Actually if you have the autotools packages installed (from the system or sage)
can you try 
autoreconf -i
then re-run configure and see if that fix it. 

> On 10/02/2018, at 00:02, François Bissey <frp.bis...@gmail.com> wrote:
> 
> Which version of ubuntu? We have seen an instance of that problem during 
> review
> but we thought it was fixed. OK, there was something nagging me but it looked 
> fixed on the patchbot.
> 
>> On 9/02/2018, at 23:56, fchapot...@gmail.com wrote:
>> 
>> An incremental build from previous beta fails on gfortran :
>> 
>> [gfortran-7.2.0] Found local metadata for gfortran-7.2.0
>> [gfortran-7.2.0] Using cached file 
>> /home/chapoton/sage/upstream/gcc-7.2.0.tar.xz
>> [gfortran-7.2.0] gfortran-7.2.0
>> [gfortran-7.2.0] ====================================================
>> [gfortran-7.2.0] Setting up build directory for gfortran-7.2.0
>> [gfortran-7.2.0] Finished extraction
>> [gfortran-7.2.0] No patch files found in ../patches
>> [gfortran-7.2.0] ****************************************************
>> [gfortran-7.2.0] Host system:
>> [gfortran-7.2.0] Linux pc-chapoton 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 
>> 25 09:13:46 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>> [gfortran-7.2.0] ****************************************************
>> [gfortran-7.2.0] C compiler: gcc
>> [gfortran-7.2.0] C compiler version:
>> [gfortran-7.2.0] Using built-in specs.
>> [gfortran-7.2.0] COLLECT_GCC=gcc
>> [gfortran-7.2.0] 
>> COLLECT_LTO_WRAPPER=/home/chapoton/sage/local/libexec/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
>> [gfortran-7.2.0] Target: x86_64-pc-linux-gnu
>> [gfortran-7.2.0] Configured with: ../src/configure 
>> --prefix=/home/chapoton/sage/local 
>> --with-local-prefix=/home/chapoton/sage/local 
>> --with-gmp=/home/chapoton/sage/local --with-mpfr=/home/chapoton/sage/local 
>> --with-mpc=/home/chapoton/sage/local --with-system-zlib --disable-multilib 
>> --disable-nls --enable-languages=c,c++,fortran --disable-libitm  
>> [gfortran-7.2.0] Thread model: posix
>> [gfortran-7.2.0] gcc version 7.2.0 (GCC) 
>> [gfortran-7.2.0] ****************************************************
>> [gfortran-7.2.0] Error: gcc is already installed
>> [gfortran-7.2.0] 
>> [gfortran-7.2.0] real        0m0.003s
>> [gfortran-7.2.0] user        0m0.004s
>> [gfortran-7.2.0] sys 0m0.000s
>> [gfortran-7.2.0] 
>> ************************************************************************
>> [gfortran-7.2.0] Error installing package gfortran-7.2.0
>> [gfortran-7.2.0] 
>> ************************************************************************
>> 
>> 
>> Le vendredi 9 février 2018 09:25:28 UTC+1, Volker Braun a écrit :
>> As always, you can get the latest beta version from the "develop" git 
>> branch. Alternatively, the self-contained source tarball is at 
>> http://www.sagemath.org/download-latest.html
>> 
>> e6cae6d88d (tag: 8.2.beta5, trac/develop) Updated SageMath version to 
>> 8.2.beta5
>> 9dd4282d36 Trac #24660: Memory leak in SubgraphSearch
>> b9aa268ecd Trac #24639: Enumerating greedy linear extensions
>> c795e950c9 Trac #24636: Rivin's test for circumcribability and inscribability
>> d70b6a253a Trac #24629: fix R build on Solaris 11
>> 4f53f24d1f Trac #24628: Build PCRE without JIT if needed
>> 867f4c9761 Trac #24618: fplll fails to build on SunOS
>> 92ac632d04 Trac #24611: Singular fails to build on SunOS
>> ac14d82c6f Trac #24590: bug in inverse_image of module homomorphism
>> 38e8a65eec Trac #24313: py3: fixes to sage.misc.temporary_file
>> b899601826 Trac #24239: Implement soliton cellular automata
>> 7d0ca44142 Trac #24139: Allow baseline to be given as part of ascii_art and 
>> unicode_art
>> 94da5b67c1 Trac #24656: Fix bug in type E bijection from cythonizing 
>> RiggedPartition
>> e8c626f7da Trac #24615: interface libgap floats
>> 9c146ffcb2 Trac #24608: Remove deprecated PowerSeries._floordiv_
>> 6b689d3bfa Trac #23978: Rich comparison for Modules
>> 70c254125d Trac #24634: add .is_polyhedral method to graphs
>> 2d1615636e Trac #24175: Optimizations to generating rigged configurations
>> 7be8a667e9 Trac #24141: Optimizations to Kleber tree
>> 8a2e3ed425 Trac #24035: Normal forms for TorsionQuadraticModules
>> 9b223d74de Trac #24633: Add jump count for a linear extension
>> 0da6392254 Trac #24632: Add is_greedy() to linear extension.
>> e185837226 Trac #24631: Faster jump number for posets
>> 4387613c32 Trac #24619: giac fails to build on SunOS
>> 58fdd676a4 Trac #24516: Cygwin test failures in lseries_ell
>> ab3c1c8da7 Trac #24411: Move gamma functions into their own file
>> 79f648c706 Trac #23714: GAP matrices
>> 295b129a35 Trac #22921: Implementation of shifted tableaux
>> c5248314f7 Trac #24625: Some small improvements to polynomial_complex_arb
>> d842b25062 Trac #24624: Stop using new_t_POL_from_int_star from cypari2
>> 75e3f2960a Trac #24617: Infinite process recursion with Solaris make
>> bb2b730403 Trac #24614: Deprecate args of Parent_old.__init__
>> 505af6e57c Trac #24613: Remove actions from old coercion model
>> b200dbae27 Trac #24610: Change richcmp() to a cpdef inline function
>> 2a71f44dae Trac #24607: Add abstract _add_ and _mul_ methods to RingElement
>> 6296a31f22 Trac #24606: Forgotten check_error in maxima spkg-install
>> f5259142ff Trac #24602: upgrade iconv to 1.15
>> e7fe097bf3 Trac #24597: Properly set LD_LIBRARY_PATH in spkg-build for 
>> python2/3 on SunOS
>> 69951df4c2 Trac #24584: Add the power poset
>> 8e3fde343d Trac #24431: Fix coercions and pushout for Laurent series
>> f313460743 Trac #24381: New Parent method _convert_method_map
>> 9f2efaef78 Trac #24357: Two bugs in NumberField.composite_fields()
>> 56c322343a Trac #24223: py3: several string conversion fixes
>> b79f27f2c6 Trac #24071: Improve docstring of MPolynomial_libsingular.reduce()
>> 950bdd8145 Trac #23696: Update matplotlib to 2.1.0
>> 36849d6c3e Trac #22928: Conversion between gmpy2 and sage objects
>> 5473d304bb Trac #5574: Implement QQbar^QQ as action
>> 129faa0c39 Trac #24599: Internal compiler error when compiling giac-1.4.9.45 
>> with gcc-7.2.0
>> 07f53b23c4 Trac #24600: another typo ticket
>> 52cd6b86d0 Trac #24563: Workaround for small race condition in parallel 
>> doctest runner
>> 80fecaaf95 Trac #24418: Doctest: bug 
>> numerical_approx(2^(450232897/4888643760))
>> 919ef40bb8 Trac #21092: Unhandled case in EllipticCurve_from_cubic
>> a3ee07f891 Trac #12426: Make Sage build with clang (3.7+) and make it the 
>> default on OS X
>> ed50684b29 Trac #24517: random failure in sage/geometry/cone.py
>> 0a674fd488 (tag: 8.2.beta4) Updated SageMath version to 8.2.beta4
>> 
>> 
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