The problem seems to interfaces/R/igraph/configure.in.

On my system, the ".in" extension tells autoconf to run version
2.13, which results in the reported errors. We can fix this by
changing the file extension to .ac, but this also means re-writing
the makefile (ugh).

The other option is to add the directive AC_PREREQ(2.50) to the
file configure.in

At least on my system, adding this autoconf directive fixes this
problem.

Note  I am still seeing odd things in the output of make, but you
also see that the tar.gz files build without (reported) error, and
the problems do not look fatal, I only list them here for your
information:

mktemp: too few X's in template `igraph'
cp: cannot create regular file `/AUTHORS': Permission denied
cp: cannot create regular file `/DESCRIPTION': Permission denied
cp: cannot create regular file `/NEWS': Permission denied
cp: cannot create directory `/R': Permission denied
cp: cannot create directory `/autom4te.cache': Permission denied
cp: cannot create regular file `/configure': Permission denied
cp: cannot create regular file `/configure.in': Permission denied
cp: cannot create regular file `/configure.win': Permission denied
cp: cannot create directory `/demo': Permission denied
cp: cannot create directory `/inst': Permission denied
cp: cannot create directory `/man': Permission denied
cp: cannot create directory `/src': Permission denied
Error in library(devtools) : there is no package called 'devtools'
Execution halted
cp: cannot stat `/DESCRIPTION': No such file or directory
cp: cannot stat `/NAMESPACE': No such file or directory
cp: cannot stat `/man/*': No such file or directory
R CMD build igraph
* checking for file 'igraph/DESCRIPTION' ... OK
* preparing 'igraph':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* creating default NAMESPACE file
* building 'igraph_0.7.999-225.tar.gz'

R CMD build igraphdata
* checking for file 'igraphdata/DESCRIPTION' ... OK
* preparing 'igraphdata':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* creating default NAMESPACE file
* building 'igraphdata_0.2.tar.gz'

+glenn

AC_INIT(igraph, @VERSION@, [email protected])
-- 
--------------------------------------------------------------
     Dr. Glenn Lawyer                    
     +352 661 967 244              
     Max-Planck-Institut für Informatik
     Computational Biology and Applied Algorithmics
     Campus E1 4
     66123 Saarbrücken, Germany
     http://bioinf.mpi-inf.mpg.de/~lawyer

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