Bug#804246: transition: gsl
On 23/11/15 01:46, Sebastiaan Couwenberg wrote:
> On 20-11-15 13:15, Emilio Pozuelo Monfort wrote:
>> On 20/11/15 12:57, Dirk Eddelbuettel wrote:
>>>
>>> On 20 November 2015 at 11:45, Sebastiaan Couwenberg wrote:
>>> | On 09-11-15 18:21, Emilio Pozuelo Monfort wrote:
>>> | > On 06/11/15 15:06, Bas Couwenberg wrote:
>>> | >> Package: release.debian.org
>>> | >> Severity: normal
>>> | >> User: release.debian.org@packages.debian.org
>>> | >> Usertags: transition
>>> | >> Forwarded: https://release.debian.org/transitions/html/auto-gsl.html
>>> | >>
>>> | >> An uncoordinated transition to GSL 2.0 has started in unstable.
>>> | >>
>>> | >> It caused nco to FTBFS and I suspect other reverse dependencies will
>>> | >> likewise need to be updated to build successfully with gsl (2.0+dfsg-1).
>>> | >>
>>> | >> The automatically created transition tracker is already available.
>>> | >>
>>> | >> The maintainer is CC'ed.
>>> | >
>>> | > Any idea how many packages fail to build against the new version? Not speaking
>>> | > of how many need to change the build dependencies from libgsl0-dev (>= x.y) to
>>> | > libgsl-dev, but of build failures in all the rdeps due to API changes.
>>> |
>>> | I haven't tested any gsl rdeps other than those maintained by the Debian
>>> | GIS team, and those rebuilds are already available in unstable.
>>> |
>>> | Can we binNMU the remaining rdeps and see what breaks?
>>>
>>> Sounds good to me.
>>
>> No, as I said that won't work as long as libgsl0-dev is still around, because
>> right now any build attempt will install that together with the old library,
>> instead of the new libgsl-dev and the new library. That's because real packages
>> are preferred over virtual ones.
>>
>> And I didn't want to request its removal until I know how many packages will
>> fail to build.
>>
>>> | Or should Dirk or someone else first rebuild the rdeps themselves before
>>> | this transition can move on?
>>>
>>> Do you happen to have a list of what has / has not rebuilt?
>>
>> See https://release.debian.org/transitions/html/gsl.html
>
> To keep this transition moving I've started a round of rebuilding the
> gsl rdeps to see what breaks.
>
>
> 3dldf (2.0.3+dfsg-3) explicitly build depends on libgsl0ldbl,
> libgsl0-dev which needs to be changed to just libgsl-dev to build with
> libgsl2. I've forwarded the patch in #805740.
>
> adun.app (0.81-7) only build depends on libgsl0-dev, but didn't pull in
> libgsl2. It built successfully with libgsl2 after changing the build
> dependency to libgsl-dev. Because of this all other reverse dependencies
> were also updated to use libgsl-dev instead of libgsl0-dev.
>
> aghermann (1.0.6-1) has the build dependency issue, and FTBFS after
> changing the build dependency to libgsl-dev with:
>
> model/borbely.cc:175:32: error: 'struct gsl_multifit_fdfsolver' has no
> member named 'J'
> gsl_multifit_covar( S->J, 0.0, covar);
> ^
> I've reported this build failure in #805746.
>
> amide (1.0.5-4) FTBFS due to the same issue as aghermann:
>
> tb_profile.c:671:31: error: 'gsl_multifit_fdfsolver
> {aka struct <anonymous>}' has no member named 'J'
> gsl_multifit_covar (solver->J, 0.0, covar);
> ^
> This is reported in #805748. And fixed with amide (1.0.5-5).
>
> Besides aghermann & amide, this common issue also affects:
>
> #805794 gbutils (5.6.7-1)
> #805799 kst (2.0.3-4)
> #805801 mathgl (2.3.3-3)
> #805819 odin (1.8.8-1.1)
> #805832 scidavis (1.D8-1)
> #805834 siril (0.9.0-1)
> #805835 voxbo (1.8.5~svn1246-1.1)
> #805841 qtiplot (0.9.8.9-10)
> #805842 ruby-gsl (1.16.0.4+dfsg1-1)
>
> altree (1.3.1-2) cannot be built after updating the build dependency to
> libgsl-dev, because some other dependency still pulls in libgsl0ldbl
> causing a conflict with libgsl2.
>
> asymptote (2.35-2) FTBFS too:
>
> gsl.cc: In function 'void trans::gen_rungsl_venv(trans::venv&)':
> gsl.cc:1091:67: error: no matching function for call to
> 'addGSLDOUBLE3Func(sym::symbol&, sym::symbol&, sym::symbol&,
> sym::symbol&)'
> addGSLDOUBLE3Func<gsl_sf_ellint_D>(SYM(D),SYM(phi),SYM(k),SYM(n));
> ^
> gsl.cc:192:6: note: candidate: template<double (* fcn)(double, double,
> double, gsl_mode_t)> void trans::addGSLDOUBLE3Func(sym::symbol,
> sym::symbol, sym::symbol, sym::symbol)
> void addGSLDOUBLE3Func(symbol name, symbol arg1, symbol arg2,
> ^
> gsl.cc:192:6: note: template argument deduction/substitution failed:
> gsl.cc:1091:67: error: could not convert template argument
> 'gsl_sf_ellint_D' to 'double (*)(double, double, double, gsl_mode_t)
> {aka double (*)(double, double, double, unsigned int)}'
> addGSLDOUBLE3Func<gsl_sf_ellint_D>(SYM(D),SYM(phi),SYM(k),SYM(n));
> ^
> Reported in #805749.
>
> ball (1.4.2+20140406-1.1) FTBFS due to a Boost issue, this seems to be
> #777791 and unrelated to GSL 2.
>
> calligra (1:2.8.5+dfsg-1.2) also FTBFS due to an issue unrelated to GSL
> 2, that seems to be #797389.
>
> gambas3 (3.5.4-2) FTBFS due to a WebKit issue:
>
> make[6]: Entering directory '/tmp/buildd/gambas3-3.5.4/gb.qt4
> /src/webkit'
> CXX gb_qt4_webkit_la-main.lo
> CXX gb_qt4_webkit_la-cwebsettings.lo
> CXX gb_qt4_webkit_la-cwebframe.lo
> main.cpp:31:21: fatal error: QDateTime: No such file or directory
>
> This is probably related to #784465.
>
> getdp (sid only) (2.4.2-1) FTBFS with make 4 as reported in #747109.
>
> mrtrix (0.2.12-1) FTBFS with type error:
>
> /usr/include/gsl/gsl_sf_legendre.h:323:33: error: 'size_t'
> does not name a type
> const size_t lmax, const double x,
> ^
> Reported in #805814.
>
> ocamlgsl (0.6.0-7) FTBFS
>
> mlgsl_fit.c:154:5: error: too many arguments to function
> 'gsl_multifit_linear_svd'
> gsl_multifit_linear_svd(&m_x, &v_y,
> ^
> Reported in #805818.
>
> openms (1.11.1-5) FTBFS due to arguments mismatch:
>
> source/ANALYSIS/MAPMATCHING/TransformationModel.C: In member function
> 'void OpenMS::TransformationModelBSpline::computeLinear_(double,
> double&, double&, double&)':
> source/ANALYSIS/MAPMATCHING/TransformationModel.C:366:70: error:
> too many arguments to function 'int gsl_bspline_deriv_eval(double,
> size_t, gsl_matrix*, gsl_bspline_workspace*)'
> gsl_bspline_deriv_eval(pos, 1, deriv, workspace_, deriv_workspace);
> ^
> In file included from
> include/OpenMS/ANALYSIS/MAPMATCHING/TransformationModel.h:40:0,
> source/ANALYSIS/MAPMATCHING/TransformationModel.C:35:
> /usr/include/gsl/gsl_bspline.h:107:1: note: declared here
> gsl_bspline_deriv_eval(const double x,
> ^
> Reported in #805823.
>
> pdl (1:2.007-4) FTBFS due to a similar issue:
>
> In file included from ELLINT.xs:39:0:
> ELLINT.xs: In function 'pdl_gsl_sf_ellint_D_readdata':
> ELLINT.xs:1720:8: error: too many arguments to function
> 'gsl_sf_ellint_D_e'
> GSLERR(gsl_sf_ellint_D_e,((phi_datap)[0] PDL_COMMENT("ACCESS()")
> ,(k_datap)[0] PDL_COMMENT("ACCESS()") ,(n_datap)[0]
> PDL_COMMENT("ACCESS()") ,GSL_PREC_DOUBLE,&r))
> ^
> Reported in #805824.
>
> r-cran-gsl (1.9-10-1) FTBFS at configure already:
>
> configure: error: Need GSL version >= 1.12
> ERROR: configuration failed for package 'gsl'
>
> Reported in #805829.
>
> root-system (5.34.19+dfsg-1.2) FTBFS due to unresolved GCC-5 issues
> (#778108).
>
> herwig++ (2.6.0-1) FTBFS due to missing /usr/lib/libgsl.a:
>
> checking for gsl location... not found
> configure: error: Can't find /usr/lib/libgsl.a or the headers in
> /usr/include
>
> Reported in #805844.
>
>
> Transition: gsl
>
> libgsl0ldbl (1.16+dfsg-4) -> libgsl2 (2.1+dfsg-1)
>
> The status of the most recent rebuilds is as follows.
>
> 3dldf (2.0.3+dfsg-3) OK
> adun.app (sid only) (0.81-7) OK
> aghermann (1.0.6-1) FTBFS
> altree (1.3.1-2) BD-Uninstallable
> amide (1.0.5-4) FTBFS
> ampliconnoise (1.29-2) OK
> apophenia (0.999e+ds-4) OK
> ardesia (sid only) (1.1-2) OK
> astrometry.net (0.64+dfsg-1) OK
> asymptote (2.35-2) FTBFS
> ball (sid only) (1.4.2+20140406-1.1) FTBFS
> bist (0.5.2-1) OK
> bogofilter (1.2.4+dfsg1-3) OK
> calligra (sid only) (1:2.8.5+dfsg-1.2) FTBFS
> chemps2 (1.6-1) OK
> clonalframe (1.2-3) OK
> cnrun (1.1.14-1) OK
> comedilib (0.10.2-3) OK
> cpl-plugin-fors (5.1.4+dfsg-1) OK
> cpl-plugin-hawki (1.8.18+dfsg-4) OK
> cpl-plugin-naco (4.4.1+dfsg-1) OK
> cpl-plugin-vimos (3.0.6+dfsg-3) OK
> cvxopt (1.1.4-1.3) OK
> dieharder (3.31.1-4) OK
> dynare (4.4.3-2) OK
> ea-utils (sid only) (1.1.2+dfsg-1) OK
> enblend-enfuse (4.1.4+dfsg-2) OK
> flowgrind (0.7.5-1) OK
> freefem++ (3.38.1-1) OK
> gambas3 (sid only) (3.5.4-2) FTBFS
> gbutils (5.6.7-1) FTBFS
> getdp (sid only) (2.4.2-1) FTBFS
> gjay (0.3.2-1.1) OK
> gnudatalanguage (sid only) (0.9.5-3) OK
> gpsshogi (sid only) (0.6.0-3+nmu1) OK
> guvcview (2.0.2+debian-1) OK
> hkl (4.99.99.1955-1) OK
> inkscape (0.91-6) OK
> kst (2.0.3-4) FTBFS
> libgpiv (0.6.1-4.2) OK
> libindi (1.0.0-3) OK
> luminance-hdr (2.4.0-6) OK
> mathgl (2.3.3-3) FTBFS
> meep (1.3-3) OK
> meep-lam4 (1.3-1) OK
> meep-mpi-default (1.3-2) OK
> meep-mpich2 (1.3-2) OK
> meep-openmpi (1.3-2) OK
> mia (2.2.7-1) OK
> mlpy (2.2.0~dfsg1-3) OK
> mrtrix (0.2.12-1) FTBFS
> ngraph-gtk (6.06.13-5) OK
> nip2 (8.0-1) OK
> ns3 (3.22+dfsg-1) OK
> ocamlgsl (0.6.0-7) FTBFS
> octave-gsl (1.0.8-6) OK
> odin (sid only) (1.8.8-1.1) FTBFS
> openms (sid only) (1.11.1-5) FTBFS
> pdl (1:2.007-4) FTBFS
> pdp (1:0.14.1-2) OK
> pfstools (2.0.4-4) OK
> proftmb (1.1.12-2) OK
> pspp (0.8.5-4) OK
> pyxplot (0.9.2-5) OK
> r-cran-gsl (1.9-10-1) FTBFS
> rivet (sid only) (1.8.3-1.2) OK
> root-system (sid only) (5.34.19+dfsg-1.2) FTBFS
> saint (2.5.0+dfsg-1) OK
> scidavis (sid only) (1.D8-1) FTBFS
> sip-tester (1:3.2-1) OK
> siril (0.9.0-1) FTBFS
> slgsl (sid only) (0.7.0-5.2) OK
> step (4:15.08.0-3) OK
> tamuanova (0.2-3) OK
> theseus (3.3.0-3) OK
> visp (2.10.0+dfsg-1) OK
> votca-tools (sid only) (1.2.4-1) OK
> voxbo (1.8.5~svn1246-1.1) FTBFS
> xaos (3.5+ds1-2) OK
>
> 3depict (sid only) (0.0.18-2) BD-Uninstallable
> gpiv (sid only) (0.6.1-2.3) OK
> gpivtools (sid only) (0.6.0-3.1) OK
> libpdl-stats-perl (0.6.5.1-1) BD-Uninstallable
> orpie (1.5.1-10) BD-Uninstallable
> psi4 (1:0.3-3) OK
> qtiplot (0.9.8.9-10) FTBFS
> ruby-gsl (sid only) (1.16.0.4+dfsg1-1) FTBFS
> thepeg (sid only) (1.8.0-1) OK
>
> herwig++ (sid only) (2.6.0-1) FTBFS
>
Would 2.1+dfsg-2 help in any way? From the changelog it sounds like it could.
Cheers,
Emilio
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