Bug#804246: transition: gsl
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
Kind Regards,
Bas
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