[Debian-med-packaging] Bug#667235: LAST fails to build with GCC-4.7.

[Charles Plessy]

Hi Martin,

we figured out in Debian that LAST does not build with GCC 4.7:

    gumbel_params/njn_approx.hpp:72:98: error: 'fabs' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]

You can see below for more context, and more in particular the instructions
under “Name lookup changes” in GCC's 4.7 porting page

    http://gcc.gnu.org/gcc-4.7/porting_to.html

Do you think you can release an updated version of LAST ?

(This email is sent to our BTS, where it is recorded.)

    http://bugs.debian.org/667235

Cheers,

-- Charles

Le Tue, Apr 03, 2012 at 11:10:04PM +0000, Matthias Klose a écrit :
> Package: last-align
> Version: 193-1
> Severity: important
> Tags: sid wheezy
> User: debian-gcc at lists.debian.org
> Usertags: ftbfs-gcc-4.7
> 
> The package fails to build in a test rebuild on at least amd64 with
> gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
> severity of this report may be raised before the wheezy release.
> 
> gumbel_params/njn_approx.hpp:72:98: error: 'fabs' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
> 
> The full build log can be found at:
> http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/last-align_193-1_unstable-gcc47.log
> The last lines of the build log are at the end of this report.
> 
> Some hints on fixing these issues can be found at
> http://gcc.gnu.org/gcc-4.7/porting_to.html
> 
> To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
> 
> [...]
> gumbel_params/sls_alp_regression.cpp: In static member function 'static double ncbi::blast::Sls::alp_reg::function_for_robust_regression_sum_with_cut_LSM(double*, double*, Int4, Int4, double, double&, double&, double&, double&, bool&)':
> gumbel_params/sls_alp_regression.cpp:389:16: warning: unused variable 'a11_error' [-Wunused-variable]
> gumbel_params/sls_alp_regression.cpp:390:16: warning: unused variable 'a12_error' [-Wunused-variable]
> gumbel_params/sls_alp_regression.cpp:391:16: warning: unused variable 'a21_error' [-Wunused-variable]
> gumbel_params/sls_alp_regression.cpp:392:16: warning: unused variable 'a22_error' [-Wunused-variable]
> gumbel_params/sls_alp_regression.cpp: In static member function 'static void ncbi::blast::Sls::alp_reg::robust_regression_sum_with_cut_LSM_beta1_is_defined(Int4, Int4, double*, double*, bool, bool, double, double&, double, double&, double, Int4&, Int4&, bool&)':
> gumbel_params/sls_alp_regression.cpp:521:16: warning: variable 'beta1_opt' set but not used [-Wunused-but-set-variable]
> gumbel_params/sls_alp_regression.cpp:523:16: warning: variable 'beta1_opt_error' set but not used [-Wunused-but-set-variable]
> gumbel_params/sls_alp_regression.cpp: In static member function 'static double ncbi::blast::Sls::alp_reg::function_for_robust_regression_sum_with_cut_LSM_beta1_is_defined(double*, double*, Int4, Int4, double, double&, double, double&, double, bool&)':
> gumbel_params/sls_alp_regression.cpp:596:16: warning: unused variable 'a11_error' [-Wunused-variable]
> gumbel_params/sls_alp_regression.cpp:597:16: warning: unused variable 'a12_error' [-Wunused-variable]
> In file included from gumbel_params/sls_alp_regression.hpp:51:0,
>                  from gumbel_params/sls_alp_regression.cpp:38:
> gumbel_params/sls_alp_data.hpp: At global scope:
> gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
> gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
> gumbel_params/sls_alp_sim.cpp: In constructor 'ncbi::blast::Sls::alp_sim::alp_sim(ncbi::blast::Sls::alp_data*)':
> gumbel_params/sls_alp_sim.cpp:477:24: warning: unused variable 'memory_after2' [-Wunused-variable]
> gumbel_params/sls_alp_sim.cpp:724:24: warning: unused variable 'memory_after3' [-Wunused-variable]
> In file included from gumbel_params/sls_alp_sim.hpp:51:0,
>                  from gumbel_params/sls_alp_sim.cpp:39:
> gumbel_params/sls_alp_data.hpp: At global scope:
> gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
> In file included from gumbel_params/sls_pvalues.cpp:41:0:
> gumbel_params/sls_alp_data.hpp:74:21: warning: 'ncbi::blast::Sls::small_long' defined but not used [-Wunused-variable]
> gumbel_params/sls_alp_data.hpp:75:23: warning: 'ncbi::blast::Sls::dbl_max_log' defined but not used [-Wunused-variable]
> make[1]: *** [lastex] Error 1
> make[1]: Leaving directory `/??PKGBUILDDIR??/src'
> make: *** [debian/stamp-makefile-build] Error 2
> dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
> 
> 
> 

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-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan