Bug#811800: fityk: FTBFS with GCC 6: error: reference is ambiguous

2016-11-06 Thread Stuart Prescott 

Hi Carlo,

> I would be happy to pass this to the Debian Science team.  My professional
> responsibilities have taken away much of the time I had to work on my
> packages.  I always hope that I can set aside some time but it never seems
> to be possible.

Sure, I understand how that happens. I'll import the historical packages into 
git within the Debian Science team and include you in Uploaders since it would 
be great to keep you involved!

cheers
Stuart

-- 
Stuart Prescotthttp://www.nanonanonano.net/   stu...@nanonanonano.net
Debian Developer   http://www.debian.org/ stu...@debian.org
GPG fingerprint90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7

Bug#811800: fityk: FTBFS with GCC 6: error: reference is ambiguous

2016-11-06 Thread Carlo Segre 


Hi Stuart:

I would be happy to pass this to the Debian Science team.  My professional 
responsibilities have taken away much of the time I had to work on my 
packages.  I always hope that I can set aside some time but it never seems 
to be possible.


Carlo

On Sun, 6 Nov 2016, Stuart Prescott wrote:


Dear Carlo,

As an alternative to the patch from Graham Inggs, this bug (and a few others)
could all be fixed by updating to the 1.3.0 release.

I attach a diff that would update to the current upstream release as well as fix
a few other bits and pieces within the packaging.

Thoughts?

(BTW I see it's been a long time since you uploaded this package -- would you
be interested co-maintaining it along with the Debian Science team?)

regards
Stuart




--
Carlo U. Segre -- Duchossois Leadership Professor of Physics
Interim Chair, Department of Chemistry
Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org

Bug#811800: fityk: FTBFS with GCC 6: error: reference is ambiguous

2016-11-06 Thread Stuart Prescott 
Dear Carlo,

As an alternative to the patch from Graham Inggs, this bug (and a few others) 
could all be fixed by updating to the 1.3.0 release.

I attach a diff that would update to the current upstream release as well as 
fix 
a few other bits and pieces within the packaging.

Thoughts?

(BTW I see it's been a long time since you uploaded this package -- would you 
be interested co-maintaining it along with the Debian Science team?)

regards
Stuart

-- 
Stuart Prescotthttp://www.nanonanonano.net/   stu...@nanonanonano.net
Debian Developer   http://www.debian.org/ stu...@debian.org
GPG fingerprint90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7--- fityk-1.2.1/debian/changelog	2014-01-02 09:44:24.0 +1100
+++ fityk-1.3.0/debian/changelog	2016-11-06 16:20:37.0 +1100
@@ -1,3 +1,24 @@
+fityk (1.3.0-0.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * New upstream release (Closes: #747161):
+- Builds successfully with GCC 6 (Closes: #811800).
+  * Update build system to suit new upstream:
+- Remove no-longer-needed compiler/linker FLAGS setting (Closes: #735777)
+- Update build-dependencies on lua
+- Add build-dependency on
+- 'swig' to build bindings
+- 'check' to run tests
+- 'texlive-latex-*', 'sphinx', 'dvipng' to build documentation
+  * Switch to debhelper compat level 10, allowing debhelper to do the necessary
+autoreconf automatically (Closes: #744571)
+  * Move d/upstream to d/upstream/metadata
+  * Fix watch file to correctly find new releases.
+  * Bump Standards-Version to 3.9.8 (no changes required).
+  * Drop no-longer-needed menu file as per #741573.
+
+ -- Stuart Prescott   Sun, 06 Nov 2016 16:20:37 +1100
+
 fityk (1.2.1-0.1) unstable; urgency=low
 
   * Non-maintainer upload.
--- fityk-1.2.1/debian/compat	2010-05-09 05:47:59.0 +1000
+++ fityk-1.3.0/debian/compat	2016-11-06 16:20:37.0 +1100
@@ -1 +1 @@
-7
+10
--- fityk-1.2.1/debian/control	2014-01-02 04:40:54.0 +1100
+++ fityk-1.3.0/debian/control	2016-11-06 16:20:37.0 +1100
@@ -2,17 +2,23 @@
 Section: science
 Priority: optional
 Maintainer: Carlo Segre 
-Build-Depends: autotools-dev (>> 20100122.1~),
-   debhelper (>> 7),
+Build-Depends: catch,
+   debhelper (>> 10),
+   dvipng,
libboost-dev,
libbz2-dev,
-   liblua5.1-0-dev,
+   liblua5.2-dev,
libreadline-dev,
libwxgtk3.0-dev,
libxy-dev,
+   lua5.2,
+   python3-sphinx,
+   swig,
+   texlive-latex-extra,
+   texlive-latex-recommended,
zlib1g-dev
 Homepage: http://fityk.nieto.pl/
-Standards-Version: 3.9.5
+Standards-Version: 3.9.8
 
 Package: fityk
 Architecture: any
--- fityk-1.2.1/debian/docs	2010-05-09 04:58:55.0 +1000
+++ fityk-1.3.0/debian/docs	2016-11-06 16:20:37.0 +1100
@@ -1,3 +1,3 @@
-README
+README.md
 debian/README.Debian
 TODO
--- fityk-1.2.1/debian/menu	2010-05-09 04:58:55.0 +1000
+++ fityk-1.3.0/debian/menu	1970-01-01 10:00:00.0 +1000
@@ -1,6 +0,0 @@
-?package(fityk):needs="X11"\
-		section="Applications/Science/Data Analysis"	\
-		title="fityk"\
-		command="/usr/bin/fityk"		\
-		icon="/usr/share/pixmaps/fityk.xpm"
-
--- fityk-1.2.1/debian/rules	2014-01-02 04:38:10.0 +1100
+++ fityk-1.3.0/debian/rules	2016-11-06 16:20:37.0 +1100
@@ -1,20 +1,16 @@
 #!/usr/bin/make -f
 
-CPPFLAGS ?= $(shell dpkg-buildflags --get CPPFLAGS) -I/usr/include/lua5.1
-CFLAGS   ?= $(shell dpkg-buildflags --get CFLAGS)
-CXXFLAGS ?= $(shell dpkg-buildflags --get CXXFLAGS)
-LDFLAGS  ?= -lstdc++ $(shell dpkg-buildflags --get LDFLAGS) # -Wl,--as-needed
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@ --with autotools_dev --parallel
+	dh $@ --buildsystem=autoconf --parallel
 
 override_dh_auto_configure:
-	dh_auto_configure -- --disable-shared --enable-static \
-	 --disable-xyconvert --with-lua-suffix=5.1 \
-	 CPPFLAGS="$(CPPFLAGS)" \
-	 CFLAGS="$(CFLAGS)" \
-	 CXXFLAGS="$(CXXFLAGS)" \
-	 LDFLAGS="$(LDFLAGS)"
+	dh_auto_configure -- --disable-shared --enable-static
+
+override_dh_auto_build:
+	dh_auto_build
+	make -C doc html
 
 override_dh_auto_install:
 	dh_auto_install
--- fityk-1.2.1/debian/watch	2011-03-24 18:00:05.0 +1100
+++ fityk-1.3.0/debian/watch	2016-11-06 16:20:37.0 +1100
@@ -1,3 +1,3 @@
 version=3
-https://github.com/wojdyr/fityk/downloads \
-  /downloads/wojdyr/fityk/fityk-(.*)\.tar\.bz2
+opts=filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/fityk-$1\.tar\.gz/ \
+  https://github.com/wojdyr/fityk/tags .*/v?(\d\S+)\.tar\.gz

Bug#811800: fityk: FTBFS with GCC 6: error: reference is ambiguous

2016-09-26 Thread Graham Inggs 

Control: tags -1 patch


Hi Maintainer

The attached patch fixes the FTBFS with GCC 6.

Regards
Graham

Description: Fix FTBFS with GCC 6
Forwarded: no
Bug-Debian: https://bugs.debian.org/811800
Author: Graham Inggs 
Last-Update: 2016-09-26
--- a/fityk/guess.cpp
+++ b/fityk/guess.cpp
@@ -20,9 +20,9 @@
 
 namespace fityk {
 
-const array Guess::linear_traits =
+const boost::array Guess::linear_traits =
 {{ "slope", "intercept", "avgy" }};
-const array Guess::peak_traits =
+const boost::array Guess::peak_traits =
 {{ "center", "height", "hwhm", "area" }};
 
 Guess::Guess(Settings const *settings) : settings_(settings)
@@ -105,7 +105,7 @@
 
 // outputs vector with: center, height, hwhm, area
 // returns values corresponding to peak_traits
-array Guess::estimate_peak_parameters()
+boost::array Guess::estimate_peak_parameters()
 {
 // find the highest point, which must be higher than the previous point
 // and not lower than the next one (-> it cannot be the first/last point)
@@ -132,11 +132,11 @@
 double center = xx_[pos];
 double area;
 double hwhm = find_hwhm(pos, ) * settings_->width_correction;
-array r = {{ center, height, hwhm, area }};
+boost::array r = {{ center, height, hwhm, area }};
 return r;
 }
 
-array Guess::estimate_linear_parameters()
+boost::array Guess::estimate_linear_parameters()
 {
 double sx = 0, sy = 0, sxx = 0, /*syy = 0,*/ sxy = 0;
 int n = yy_.size();
@@ -152,7 +152,7 @@
 double slope = (n * sxy - sx * sy) / (n * sxx - sx * sx);
 double intercept = (sy - slope * sx) / n;
 double avgy = sy / n;
-array r = {{ slope, intercept, avgy }};
+boost::array r = {{ slope, intercept, avgy }};
 return r;
 }
 
--- a/wxgui/frame.cpp
+++ b/wxgui/frame.cpp
@@ -1028,7 +1028,7 @@
 return;
 }
 try {
-shared_ptr d =
+std::tr1::shared_ptr d =
 xylib::cached_load_file(f, "", "");
 if (d->get_block_count() > 1) {
 wxArrayString choices;

Bug#811800: fityk: FTBFS with GCC 6: error: reference is ambiguous

2016-01-19 Thread Martin Michlmayr 
Package: fityk
Version: 1.2.1-0.1
Severity: important
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-6 gcc-6-reference-ambiguous

This package fails to build with GCC 6.  GCC 6 has not been released
yet, but it's expected that GCC 6 will become the default compiler for
stretch.

Note that only the first error is reported; there might be more.  You
can find a snapshot of GCC 6 in experimental.  To build with GCC 6,
you can set CC=gcc-6 CXX=g++-6 explicitly.

You may be able to find out more about this issue at
https://gcc.gnu.org/gcc-6/changes.html

> sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
> 
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time 
> -D_FORTIFY_SOURCE=2 -I/usr/include/lua5.1 -g -O2 -fstack-protector-strong 
> -Wformat -Werror=format-security -c swig/fityk_lua.cpp -o 
> swig/libfityk_la-fityk_lua.o
> /bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..  
>  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/lua5.1  -g -O2 
> -fstack-protector-strong -Wformat -Werror=format-security -c -o 
> cmpfit/libfityk_la-mpfit.lo `test -f 'cmpfit/mpfit.c' || echo 
> './'`cmpfit/mpfit.c
> mgr.cpp: In member function 'int 
> fityk::VariableManager::add_variable(fityk::Variable*)':
> mgr.cpp:251:5: warning: 'template class std::auto_ptr' is deprecated 
> [-Wdeprecated-declarations]
>  auto_ptr var(new_var);
>  ^~~~
> 
> In file included from /usr/include/c++/6/memory:81:0,
>  from /usr/include/boost/config/no_tr1/memory.hpp:21,
>  from /usr/include/boost/smart_ptr/shared_ptr.hpp:23,
>  from /usr/include/boost/shared_ptr.hpp:17,
>  from tplate.h:9,
>  from mgr.h:9,
>  from mgr.cpp:5:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
>template class auto_ptr;
> ^~~~
> 
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 
> -D_FORTIFY_SOURCE=2 -I/usr/include/lua5.1 -g -O2 -fstack-protector-strong 
> -Wformat -Werror=format-security -c cmpfit/mpfit.c -o 
> cmpfit/libfityk_la-mpfit.o
> logic.cpp: In member function 'void fityk::Ftk::import_dataset(int, const 
> string&, const string&, const string&)':
> logic.cpp:234:13: warning: 'template class std::auto_ptr' is 
> deprecated [-Wdeprecated-declarations]
>  auto_ptr data(new Data(this));
>  ^~~~
> 
> In file included from /usr/include/c++/6/memory:81:0,
>  from /usr/include/boost/smart_ptr/scoped_ptr.hpp:21,
>  from /usr/include/boost/scoped_ptr.hpp:14,
>  from logic.h:8,
>  from logic.cpp:5:
> /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
>template class auto_ptr;
> ^~~~
> 
> guess.cpp:23:7: error: reference to 'array' is ambiguous
>  const array Guess::linear_traits =
>^
> 
> In file included from guess.h:9:0,
>  from guess.cpp:5:
> /usr/include/boost/array.hpp:60:11: note: candidates are: template long unsigned int N> class boost::array
>  class array {
>^
> 
> In file included from /usr/include/c++/6/tuple:39:0,
>  from /usr/include/c++/6/functional:55,
>  from /usr/include/c++/6/memory:79,
>  from model.h:9,
>  from guess.cpp:12:
> /usr/include/c++/6/array:90:12: note: template long unsigned int _Nm> struct std::array
>  struct array
> ^
> 
> guess.cpp:25:7: error: reference to 'array' is ambiguous
>  const array Guess::peak_traits =
>^
> 
> In file included from guess.h:9:0,
>  from guess.cpp:5:
> /usr/include/boost/array.hpp:60:11: note: candidates are: template long unsigned int N> class boost::array
>  class array {
>^
> 
> In file included from /usr/include/c++/6/tuple:39:0,
>  from /usr/include/c++/6/functional:55,
>  from /usr/include/c++/6/memory:79,
>  from model.h:9,
>  from guess.cpp:12:
> /usr/include/c++/6/array:90:12: note: template long unsigned int _Nm> struct std::array
>  struct array
> ^
> 
> guess.cpp:108:1: error: reference to 'array' is ambiguous
>  array Guess::estimate_peak_parameters()
>  ^
> 
> In file included from guess.h:9:0,
>  from guess.cpp:5:
> /usr/include/boost/array.hpp:60:11: note: candidates are: template long unsigned int N> class boost::array
>  class array {
>^
> 
> In file included from /usr/include/c++/6/tuple:39:0,
>  from /usr/include/c++/6/functional:55,
>  from /usr/include/c++/6/memory:79,
>  from model.h:9,
>  from guess.cpp:12:
> /usr/include/c++/6/array:90:12: note: template long unsigned int