Control: tags -1 patch
On 22-11-15 21:06, Bas Couwenberg wrote:
> Your package fails to build with GSL 2:
>
> fitting.cpp: In member function 'virtual bool
> FunctionFitDerivative::fit(const blitz::Array<float, 1>&, const
> blitz::Array<float, 1>&, const blitz::Array<float, 1>&, unsigned int,
> double)':
> fitting.cpp:222:40: error: 'struct gsl_multifit_fdfsolver' has no member
> named 'J'
> gsl_multifit_covar (gsldata->solver->J, 0.0, gsldata->covar);
> ^
>
> This needs to be fixed for the ongoing gsl transition (#804246).
>
> The full build log is attached, as is a patch to update the build
> dependencies for GSL 2 (changing libgsl0-dev to libgsl-dev).
The attached debdiff includes a patch with the GSL 2 related changes
from the upstream VCS in addition to the updated dependencies.
http://sourceforge.net/p/od1n/code/8551/
With the updated dependencies and the changes in gsl-2.patch, odin
builds successfully with libgsl2.
Please include the changes from the debdiff in the next upload.
Also consider using dh-autoreconf to automatically regenerate the build
system, so you don't need to patch generated files as was required for
the gsl-2.patch.
https://wiki.debian.org/Autoreconf
Kind Regards,
Bas
--
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diff -Nru odin-1.8.8/debian/changelog odin-1.8.8/debian/changelog
--- odin-1.8.8/debian/changelog 2015-09-16 16:30:32.000000000 +0200
+++ odin-1.8.8/debian/changelog 2015-12-04 14:15:17.000000000 +0100
@@ -1,3 +1,11 @@
+odin (1.8.8-1.2) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Update build dependencies for GSL 2, change libgsl0-dev to libgsl-dev.
+ * Add patch for GSL 2 support.
+
+ -- Bas Couwenberg <sebas...@debian.org> Sun, 22 Nov 2015 20:37:25 +0100
+
odin (1.8.8-1.1) unstable; urgency=medium
* Non-maintainer upload.
diff -Nru odin-1.8.8/debian/control odin-1.8.8/debian/control
--- odin-1.8.8/debian/control 2014-10-09 08:42:34.000000000 +0200
+++ odin-1.8.8/debian/control 2015-12-03 15:39:55.000000000 +0100
@@ -6,7 +6,7 @@
Yaroslav Halchenko <deb...@onerussian.com>
Build-Depends: debhelper (>= 7.0.50~),
autotools-dev,
- libgsl0-dev,
+ libgsl-dev,
libblitz0-dev (>= 0.8) | libblitz-dev,
libnifti-dev,
libvtk5-dev,
@@ -26,7 +26,7 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
libodin-dev,
- libgsl0-dev,
+ libgsl-dev,
libc6-dev | libc-dev,
g++,
libblas-dev | libatlas-base-dev,
diff -Nru odin-1.8.8/debian/patches/gsl-2.patch
odin-1.8.8/debian/patches/gsl-2.patch
--- odin-1.8.8/debian/patches/gsl-2.patch 1970-01-01 01:00:00.000000000
+0100
+++ odin-1.8.8/debian/patches/gsl-2.patch 2015-12-04 13:36:49.000000000
+0100
@@ -0,0 +1,126 @@
+Description: porting to GSL2
+Origin: http://sourceforge.net/p/od1n/code/8551/
+Bug-Debian: https://bugs.debian.org/805819
+
+--- a/odindata/fitting.cpp
++++ b/odindata/fitting.cpp
+@@ -107,6 +107,7 @@ int FunctionFitDerivative_func_fdf (cons
+
+
+ bool FunctionFitDerivative::init(ModelFunction& model_func, unsigned int
nvals) {
++ Log<OdinData> odinlog("FunctionFitDerivative","init");
+
+ data4fit= new ModelData(nvals);
+
+@@ -114,8 +115,10 @@ bool FunctionFitDerivative::init(ModelFu
+
+ gsldata=new GslData4Fit;
+
+- // allocate and initialize GSL stuff
+ unsigned int npars=model_func.numof_fitpars();
++ ODINLOG(odinlog,normalDebug) << "npars=" << npars << STD_endl;
++
++ // allocate and initialize GSL stuff
+ gsldata->covar = gsl_matrix_alloc (npars, npars);
+ gsldata->solver = gsl_multifit_fdfsolver_alloc
(gsl_multifit_fdfsolver_lmsder, data4fit->n, npars);
+
+@@ -164,7 +167,7 @@ bool FunctionFitDerivative::fit(const Ar
+
+ ModelFunction* func=data4fit->modelfunc;
+ unsigned int npars=func->numof_fitpars();
+- ODINLOG(odinlog,normalDebug) << "n/numof_fitpars=" << data4fit->n << "/" <<
npars << STD_endl;
++ ODINLOG(odinlog,normalDebug) << "n/npars=" << data4fit->n << "/" << npars
<< STD_endl;
+
+ // copy Blitz arrays to data4fit
+ for (unsigned long i=0;i<data4fit->n;i++) {
+@@ -219,7 +222,30 @@ bool FunctionFitDerivative::fit(const Ar
+ return false;
+ }
+
+- gsl_multifit_covar (gsldata->solver->J, 0.0, gsldata->covar);
++
++ gsl_matrix* J=0;
++#ifdef HAVE_GSL_MULTIFIT_FDFSOLVER_JAC // for GSL2
++ ODINLOG(odinlog,normalDebug) << "solver->f->size=" <<
gsldata->solver->f->size << STD_endl;
++ ODINLOG(odinlog,normalDebug) << "solver->x->size=" <<
gsldata->solver->x->size << STD_endl;
++ J = gsl_matrix_alloc(gsldata->solver->f->size, gsldata->solver->x->size);
++ status = gsl_multifit_fdfsolver_jac(gsldata->solver, J);
++ if(status!=GSL_SUCCESS) {
++ ODINLOG(odinlog,errorLog) << gsl_strerror(status) << STD_endl;
++ return false;
++ }
++#else // pre GSL2
++ J=gsldata->solver->J;
++#endif
++
++ status = gsl_multifit_covar(J, 0.0, gsldata->covar);
++ if(status!=GSL_SUCCESS) {
++ ODINLOG(odinlog,errorLog) << gsl_strerror(status) << STD_endl;
++ return false;
++ }
++
++#ifdef HAVE_GSL_MULTIFIT_FDFSOLVER_JAC // for GSL2
++ gsl_matrix_free(J);
++#endif
+
+ // copy results
+ for(unsigned int i=0;i<npars;i++) {
+--- a/configure.in
++++ b/configure.in
+@@ -281,14 +281,14 @@ else
+ dnl GSL is used in tjutils and odindata so we add it to the global LIBS
+ valid_gsl=yes
+ AC_CHECK_LIB(gslcblas,main,LIBS="-lgslcblas $LIBS"; BASELIBS="-lgslcblas
$BASELIBS")
+- AC_CHECK_LIB(gsl,gsl_multifit_fdfsolver_iterate,BASELIBS="-lgsl
$BASELIBS",valid_gsl=no)
++ AC_CHECK_LIB(gsl,gsl_multifit_fdfsolver_iterate,LIBS="-lgsl $LIBS";
BASELIBS="-lgsl $BASELIBS",valid_gsl=no)
+ AC_CHECK_HEADER(gsl/gsl_multifit_nlin.h,,valid_gsl=no)
+ AC_CHECK_HEADER(gsl/gsl_multimin.h,,valid_gsl=no)
+ if test "x$valid_gsl" = "xno" ; then
+ AC_MSG_ERROR([Please install the GNU Scientific Library (There is
probably a precompiled package for your UNIX/Linux distribution, otherwise see
http://www.gnu.org/software/gsl)])
+ fi
+
AC_CHECK_DECL(gsl_multimin_fminimizer_nmsimplex2,have_gsl_multimin_fminimizer_nmsimplex2=yes,,[#include
<gsl/gsl_multimin.h>])
+-
++ AC_CHECK_FUNCS(gsl_multifit_fdfsolver_jac)
+
+ if test "x$macos" = "xyes" ; then
+ AC_MSG_NOTICE([Using vecLib for lapack support])
+--- a/configure
++++ b/configure
+@@ -15891,7 +15891,7 @@ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result:
$ac_cv_lib_gsl_gsl_multifit_fdfsolver_iterate" >&5
+ $as_echo "$ac_cv_lib_gsl_gsl_multifit_fdfsolver_iterate" >&6; }
+ if test "x$ac_cv_lib_gsl_gsl_multifit_fdfsolver_iterate" = xyes; then :
+- BASELIBS="-lgsl $BASELIBS"
++ LIBS="-lgsl $LIBS"; BASELIBS="-lgsl $BASELIBS"
+ else
+ valid_gsl=no
+ fi
+@@ -15921,6 +15921,16 @@ if test "x$ac_cv_have_decl_gsl_multimin_
+ have_gsl_multimin_fminimizer_nmsimplex2=yes
+ fi
+
++ for ac_func in gsl_multifit_fdfsolver_jac
++do :
++ ac_fn_cxx_check_func "$LINENO" "gsl_multifit_fdfsolver_jac"
"ac_cv_func_gsl_multifit_fdfsolver_jac"
++if test "x$ac_cv_func_gsl_multifit_fdfsolver_jac" = xyes; then :
++ cat >>confdefs.h <<_ACEOF
++#define HAVE_GSL_MULTIFIT_FDFSOLVER_JAC 1
++_ACEOF
++
++fi
++done
+
+
+ if test "x$macos" = "xyes" ; then
+--- a/tjutils/config.h.in
++++ b/tjutils/config.h.in
+@@ -81,6 +81,9 @@
+ /* Define to 1 if you have the `gettimeofday' function. */
+ #undef HAVE_GETTIMEOFDAY
+
++/* Define to 1 if you have the `gsl_multifit_fdfsolver_jac' function. */
++#undef HAVE_GSL_MULTIFIT_FDFSOLVER_JAC
++
+ /* "existence of newer gsl_multimin_fminimizer_nmsimplex2 algorithm" */
+ #undef HAVE_GSL_MULTIMIN_FMINIMIZER_NMSIMPLEX2
+
diff -Nru odin-1.8.8/debian/patches/series odin-1.8.8/debian/patches/series
--- odin-1.8.8/debian/patches/series 2015-09-16 16:29:42.000000000 +0200
+++ odin-1.8.8/debian/patches/series 2015-12-03 15:07:52.000000000 +0100
@@ -1 +1,2 @@
ld-as-needed.diff
+gsl-2.patch
