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

Thu Apr 5 06:37:46 UTC 2012

Hi Charles,

many thanks for letting me know about this.  I believe the problem is fixed
in the latest LAST.  (I've also tried to improve the makefiles: not sure if
that will affect you.)

Have a nice day,
Martin

On Wed, Apr 4, 2012 at 1:24 PM, Charles Plessy <plessy at debian.org> wrote:

> 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
> >
> >
> >
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
>
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