install igraph.

Hope this is helpful to someone out there. #+END_SRC