Bug#895506: apertium-swe-nor FTBFS: test failure

[Adrian Bunk]

Source: apertium-swe-nor
Version: 0.2.0~r69544-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/apertium-swe-nor.html

...
   dh_auto_test -O--fail-missing
make -j1 test VERBOSE=1
make[1]: Entering directory '/build/1st/apertium-swe-nor-0.2.0~r69544'
echo "Såg hon inte orden?" | apertium -d . swe-nno | tee .test-mt
Såg kummen ikkje orda?
1c1
< Såg ho ikkje orda?
---
> Såg kummen ikkje orda?
make[1]: *** [Makefile:878: test] Error 1
-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#895492: tiemu FTBFS: error: macro "abort" passed 1 arguments, but takes just 0

[Adrian Bunk]

Source: tiemu
Version: 3.04~git20110801-nogdb+dfsg-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/tiemu.html

...
gcc -I.. -I -DPREFIX=\"/usr\" -I. -I./core -I./core/uae -I./core/ti_hw 
-I./core/ti_sw -I./core/dbg -I./sound -I./gui -I./gui/calc -I./gui/debugger 
-I./ipc/dcop -I./ipc/dbus -I./ipc/com -I./kde -I./misc -DHAVE_CONFIG_H 
-DSHARE_DIR=\"/usr/share/tiemu\" -DLOCALEDIR=\"/usr/share/locale\" -c -g -O2 
-fstack-protector-strong -Wformat -Werror=format-security -D__LINUX__ 
-fvisibility=hidden -DGTK_DISABLE_DEPRECATED -DDEBUGGER -DNO_GDB 
-I/usr/include/tilp2 -I/usr/include/glib-2.0 
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/tilp2 
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include 
-I/usr/include/tilp2 -I/usr/include/glib-2.0 
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/tilp2 
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include 
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -pthread 
-I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include 
-I/usr/include/gio-unix-2.0/ -I/usr/include/cairo -I/usr/include/pango-1.0 
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 
-I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/pango-1.0 
-I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi 
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -pthread 
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 
-I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/gio-unix-2.0/ 
-I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 
-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz 
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0 
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi 
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 
-I/usr/include/libxml2 -I/usr/include/SDL -D_GNU_SOURCE=1 -D_REENTRANT  
core/state.c -o core/state.o
In file included from /usr/include/glib-2.0/glib/gutils.h:306:0,
 from /usr/include/glib-2.0/glib/gthread.h:34,
 from /usr/include/glib-2.0/glib/gasyncqueue.h:32,
 from /usr/include/glib-2.0/glib.h:32,
 from core/ti68k_def.h:39,
 from core/ti68k_int.h:31,
 from core/state.c:39:
/usr/include/stdlib.h:588:24: error: macro "abort" passed 1 arguments, but 
takes just 0
 extern void abort (void) __THROW __attribute__ ((__noreturn__));
^

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#895215: cypari2 FTBFS with dh-python >= 3.20180313

[Adrian Bunk]

Source: cypari2
Version: 1.1.4-2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/cypari2.html

...
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/1st/cypari2-1.1.4'
python2 tests/rundoctest.py
Traceback (most recent call last):
  File "tests/rundoctest.py", line 16, in 
import cypari2
  File "/build/1st/cypari2-1.1.4/cypari2/__init__.py", line 1, in 
from .pari_instance import Pari
ImportError: No module named pari_instance
make[1]: *** [debian/rules:16: override_dh_auto_test] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#895068: freecad does not start : "Illegal Instruction" returned

[Adrian Bunk]

Control: reassign -1 src:xerces-c 3.1.4+debian-2
Control: retitle -1 xerces-c: baseline violation on i386
Control: affects -1 freecad

On Sat, Apr 07, 2018 at 12:30:26AM +0200, Giuliano Cabrele wrote:
> Package: freecad
> Version: 0.16+dfsg2-3
> Severity: grave
> Justification: renders package unusable
> 
> Dear Maintainer,
> 
> A freshly installed Freecad did not start when launched from Xfce desktop.
> Trying to start from terminal produced the warning "Illegal Instruction" and 
> stop of the program.  
> The dmsg returns just a line:
> traps: freecad[12387] trap invalid opcode ip:b651da3d sp:bf9062e8 error:0
>   in libxerces-c-3.1.so[b62ab000+34a000].
> Thanks for the attention
>...

Thanks for your report, the root cause is that the --disable-sse2 was 
lost at some point in xerces-c, and the packages in stable and unstable
are therefore violating the i386 baseline due to using SSE2.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#894699: ros-rosinstall FTBFS with ros-wstool 0.1.17-1

[Adrian Bunk]

Source: ros-rosinstall
Version: 0.7.7-6
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ros-rosinstall.html

...
==
ERROR: test_info_only (test.local.test_rosws.RosWsTest)
--
Traceback (most recent call last):
  File "test/local/test_rosws.py", line 259, in test_info_only
self.assertEqual(0, cli.cmd_info(workspace, ['--only=localname']))
  File "rosinstall/rosws_cli.py", line 335, in cmd_info
localnames=args)
TypeError: get_info_table_raw_csv() takes exactly 4 arguments (3 given)

--
Ran 53 tests in 559.163s

FAILED (errors=1)
[ros] Fetching /tmp/tmp1OXbvj/ros (version None) to /tmp/tmp1OXbvj/ws7/ros
[ros] Done.
[gitrepo] Fetching /tmp/tmp1OXbvj/gitrepo (version None) to 
/tmp/tmp1OXbvj/ws7/gitrepo
[gitrepo] Done.
(Over-)Writing setup.sh, setup.bash, and setup.zsh in /tmp/tmp1OXbvj/ws7

rosinstall update complete.

Type 'source /tmp/tmp1OXbvj/ws7/setup.bash' to change into this environment. 
Add that source command to the bottom of your ~/.bashrc to set it up every time 
you log in.

If you are not using bash please see 
http://www.ros.org/wiki/rosinstall/NonBashShells 
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd 
/build/1st/ros-rosinstall-0.7.8/.pybuild/cpython2_2.7_rosinstall/build; 
python2.7 -m unittest discover -v 
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
make: *** [debian/rules:7: build] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Accepted r-cran-mi 1.0-4+deb9u1 (source) into proposed-updates->stable-new, proposed-updates

[Adrian Bunk]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 13 Mar 2018 21:53:01 +0200
Source: r-cran-mi
Binary: r-cran-mi
Architecture: source
Version: 1.0-4+deb9u1
Distribution: stretch
Urgency: medium
Maintainer: Debian Science Team 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Adrian Bunk <b...@debian.org>
Description:
 r-cran-mi  - GNU R package for Missing Data Imputation and Model Checking -- m
Closes: 877433
Changes:
 r-cran-mi (1.0-4+deb9u1) stretch; urgency=medium
 .
   * Non-maintainer upload.
   * Add the missing dependency on r-cran-arm. (Closes: #877433)
Checksums-Sha1:
 48e25a3e453c8c73095a4fa82dbac15797cf49ac 2042 r-cran-mi_1.0-4+deb9u1.dsc
 cd289f2b78eae7b91e80edb78ea656a7b8f28a0a 1872 
r-cran-mi_1.0-4+deb9u1.debian.tar.xz
Checksums-Sha256:
 64ba70be2d2999d84f173fcf635e795912a0709af6b33f5c0a3edc08360493d2 2042 
r-cran-mi_1.0-4+deb9u1.dsc
 17101211e189eec04d5eff5fc178e67d5d8eab6afdde170423d04cd1cfedfcb6 1872 
r-cran-mi_1.0-4+deb9u1.debian.tar.xz
Files:
 58f6304e4de060854253b896b1d61932 2042 gnu-r optional r-cran-mi_1.0-4+deb9u1.dsc
 6fef9fb1d1079c62e2ffe503c6b28f89 1872 gnu-r optional 
r-cran-mi_1.0-4+deb9u1.debian.tar.xz

-BEGIN PGP SIGNATURE-
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=qo7e
-END PGP SIGNATURE-


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#894623: numexpr FTBFS with dh-python >= 3.20180313

[Adrian Bunk]

Source: numexpr
Version: 2.6.4-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/numexpr.html

...
make[1]: Entering directory '/build/1st/numexpr-2.6.4'
pyversions: missing X(S)-Python-Version in control file, fall back to 
debian/pyversions
py3versions: no X-Python3-Version in control file, using supported versions
set -e -x;\
for py in 2.7 3.6; do \
cd /build/1st/numexpr-2.6.4/.pybuild/pythonX.Y_$py/build;\
env PYTHONPATH=. python$py numexpr/tests/test_numexpr.py -v;\
cd /build/1st/numexpr-2.6.4/.pybuild/pythonX.Y-dbg_$py/build;\
env PYTHONPATH=. python$py-dbg numexpr/tests/test_numexpr.py -v;\
done
+ cd /build/1st/numexpr-2.6.4/.pybuild/pythonX.Y_2.7/build
/bin/sh: 3: cd: can't cd to 
/build/1st/numexpr-2.6.4/.pybuild/pythonX.Y_2.7/build
make[1]: *** [debian/rules:36: override_dh_auto_test] Error 2

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#894572: statsmodels FTBFS with dh-python >= 3.20180313

[Adrian Bunk]

Source: statsmodels
Version: 0.8.0-6
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/statsmodels.html

...
 make -C docs html
make[2]: Entering directory '/build/1st/statsmodels-0.8.0/docs'
Make static directory for images
mkdir -p build/html/_static
# generate the examples rst files
Generating reST from examples folder
#../tools/examples_rst.py
Generating datasets from installed statsmodels.datasets
python3 ../tools/dataset_rst.py
Traceback (most recent call last):
  File "../tools/dataset_rst.py", line 8, in 
import statsmodels.api as sm
ModuleNotFoundError: No module named 'statsmodels'
make[2]: *** [Makefile:68: html] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#886361: closed by Kartik Mistry <kar...@debian.org> (Bug#886361: fixed in apertium 3.4.2~r68466-4)

[Adrian Bunk]

Control: reopen -1
Control: fixed -1 3.4.2~r68466-4
Control: found -1 3.5.0~r84331-1 

On Fri, Jan 05, 2018 at 05:09:03AM +, Debian Bug Tracking System wrote:
>...
>  apertium (3.4.2~r68466-4) unstable; urgency=medium
>  .
>* debian/patches/00-parallel-ftbfs.patch:
>  + Added patch to fix frequent parallel FTBFS. Patch by Adrian Bunk
><b...@debian.org> (Closes: #886361)
>...


The patch was lost when upgrading to 3.5.0~r84331-1:
https://buildd.debian.org/status/fetch.php?pkg=apertium=ppc64el=3.5.0~r84331-1=1521631792=0

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893735: paraview FTBFS on armel/armhf: QVTKOpenGLWidget.cxx:458:3: error: 'QOpenGLFunctions_3_2_Core' was not declared in this scope

[Adrian Bunk]

Source: paraview
Version: 5.4.1+dfsg4-1
Severity: serious

https://buildd.debian.org/status/package.php?p=paraview=sid

...
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx: In 
member function 'virtual void QVTKOpenGLWidget::paintGL()':
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx:458:3:
 error: 'QOpenGLFunctions_3_2_Core' was not declared in this scope
   QOpenGLFunctions_3_2_Core* f =
   ^
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx:458:3:
 note: suggested alternative: 'QOpenGLFunctionsPrivate'
   QOpenGLFunctions_3_2_Core* f =
   ^
   QOpenGLFunctionsPrivate
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx:458:30:
 error: 'f' was not declared in this scope
   QOpenGLFunctions_3_2_Core* f =
  ^
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx:459:83:
 error: no matching function for call to 
'QOpenGLContext::versionFunctions()'
 
QOpenGLContext::currentContext()->versionFunctions();

   ^
In file included from 
/usr/include/arm-linux-gnueabihf/qt5/QtGui/QOpenGLContext:1:0,
 from 
/<>/paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx:18:
/usr/include/arm-linux-gnueabihf/qt5/QtGui/qopenglcontext.h:193:11: note: 
candidate: template TYPE* QOpenGLContext::versionFunctions() const
 TYPE *versionFunctions() const
   ^~~~
/usr/include/arm-linux-gnueabihf/qt5/QtGui/qopenglcontext.h:193:11: note:   
template argument deduction/substitution failed:
VTK/GUISupport/Qt/CMakeFiles/vtkGUISupportQt.dir/build.make:453: recipe for 
target 
'VTK/GUISupport/Qt/CMakeFiles/vtkGUISupportQt.dir/QVTKOpenGLWidget.cxx.o' failed
make[3]: *** 
[VTK/GUISupport/Qt/CMakeFiles/vtkGUISupportQt.dir/QVTKOpenGLWidget.cxx.o] Error 
1


On armel/armhf (and on arm64 in Ubuntu) Qt is compiled for OpenGL ES
instead of full OpenGL.

This is caused by:
https://gitlab.kitware.com/vtk/vtk/commit/53c566782950cd94ccd877cb906607e4cc33e1f7

The following fixes the build:

--- paraview-5.4.1+dfsg4.orig/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx
+++ paraview-5.4.1+dfsg4/VTK/GUISupport/Qt/QVTKOpenGLWidget.cxx
@@ -19,7 +19,7 @@
 #include 
 #include 
 #include 
-#include 
+//#include 
 #include 
 #include 
 #include 
@@ -453,6 +453,7 @@ void QVTKOpenGLWidget::paintGL()
   // before proceeding with blit-ing.
   this->makeCurrent();
 
+#if 0
   // blit from this->FBO to QOpenGLWidget's FBO.
   vtkQVTKOpenGLWidgetDebugMacro("paintGL::blit-to-defaultFBO");
   QOpenGLFunctions_3_2_Core* f =
@@ -485,6 +486,7 @@ void QVTKOpenGLWidget::paintGL()
 f->glColorMask(colorMask[0], colorMask[1], colorMask[2], colorMask[3]);
 f->glClearColor(clearColor[0], clearColor[1], clearColor[2], 
clearColor[3]);
   }
+#endif  /* 0 */
 }
 
 //-


This is obviously not a patch that should be applied,
it serves only to show that it is really just a small piece
of recently added code that prevents compilation here.

If possible, this should be fixed.


In case fixing is not possible or desirable, please:
- change the build dependency from libqt5opengl5-dev
  to libqt5opengl5-desktop-dev, and
- file a removal bug for the old armel+armhf binaries
  against ftp.debian.org

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893653: petsc4py FTBFS

[Adrian Bunk]

Source: petsc4py
Version: 3.8.1-2
Severity: serious

Some recent change in unstable makes petsc4py FTBFS:

https://tests.reproducible-builds.org/debian/history/petsc4py.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/petsc4py.html

...
# petsc4py embeds the deep PETSC_DIR path as RPATH in its library.
# Swap it out for a standard path, or else dh_shlibdeps gets confused
chrpath -d .pybuild/pythonX.Y_*/build/petsc4py/lib/PETSc*.so
open: No such file or directory
elf_open: Invalid argument
make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893423: thepeg FTBFS with openjdk-9

[Adrian Bunk]

Source: thepeg
Version: 1.8.0-3
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/thepeg.html

...
checking for javac... /usr/bin/javac
checking for java... /usr/bin/java
checking for jar... /usr/bin/jar
checking if java works... no
configure: Java GUI disabled
...
   debian/rules override_dh_install-indep
make[1]: Entering directory '/build/1st/thepeg-1.8.0'
dh_install
dh_install: Cannot find (any matches for) "usr/bin/thepeg" (tried in ., 
debian/tmp)

dh_install: thepeg-gui missing files: usr/bin/thepeg
dh_install: Cannot find (any matches for) "usr/lib/*/ThePEG/ThePEG.jar" (tried 
in ., debian/tmp)

dh_install: thepeg-gui missing files: usr/lib/*/ThePEG/ThePEG.jar
dh_install: missing files, aborting
make[1]: *** [debian/rules:38: override_dh_install-indep] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893381: openstereogram FTBFS with openjdk-9

[Adrian Bunk]

Source: openstereogram
Version: 0.1+20080921-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/openstereogram.html

...
-do-compile:
[javac] Using javac -source 1.5 is no longer supported, switching to 1.6
[javac] Compiling 12 source files to 
/build/1st/openstereogram-0.1+20080921/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with 
-source 1.6
[javac] warning: [options] source value 1.6 is obsolete and will be removed 
in a future release
[javac] warning: [options] target value 1.6 is obsolete and will be removed 
in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use 
-Xlint:-options.
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:34:
 error: unmappable character (0xF3) for encoding ANSI_X3.4-1968
[javac] // //GEN-BEGIN:initComponents
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:52:
 error: unmappable character (0xE7) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]   ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:52:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:52:
 error: unmappable character (0xE1) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:52:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]   ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:53:
 error: unmappable character (0xE7) for encoding ANSI_X3.4-1968
[javac] // Fim da declara??o de vari?veis//GEN-END:variables
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:53:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Fim da declara??o de vari?veis//GEN-END:variables
[javac]   ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePanel.java:53:
 error: unmappable character (0xE1) for encoding ANSI_X3.4-1968
[javac] // Fim da declara??o de vari?veis//GEN-END:variables
[javac] ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:53:
 error: unmappable character (0xF3) for encoding ANSI_X3.4-1968
[javac] // //GEN-BEGIN:initComponents
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:70:
 error: unmappable character (0xE7) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]   ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:70:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:70:
 error: unmappable character (0xE1) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:70:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Declara??o de vari?veis - n?o modifique//GEN-BEGIN:variables
[javac]   ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:71:
 error: unmappable character (0xE7) for encoding ANSI_X3.4-1968
[javac] // Fim da declara??o de vari?veis//GEN-END:variables
[javac]  ^
[javac] 
/build/1st/openstereogram-0.1+20080921/src/br/gfca/openstereogram/gui/ImagePreviewPanel.java:71:
 error: unmappable character (0xE3) for encoding ANSI_X3.4-1968
[javac] // Fim da declara??o de vari?veis//GEN-END:variables
[javac]   ^

Bug#893273: bcolz: FTBFS and Debci failure

[Adrian Bunk]

Source: bcolz
Version: 1.1.0+ds1-5
Severity: serious

https://ci.debian.net/packages/b/bcolz/unstable/amd64/
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/bcolz.html

...
==
FAIL: test01a (bcolz.tests.test_carray.bloscFiltersTest)
Testing all available filters in big arrays (setdefaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2283, in test01a
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

==
FAIL: test01b (bcolz.tests.test_carray.bloscFiltersTest)
Testing all available filters in big arrays (bcolz.defaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2303, in test01b
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

==
FAIL: test01 (bcolz.tests.test_carray.copyDiskTest)
Testing copy() with higher compression
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 685, in test01
self.assertTrue(b.cbytes > c.cbytes, "clevel not changed")
AssertionError: clevel not changed

==
FAIL: test01 (bcolz.tests.test_carray.copyMemoryTest)
Testing copy() with higher compression
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 685, in test01
self.assertTrue(b.cbytes > c.cbytes, "clevel not changed")
AssertionError: clevel not changed

==
FAIL: test01a (bcolz.tests.test_carray.filtersDiskTest)
Testing all available filters in big arrays (setdefaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2283, in test01a
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

==
FAIL: test01b (bcolz.tests.test_carray.filtersDiskTest)
Testing all available filters in big arrays (bcolz.defaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2303, in test01b
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

==
FAIL: test01a (bcolz.tests.test_carray.filtersMemoryTest)
Testing all available filters in big arrays (setdefaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2283, in test01a
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

==
FAIL: test01b (bcolz.tests.test_carray.filtersMemoryTest)
Testing all available filters in big arrays (bcolz.defaults)
--
Traceback (most recent call last):
  File "bcolz/tests/test_carray.py", line 2303, in test01b
"carray does not seem to compress at all")
AssertionError: carray does not seem to compress at all

--
Ran 1254 tests in 31.476s

FAILED (failures=8, skipped=156)
E: pybuild pybuild:323: test: plugin distutils failed with: exit code=1: cd 
/build/1st/bcolz-1.1.0+ds1/.pybuild/cpython2_2.7_bcolz/build; python2.7 -m 
unittest discover -v 
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
make: *** [debian/rules:14: build] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893075: liblttoolbox3-3.3-0v5 must be dropped since it now depends on the wrong soversion

[Adrian Bunk]

On Fri, Mar 16, 2018 at 08:50:49AM +0100, Tino Didriksen wrote:
> This will fix itself when apertium is updated, which is next. Just needed
> lttoolbox through first.

apertium needs a rebuild for this library transition.

But this won't fix the bug that liblttoolbox3-3.3-0v5 must be removed.

> -- Tino Didriksen

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893075: liblttoolbox3-3.3-0v5 must be dropped since it now depends on the wrong soversion

[Adrian Bunk]

Package: liblttoolbox3-3.3-0v5
Version: 3.4.0~r84331-1
Severity: grave
Control: affects -1 apertium src:apertium-es-pt

$ apertium-preprocess-transfer
apertium-preprocess-transfer: error while loading shared libraries: 
liblttoolbox3-3.3.so.0: cannot open shared object file: No such file or 
directory
$


Root cause:

Package: liblttoolbox3-3.3-0v5
Version: 3.4.0~r84331-1
Depends: liblttoolbox3-3.4-1 (>= 3.4.0~r84331-1)
Description-en: Transitional package to undo g++-5 renaming
 This is a transitional dummy package. It can safely be removed.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#893023: librsl FTBFS with flex 2.6.4-6

[Adrian Bunk]

Source: librsl
Version: 1.43-1.2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/librsl.html

...
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2 
-fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro 
-o any_to_gif any_to_gif.o -L/usr/lib -lmfhdf -ldf -ljpeg -lz -lm -lfl 
../.libs/librsl.a  -L/usr/lib -lmfhdf -ldf -ljpeg -lz -lm -lfl
libtool: link: gcc -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -Wl,-z -Wl,relro -o any_to_gif any_to_gif.o  -L/usr/lib 
../.libs/librsl.a /usr/lib/libmfhdf.so /usr/lib/libdf.so -ljpeg -lz -lm -lfl
/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/libfl.so: undefined 
reference to `yylex'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:487: any_to_gif] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877433: stretch update for r-cran-mi

[Adrian Bunk]

On Sun, Oct 01, 2017 at 09:39:04PM +, Debian Bug Tracking System wrote:
>...
>  r-cran-mi (1.0-5) unstable; urgency=medium
>...
>* Convert to dh-r.
>  Incidentally, this implies that r-cran-arm is a Depends. (Closes: 
> #877433)
>...

Thanks a lot for fixing this bug for unstable.

It is still present in stretch, could you also fix it there?
Alternatively, I can fix it for stretch if you don't object.

Thanks
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890254: stretch update for gf2x

[Adrian Bunk]

On Mon, Feb 12, 2018 at 05:51:03PM +, Debian Bug Tracking System wrote:
>...
>  gf2x (1.2-4) unstable; urgency=medium
>  .
>* Team upload.
>* Actually disable HW-specific code also on i386. (Closes: #890254)
>...

Thanks a lot for fixing this bug for unstable.

It is still present in stretch, could you also fix it there?
Alternatively, I can fix it for stretch if you don't object.

Thanks
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#892739: nmu: getdp_2.11.3+dfsg1-1 and deal.ii_8.4.2-2

[Adrian Bunk]

Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: binnmu

nmu getdp_2.11.3+dfsg1-1 . ANY . unstable . -m "Rebuild with slepc 3.8"
nmu deal.ii_8.4.2-2 . ANY . unstable . -m "Rebuild with slepc 3.8"

Technically this is a transition, but the new slepc is already
in testing.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890237: closed by Anton Gladky <gl...@debian.org> (Bug#890237: fixed in yade 2018.02b-1)

[Adrian Bunk]

Control: reopen -1

On Tue, Feb 20, 2018 at 07:42:07PM +, Debian Bug Tracking System wrote:
>...
>  yade (2018.02b-1) unstable; urgency=medium
>...
>    [ Adrian Bunk ]
>* [a5eddfb] Fix compilation on weak archs. (Closes: #890237)
>...

It did build for me with 2018.02a-2, but for 2018.02b-1 I need -g0:

--- debian/rules.old2018-02-22 22:06:44.675263179 +
+++ debian/rules2018-02-22 22:07:26.598594150 +
@@ -11,10 +11,10 @@
 
 export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed,-no-keep-memory
 
-# less debug info to avoid running
+# no debug info to avoid running
 # out of address space when linking
 ifneq (,$(filter $(DEB_HOST_ARCH), mips mipsel))
-   export DEB_CXXFLAGS_MAINT_APPEND += -g1
+   export DEB_CXXFLAGS_MAINT_APPEND += -g0
 endif
 
 # Check, whether Build-Depends-Indep are installed


cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#892288: arrayfire FTBFS on i386: test segfaults

[Adrian Bunk]

Source: arrayfire
Version: 3.3.2+dfsg1-4
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/i386/arrayfire.html

...
98% tests passed, 2 tests failed out of 95

Total Test time (real) =  53.16 sec

The following tests FAILED:
  4 - Test_assign_cpu (SEGFAULT)
 43 - Test_index_cpu (SEGFAULT)
Errors while running CTest
Makefile:143: recipe for target 'test' failed
make[2]: *** [test] Error 8


Whatever broke it was not yet in unstable on 2017-12-31,
but likely entered buster before 2018-01-31:
https://tests.reproducible-builds.org/debian/history/arrayfire.html

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Accepted graywolf 0.1.4+20170307gite1bf319-2.1 (source) into unstable

[Adrian Bunk]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 01 Mar 2018 23:32:40 +0200
Source: graywolf
Binary: libycadgraywolf1 libycadgraywolf-dev libycadgraywolf1-dbg graywolf
Architecture: source
Version: 0.1.4+20170307gite1bf319-2.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Adrian Bunk <b...@debian.org>
Description:
 graywolf   - Placement for digital VLSI design
 libycadgraywolf-dev - Library for graywolf - development files
 libycadgraywolf1 - Library for common functions used by graywolf
 libycadgraywolf1-dbg - debug symbols for libycadgraywolf1
Closes: 887760
Changes:
 graywolf (0.1.4+20170307gite1bf319-2.1) unstable; urgency=medium
 .
   * Non-maintainer upload.
   * Add upstream fix for FTBFS with glibc 2.26,
 thanks to Juhani Numminen. (Closes: #887760)
Checksums-Sha1:
 8904b1aee3c46e1bff1283498794c1c6cdfb1e3c 2358 
graywolf_0.1.4+20170307gite1bf319-2.1.dsc
 cea1d6c81e6f931e60b3fe544ec51b0114e2a7d0 8924 
graywolf_0.1.4+20170307gite1bf319-2.1.debian.tar.xz
Checksums-Sha256:
 83518cd882033597cdb77fc87aad874ae8a07201d39bd3dcb1a20dcf46431c25 2358 
graywolf_0.1.4+20170307gite1bf319-2.1.dsc
 3467869a17ac9b593b463ba7fdbe97d8ee5b8e782c71ef8374f4893c051ba832 8924 
graywolf_0.1.4+20170307gite1bf319-2.1.debian.tar.xz
Files:
 5bc87226f410e3c24971417e79204dff 2358 electronics optional 
graywolf_0.1.4+20170307gite1bf319-2.1.dsc
 fe0c5ba4897adfc2153e18aaffd5b96f 8924 electronics optional 
graywolf_0.1.4+20170307gite1bf319-2.1.debian.tar.xz

-BEGIN PGP SIGNATURE-
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=Vvbo
-END PGP SIGNATURE-


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#892125: RM: gazebo [arm64 armel armhf mips mips64el mipsel s390x] -- NBS; gazebo is now only built on amd64 and i386

[Adrian Bunk]

Package: ftp.debian.org
Severity: normal

gazebo (9.0.0+dfsg5-4) unstable; urgency=medium

  * libqtpropertybrowser-dev is not an optional dependency. Remove arch 
conditionals
(Closes: #891646)

 -- Jose Luis Rivero   Thu, 01 Mar 2018 12:12:16 
+

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#892107: vlfeat FTBFS: No symbol version section for versioned symbol `memcpy@GLIBC_2.2.5'

[Adrian Bunk]

Source: vlfeat
Version: 0.9.21+dfsg0-1
Severity: serious

https://buildd.debian.org/status/package.php?p=vlfeat=sid

...
"cc" -shared\
bin/debian/objs/rodrigues.o bin/debian/objs/gmm.o bin/debian/objs/liop.o 
bin/debian/objs/aib.o bin/debian/objs/host.o bin/debian/objs/kdtree.o 
bin/debian/objs/hog.o bin/debian/objs/lbp.o bin/debian/objs/svmdataset.o 
bin/debian/objs/mathop_sse2.o bin/debian/objs/pgm.o bin/debian/objs/hikmeans.o 
bin/debian/objs/generic.o bin/debian/objs/mathop.o bin/debian/objs/imopv_sse2.o 
bin/debian/objs/covdet.o bin/debian/objs/stringop.o bin/debian/objs/vlad.o 
bin/debian/objs/quickshift.o bin/debian/objs/mser.o bin/debian/objs/kmeans.o 
bin/debian/objs/mathop_avx.o bin/debian/objs/imopv.o bin/debian/objs/fisher.o 
bin/debian/objs/slic.o bin/debian/objs/random.o bin/debian/objs/scalespace.o 
bin/debian/objs/svm.o bin/debian/objs/homkermap.o bin/debian/objs/array.o 
bin/debian/objs/ikmeans.o\
-Wl,-z,relro -Wl,-z,now -Wl,--as-needed -lpthread -lm -lm -lpthread 
-fopenmp\
-Wl,-soname,libvl.so.1\
-o "bin/debian/libvl.so"
/usr/bin/ld: bin/debian/libvl.so: No symbol version section for versioned 
symbol `memcpy@GLIBC_2.2.5'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
make/dll.mak:118: recipe for target 'bin/debian/libvl.so' failed
make[2]: *** [bin/debian/libvl.so] Error 1


This FTBFS is caused by changes in vl/host.h, not changes in glibc 2.27.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887760: graywolf: diff for NMU version 0.1.4+20170307gite1bf319-2.1

[Adrian Bunk]

Control: tags 887760 + pending

Dear maintainer,

I've prepared an NMU for graywolf (versioned as 
0.1.4+20170307gite1bf319-2.1) and uploaded it to DELAYED/5.
Please feel free to tell me if I should cancel it.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

diff -Nru graywolf-0.1.4+20170307gite1bf319/debian/changelog graywolf-0.1.4+20170307gite1bf319/debian/changelog
--- graywolf-0.1.4+20170307gite1bf319/debian/changelog	2017-03-08 10:45:52.0 +0200
+++ graywolf-0.1.4+20170307gite1bf319/debian/changelog	2018-03-01 23:32:40.0 +0200
@@ -1,3 +1,11 @@
+graywolf (0.1.4+20170307gite1bf319-2.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Add upstream fix for FTBFS with glibc 2.26,
+thanks to Juhani Numminen. (Closes: #887760)
+
+ -- Adrian Bunk <b...@debian.org>  Thu, 01 Mar 2018 23:32:40 +0200
+
 graywolf (0.1.4+20170307gite1bf319-2) unstable; urgency=medium
 
   * debian/copyright:
diff -Nru graywolf-0.1.4+20170307gite1bf319/debian/patches/0001-cfree-has-been-removed-from-glibc-2.26.patch graywolf-0.1.4+20170307gite1bf319/debian/patches/0001-cfree-has-been-removed-from-glibc-2.26.patch
--- graywolf-0.1.4+20170307gite1bf319/debian/patches/0001-cfree-has-been-removed-from-glibc-2.26.patch	1970-01-01 02:00:00.0 +0200
+++ graywolf-0.1.4+20170307gite1bf319/debian/patches/0001-cfree-has-been-removed-from-glibc-2.26.patch	2018-03-01 23:08:31.0 +0200
@@ -0,0 +1,25 @@
+From 23c6f4adb38f3314ef55139929e4295aac4c72b3 Mon Sep 17 00:00:00 2001
+From: KokaKiwi <kokakiwi+...@kokakiwi.net>
+Date: Thu, 16 Nov 2017 17:48:06 +0100
+Subject: cfree has been removed from glibc 2.26
+
+---
+ src/Ylib/okmalloc.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Ylib/okmalloc.c b/src/Ylib/okmalloc.c
+index 10f7a33..8a5ef68 100644
+--- a/src/Ylib/okmalloc.c
 b/src/Ylib/okmalloc.c
+@@ -901,7 +901,7 @@ VOIDPTR ptr;
+ VOID Ysafe_cfree(ptr)
+ VOIDPTR ptr;
+ {
+-cfree(ptr);
++free(ptr);
+ return;
+ }
+ 
+-- 
+2.11.0
+
diff -Nru graywolf-0.1.4+20170307gite1bf319/debian/patches/series graywolf-0.1.4+20170307gite1bf319/debian/patches/series
--- graywolf-0.1.4+20170307gite1bf319/debian/patches/series	2017-03-08 10:45:52.0 +0200
+++ graywolf-0.1.4+20170307gite1bf319/debian/patches/series	2018-03-01 23:32:40.0 +0200
@@ -2,3 +2,4 @@
 02_dont_create_link.patch
 04_install_directory_multiarch.patch
 0004-Fixes-some-spelling-errors.patch
+0001-cfree-has-been-removed-from-glibc-2.26.patch
-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#891646: gazebo FTBFS without libqtpropertybrowser-dev

[Adrian Bunk]

Source: gazebo
Version: 9.0.0+dfsg5-3
Severity: serious

https://buildd.debian.org/status/package.php?p=gazebo=sid

...
/<>/gazebo-9.0.0+dfsg5/gazebo/gui/ModelListWidget.cc:46:10: fatal 
error: qtpropertybrowser/qttreepropertybrowser.h: No such file or directory
 #include "qtpropertybrowser/qttreepropertybrowser.h"
  ^~~
compilation terminated.
gazebo/gui/CMakeFiles/gazebo_gui.dir/build.make:662: recipe for target 
'gazebo/gui/CMakeFiles/gazebo_gui.dir/ModelListWidget.cc.o' failed
make[3]: *** [gazebo/gui/CMakeFiles/gazebo_gui.dir/ModelListWidget.cc.o] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#891518: ros-geometry2 FTBFS: error: 'logWarn' was not declared in this scope

[Adrian Bunk]

Source: ros-geometry2
Version: 0.5.16-1
Severity: serious

https://buildd.debian.org/status/package.php?p=ros-geometry2=sid

...
/<>/tf2/src/buffer_core.cpp: In member function 'bool 
tf2::BufferCore::warnFrameId(const char*, const string&) const':
/<>/tf2/src/buffer_core.cpp:126:5: error: 'logWarn' was not 
declared in this scope
 logWarn("%s",ss.str().c_str());
 ^~~
/<>/tf2/src/buffer_core.cpp:134:5: error: 'logWarn' was not 
declared in this scope
 logWarn("%s",ss.str().c_str());
 ^~~

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#891516: ros-geometric-shapes FTBFS: error: 'logError' was not declared in this scope

[Adrian Bunk]

Source: ros-geometric-shapes
Version: 0.5.3-1
Severity: serious

https://buildd.debian.org/status/package.php?p=ros-geometric-shapes=sid

...
/<>/src/body_operations.cpp: In function 'bodies::Body* 
bodies::createBodyFromShape(const shapes::Shape*)':
/<>/src/body_operations.cpp:62:7: error: 'logError' was not 
declared in this scope
   logError("Creating body from shape: Unknown shape type %d", 
(int)shape->type);
   ^~~~

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#891207: simbody binary-all FTBFS: tests not run

[Adrian Bunk]

Source: simbody
Version: 3.5.4+dfsg2-1
Severity: serious

https://buildd.debian.org/status/fetch.php?pkg=simbody=all=3.5.4%2Bdfsg2-1=1519350416=0

...

0% tests passed, 101 tests failed out of 101

Total Test time (real) =   0.14 sec

The following tests FAILED:
  1 - BNTTest (Not Run)
  2 - MatVecTest (Not Run)
  3 - OrientationTest (Not Run)
  4 - PolynomialTest (Not Run)
  5 - RandomTest (Not Run)
  6 - RotationTest (Not Run)
  7 - SFMTTest (Not Run)
  8 - SpatialAlgebraTest (Not Run)
  9 - StateTest (Not Run)
 10 - TestArray (Not Run)
 11 - TestAtomicInteger (Not Run)
 12 - TestBigMatrix (Not Run)
 13 - TestFunction (Not Run)
 14 - TestMassProperties (Not Run)
 15 - TestParallel2DExecutor (Not Run)
 16 - TestParallelExecutor (Not Run)
 17 - TestParallelWorkQueue (Not Run)
 18 - TestPlugin (Not Run)
 19 - TestPolygonalMesh (Not Run)
 20 - TestPrivateImplementation (Not Run)
 21 - TestScalar (Not Run)
 22 - TestSimulation (Not Run)
 23 - TestSmallMatrix (Not Run)
 24 - TestVectorMath (Not Run)
 25 - TestXml (Not Run)
 26 - cpsAdvDiff_bnd (Not Run)
 27 - cpsAdvDiff_bndL (Not Run)
 28 - cpsAdvDiff_non (Not Run)
 29 - cpsNewtCrd_dns (Not Run)
 30 - cpsPend_dns (Not Run)
 31 - cpsPend_dnsL (Not Run)
 32 - cpsRoberts_dns (Not Run)
 33 - cpsRoberts_dnsL (Not Run)
 34 - cpsVanDPol_non (Not Run)
 35 - cpsadamsx (Not Run)
 36 - cpsbanx (Not Run)
 37 - cpsbanx_lap (Not Run)
 38 - cpsdenx (Not Run)
 39 - cpsdenx_lap (Not Run)
 40 - initroot1 (Not Run)
 41 - newton (Not Run)
 42 - pend (Not Run)
 43 - pendEs (Not Run)
 44 - pendLr (Not Run)
 45 - pend_test (Not Run)
 46 - CpsAdamsXCpp (Not Run)
 47 - PendLrCpp (Not Run)
 48 - BestAvailableTest (Not Run)
 49 - CMAESTest (Not Run)
 50 - CPodesIntegratorTest (Not Run)
 51 - DifferentiatorTest (Not Run)
 52 - EigenTest (Not Run)
 53 - ExplicitEulerIntegratorTest (Not Run)
 54 - FactorLUTest (Not Run)
 55 - FactorQTZTest (Not Run)
 56 - FactorSVDTest (Not Run)
 57 - IntegratorTest (Not Run)
 58 - IpoptDiffTest (Not Run)
 59 - IpoptTest (Not Run)
 60 - LBFGSBDiffTest (Not Run)
 61 - LBFGSBTest (Not Run)
 62 - LBFGSDiffTest (Not Run)
 63 - LBFGSTest (Not Run)
 64 - RungeKutta2IntegratorTest (Not Run)
 65 - RungeKutta3IntegratorTest (Not Run)
 66 - RungeKuttaFeldbergIntegratorTest (Not Run)
 67 - RungeKuttaMersonIntegratorTest (Not Run)
 68 - SemiExplicitEuler2IntegratorTest (Not Run)
 69 - SemiExplicitEulerIntegratorTest (Not Run)
 70 - SimpleDifferentiatorTest (Not Run)
 71 - TestBicubicSurface (Not Run)
 72 - TestContactGeometry (Not Run)
 73 - TestGeo (Not Run)
 74 - TestSpline (Not Run)
 75 - TestTriangleMesh (Not Run)
 76 - TimeStepperTest (Not Run)
 77 - VerletIntegratorTest (Not Run)
 78 - GazeboInelasticCollision (Not Run)
 79 - GazeboReactionForce (Not Run)
 80 - GazeboReactionForceWithAppliedForceCompliant (Not Run)
 81 - GazeboReactionForceWithAppliedForceRigid (Not Run)
 82 - TestAngleConversions (Not Run)
 83 - TestCollisionDetectionAlgorithm (Not Run)
 84 - TestConstraints (Not Run)
 85 - TestCustomConstraints (Not Run)
 86 - TestCustomMobilizedBodies (Not Run)
 87 - TestElasticFoundationForce (Not Run)
 88 - TestForces (Not Run)
 89 - TestFunctionBasedMobilizedBodies (Not Run)
 90 - TestGravity (Not Run)
 91 - TestHuntCrossleyForce (Not Run)
 92 - TestLinearBushing (Not Run)
 93 - TestLoneParticle (Not Run)
 94 - TestMassMatrix (Not Run)
 95 - TestMobilizedBody (Not Run)
 96 - TestMobilizerReactionForces (Not Run)
 97 - TestNoseHooverThermostat (Not Run)
 98 - TestObservedPointFitter (Not Run)
 99 - TestOrientedBoundingBox (Not Run)
100 - TestPimpl1 (Not Run)
101 - TestReverseMobilizers (Not Run)
Errors while running CTest
make[1]: *** [Makefile:122: test] Error 8

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#891151: dune-uggrid FTBFS with cmake 3.10.2-1

[Adrian Bunk]

Source: dune-uggrid
Version: 2.5.1-1
Severity: serious
Tags: patch
Control: fixed -1 2.6~20180108-1
Control: close -1

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/dune-uggrid.html

...
cd /build/1st/dune-uggrid-2.5.1/build/parallel/dddif && /usr/bin/c++  
-D-pthread -DENABLE_MPI=1 -DFOR_DUNE -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX 
-DMPIPP_H -DModelP -DUGLIB -DUG_DIM_3 -DUG_USE_NEW_DIMENSION_DEFINES 
-DUG_USE_SYSTEM_HEAP=1 -I/build/1st/dune-uggrid-2.5.1/build 
-I/build/1st/dune-uggrid-2.5.1 
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi 
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
 
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
 -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/1st/dune-uggrid-2.5.1/low 
-I/build/1st/dune-uggrid-2.5.1/gm -I/build/1st/dune-uggrid-2.5.1/dev 
-I/build/1st/dune-uggrid-2.5.1/dom -I/build/1st/dune-uggrid-2.5.1/np 
-I/build/1st/dune-uggrid-2.5.1/ui -I/build/1st/dune-uggrid-2.5.1/np/algebra 
-I/build/1st/dune-uggrid-2.5.1/np/udm -I/build/1st/dune-uggrid-2.5.1/parallel 
-I/build/1st/dune-uggrid-2.5.1/parallel/ddd 
-I/build/1st/dune-uggrid-2.5.1/parallel/pp
 if -I/build/1st/dune-uggrid-2.5.1/parallel/dddif 
-I/build/1st/dune-uggrid-2.5.1/parallel/util 
-I/build/1st/dune-uggrid-2.5.1/parallel/ddd/include  -g -O2 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -std=c++14  -fPIC   -o CMakeFiles/dddif3.dir/memmgr.cc.o -c 
/build/1st/dune-uggrid-2.5.1/parallel/dddif/memmgr.cc
:0:1: error: macro names must be identifiers


Felix Geyer mentioned that the root cause is that the
COMPILE_DEFINITIONS in parallel/CMakeLists.txt should
be replaced with COMPILE_OPTIONS.

The version in experimental seems already fixed.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#852307: bcolz: test_leftover_ptr_with_statement_create_open fails on s390x, powerpc

[Adrian Bunk]

Control: retitle -1 bcolz: test_leftover_ptr_with_statement_create_open fails 
on big endian
Control: severity -1 important

On Mon, Jan 23, 2017 at 02:20:35PM +0100, Daniel Stender wrote:
> Package: bcolz
> Version: 1.1.0+ds1-2
> Severity: serious
> Justification: fails to build from source
> Control: forwarded -1 https://github.com/Blosc/bcolz/issues/329
> 
> There is a test failure on s390x and powerpc [1]:
>...

Actually on all big endian architectures.

And not RC since the package never built on these architectures.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890384: ignition-math4: baseline violation on amd64

[Adrian Bunk]

Source: ignition-math4
Version: 4.0.0+dfsg1-1
Severity: serious

https://sources.debian.org/src/ignition-math4/4.0.0+dfsg1-1/debian/rules/#L10

ifeq ($(DEB_HOST_ARCH),amd64)
SSE_FLAGS = -mfpmath=sse -msse -msse2 -msse3 -mssse3 -DSSE
endif

SSE3 and SSSE3 are not part of the amd64 baseline.

"-mfpmath=sse -msse -msse2" are already enabled
by default on amd64, no need to do that manually.

The SSE define does not seem to be used anywhere in the code.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890383: ignition-common FTBFS on big endian: UNIT_Util_TEST (Failed)

[Adrian Bunk]

Source: ignition-common
Version: 1.0.1-1
Severity: important

https://buildd.debian.org/status/package.php?p=ignition-common=sid

...

98% tests passed, 1 tests failed out of 59

Total Test time (real) =  10.32 sec

The following tests FAILED:
 49 - UNIT_Util_TEST (Failed)
Errors while running CTest
Makefile:143: recipe for target 'test' failed
make[2]: *** [test] Error 8

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890254: control

[Adrian Bunk]

Control: not fixed -1 1.2-3

On Mon, Feb 12, 2018 at 02:14:00PM +, Ximin Luo wrote:
> Control: fixed -1 1.2-3
> 
> Already fixed there, version in stretch still affected.

That only fixed it for amd64, i386 still builds with -msse2:
https://buildd.debian.org/status/fetch.php?pkg=gf2x=i386=1.2-3=1518451597=0

> X

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890254: gf2x: baseline violations on i386/amd64

[Adrian Bunk]

Source: gf2x
Version: 1.1-2
Severity: serious
Control: affects -1 src:sagemath

A FTBFS in sagemath boiled down to gf2x violating
the amd64 baseline by building with
"-msse2 -msse3 -mssse3 -msse4.1 -mpclmul".

The same problem exists on i386 with
"-msse2 -msse3 -mssse3".

gf2x 1.1-2 has similar problems by building with
"-msse2 -mpclmul" if supported during the build,
and building with "-msse2" on i386.

gf2x must not ever set any of these flags
(-msse2 on amd64 is harmless since it is
 already enabled by default, but therefore
 also pointless).

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890237: yade FTBFS on mips/mipsel: virtual memory exhausted: Cannot allocate memory

[Adrian Bunk]

Source: yade
Version: 2018.02a-2
Severity: important
Tags: patch

https://buildd.debian.org/status/package.php?p=yade

...
virtual memory exhausted: Cannot allocate memory
CMakeFiles/yade.dir/build.make:521: recipe for target 
'CMakeFiles/yade.dir/pkg/common/Cylinder.cpp.o' failed
make[3]: *** [CMakeFiles/yade.dir/pkg/common/Cylinder.cpp.o] Error 1


Fix:

--- debian/rules.old2018-02-11 13:26:34.803924197 +
+++ debian/rules2018-02-11 13:29:11.853915345 +
@@ -1,4 +1,7 @@
 #!/usr/bin/make -f
+
+include /usr/share/dpkg/architecture.mk
+
 BUILDDIR = $(CURDIR)/debian/build
 tmpInstall = $(CURDIR)/debian/tmp
 tmpDirMatplotLib = $(CURDIR)/debian/matplotlib
@@ -8,6 +11,12 @@
 
 export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed,-no-keep-memory
 
+# less debug info to avoid running
+# out of address space when linking
+ifneq (,$(filter $(DEB_HOST_ARCH), mips mipsel))
+  export DEB_CXXFLAGS_MAINT_APPEND += -g1
+endif
+
 # Check, whether Build-Depends-Indep are installed
 BUILD_DOC=$(shell dpkg -s python-sphinx | grep -q "^Status:.* installed$$" && 
echo yes)
 

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#890054: yade: frequent parallel FTBFS

[Adrian Bunk]

On Sat, Feb 10, 2018 at 05:47:34PM +0200, Adrian Bunk wrote:
> Source: yade
> Version: 2018.02a-1
> Severity: serious
> 
> https://buildd.debian.org/status/package.php?p=yade=sid
> 
> On plummer (ppc64el porterbox) "dpkg-buildpackage -J100 -B"
> failed immediately while "dpkg-buildpackage -J1 -B"
> succeeded.
>...

I forgot to copy the error message from the buildd:

...
Generating MOC predefs moc_predefs.h
Generating MOC compilation mocs_compilation.cpp
make[3]: Leaving directory '/<>/debian/build'
Generating MOC predefs moc_predefs.h
Generating MOC compilation mocs_compilation.cpp
Generating MOC predefs moc_predefs.h
Generating MOC compilation mocs_compilation.cpp
...
cd /<>/debian/build/py && /usr/bin/c++  
-DBOOST_MATH_DISABLE_FLOAT128=1 -DNDEBUG -DYADE_ODEINT -DYADE_SPH 
-D_polyhedra_utils_EXPORTS 
-I/<>/debian/build/py/_polyhedra_utils_autogen/include 
-I/<> -I/usr/lib/python2.7/dist-packages/numpy/core/include 
-I/usr/include/python2.7 -I/usr/include/eigen3 -I/usr/include/vtk-6.3 
-I/usr/include/powerpc64le-linux-gnu -I/usr/include/glib-2.0 
-I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include 
-I/<>/debian/build  -g -O2 -fdebug-prefix-map=/<>=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -O2 --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security -Wall -std=c++11 -DYADE_VTK 
-DYADE_OPENMP -fopenmp -DYADE_GTS  -DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_QT5 
-DYADE_GL2PS -DLBM_ENGINE -fPIC   -ftrack-macro-expansion=0 -save-temps 
-fstack-protector-strong -DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN 
-DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT -o 
CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils.cpp.o -c 
/<>/py/_polyhedra_utils.cpp
cd /<>/debian/build/py && /usr/bin/c++  
-DBOOST_MATH_DISABLE_FLOAT128=1 -DNDEBUG -DYADE_ODEINT -DYADE_SPH 
-D_polyhedra_utils_EXPORTS 
-I/<>/debian/build/py/_polyhedra_utils_autogen/include 
-I/<> -I/usr/lib/python2.7/dist-packages/numpy/core/include 
-I/usr/include/python2.7 -I/usr/include/eigen3 -I/usr/include/vtk-6.3 
-I/usr/include/powerpc64le-linux-gnu -I/usr/include/glib-2.0 
-I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include 
-I/<>/debian/build  -g -O2 -fdebug-prefix-map=/<>=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -O2 --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security -Wall -std=c++11 -DYADE_VTK 
-DYADE_OPENMP -fopenmp -DYADE_GTS  -DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_QT5 
-DYADE_GL2PS -DLBM_ENGINE -fPIC   -ftrack-macro-expansion=0 -save-temps 
-fstack-protector-strong -DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN 
-DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT -o 
CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils_autogen/mocs_compilation.cpp.o 
-c 
/<>/debian/build/py/_polyhedra_utils_autogen/mocs_compilation.cpp
cd /<>/debian/build/py && /usr/bin/c++  
-DBOOST_MATH_DISABLE_FLOAT128=1 -DNDEBUG -DYADE_ODEINT -DYADE_SPH 
-D_packObb_EXPORTS -I/<>/debian/build/py/_packObb_autogen/include 
-I/<> -I/usr/lib/python2.7/dist-packages/numpy/core/include 
-I/usr/include/python2.7 -I/usr/include/eigen3 -I/usr/include/vtk-6.3 
-I/usr/include/powerpc64le-linux-gnu -I/usr/include/glib-2.0 
-I/usr/lib/powerpc64le-linux-gnu/glib-2.0/include 
-I/<>/debian/build  -g -O2 -fdebug-prefix-map=/<>=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -O2 --param=ssp-buffer-size=4 -Wformat 
-Wformat-security -Werror=format-security -Wall -std=c++11 -DYADE_VTK 
-DYADE_OPENMP -fopenmp -DYADE_GTS  -DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_QT5 
-DYADE_GL2PS -DLBM_ENGINE -fPIC   -ftrack-macro-expansion=0 -save-temps 
-fstack-protector-strong -DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN 
-DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT -o 
CMakeFiles/_packObb.dir/_packObb_autogen/mocs_compilation.cpp.o -c 
/<>/debian/build/py/_packObb_autogen/mocs_compilation.cpp
/<>/debian/build/py/_packObb_autogen/mocs_compilation.cpp:3:1: 
error: 'than_nothing' does not name a type
/<>/debian/build/py/_packObb_autogen/mocs_compilation.cpp:3:14: 
error: expected declaration before '}' token
py/CMakeFiles/_polyhedra_utils.dir/build.make:89: recipe for target 
'py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils_autogen/mocs_compilation.cpp.o'
 failed
make[3]: *** 
[py/CMakeFiles/_polyhedra_utils.dir/_polyhedra_utils_autogen/mocs_compilation.cpp.o]
 Error 1
make[3]: *** Waiting for unfinished jobs
/<>/debian/build/py/_packObb_autogen/mocs_compilation.cpp:3:1: 
error: 'than_nothing' does not name a type
/<>/debian/build/py/_packObb_autogen/mocs_compilation.cpp:3:14: 
error: expected declaration before '}' token
make[3]: Leaving directory '/<>/debian/build'
CMakeFiles/Makefile2:550: recipe for target 
'py/CMakeFiles/_polyhed

Bug#890054: yade: frequent parallel FTBFS

[Adrian Bunk]

Source: yade
Version: 2018.02a-1
Severity: serious

https://buildd.debian.org/status/package.php?p=yade=sid

On plummer (ppc64el porterbox) "dpkg-buildpackage -J100 -B"
failed immediately while "dpkg-buildpackage -J1 -B"
succeeded.

Please disable parallel building by passing --no-parallel
to dh as long as the build does not work properly with
parallel building.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#889878: closed by Picca Frédéric-Emmanuel <pi...@debian.org> (Bug#889878: fixed in hkl 5.0.0.2449-1)

[Adrian Bunk]

Control: reopen -1

On Thu, Feb 08, 2018 at 11:12:07AM +, Debian Bug Tracking System wrote:
>...
>  hkl (5.0.0.2449-1) unstable; urgency=medium
>  .
>* New upstream version 5.0.0.2449 (Closes: #889878)
>...
> Source: hkl
> Version: 5.0.0.2447-1
> Severity: serious
> 
> https://buildd.debian.org/status/package.php?p=hkl=sid
> 
> ...
> make[4]: Entering directory '/<>/Documentation/figures'
> gcc -DHAVE_CONFIG_H -I. -I../..  -Wextra -D_DEFAULT_SOURCE -I../.. 
> -I../../hkl -I/usr/include/glib-2.0 
> -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/glib-2.0 
> -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include -Wdate-time 
> -D_FORTIFY_SOURCE=2  -g -O2 -fdebug-prefix-map=/<>=. 
> -fstack-protector-strong -Wformat -Werror=format-security -c -o sirius.o 
> sirius.c
> /bin/bash ../../libtool  --tag=CC   --mode=link gcc  -g -O2 
> -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
> -Werror=format-security 
> -Wl,--whole-archive,../../hkl/.libs/libhkl.a,--no-whole-archive -Wl,-z,relro 
> -Wl,--as-needed -o sirius sirius.o ../../hkl/libhkl.la 
> ../../hkl/api2/libhkl2.la -lglib-2.0 -lgobject-2.0 -lglib-2.0 
> -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lyaml 
> libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. 
> -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive 
> -Wl,../../hkl/.libs/libhkl.a -Wl,--no-whole-archive -Wl,-z -Wl,relro 
> -Wl,--as-needed -o .libs/sirius sirius.o  ../../hkl/.libs/libhkl.so 
> ../../hkl/api2/.libs/libhkl2.a -lgobject-2.0 -lglib-2.0 
> -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lyaml
> cd . && ./sirius
> Makefile:728: recipe for target 'sirius-stamp' failed
> make[4]: *** [sirius-stamp] Segmentation fault
>...

This seems to be fixed on arm64 only and still FTBFS on 
amd64/ppc64el/s390x:
  https://buildd.debian.org/status/package.php?p=hkl=sid

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#889886: neuron FTBFS on !x86/ppc: #error "This code has only been tested on x86 and powerpc platforms."

[Adrian Bunk]

Source: neuron
Version: 7.5-1
Severity: important

https://buildd.debian.org/status/package.php?p=neuron=sid

...
In file included from ../../src/Random123/features/compilerfeatures.h:213:0,
 from ../../src/Random123/philox.h:37,
 from nrnran123.c:7:
../../src/Random123/features/gccfeatures.h:38:4: error: #error "This code has 
only been tested on x86 and powerpc platforms."
 #  error "This code has only been tested on x86 and powerpc platforms."
^


The supported platforms already cover all combinations of
32/64bit and big/little endian, making it unlikely that
the package would be completely broken everywhere else.

It builds for me on arm64 after removing the #error block.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#889878: hkl FTBFS on amd64/arm64/ppc64el/s390x: sirius segfaults

[Adrian Bunk]

Source: hkl
Version: 5.0.0.2447-1
Severity: serious

https://buildd.debian.org/status/package.php?p=hkl=sid

...
make[4]: Entering directory '/<>/Documentation/figures'
gcc -DHAVE_CONFIG_H -I. -I../..  -Wextra -D_DEFAULT_SOURCE -I../.. -I../../hkl 
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include 
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include 
-I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
-Werror=format-security -c -o sirius.o sirius.c
/bin/bash ../../libtool  --tag=CC   --mode=link gcc  -g -O2 
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
-Werror=format-security 
-Wl,--whole-archive,../../hkl/.libs/libhkl.a,--no-whole-archive -Wl,-z,relro 
-Wl,--as-needed -o sirius sirius.o ../../hkl/libhkl.la 
../../hkl/api2/libhkl2.la -lglib-2.0 -lgobject-2.0 -lglib-2.0 
-L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lyaml 
libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive 
-Wl,../../hkl/.libs/libhkl.a -Wl,--no-whole-archive -Wl,-z -Wl,relro 
-Wl,--as-needed -o .libs/sirius sirius.o  ../../hkl/.libs/libhkl.so 
../../hkl/api2/.libs/libhkl2.a -lgobject-2.0 -lglib-2.0 
-L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lyaml
cd . && ./sirius
Makefile:728: recipe for target 'sirius-stamp' failed
make[4]: *** [sirius-stamp] Segmentation fault


Backtrace:

#0  generator_argp_ (ret=0xcdaab730) at ../../hkl/ccan/generator/generator.h:44
#1  trajectory_gen_generator__ (ret=0xcdaab730) at hkl2.c:246
#2  0x7f3078908d70 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#3  0x in ?? ()

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#889560: trilinos: cmake files seem to be missing

[Adrian Bunk]

Source: trilinos
Version: 12.12.1-3
Severity: serious
Control: affects -1 src:deal.ii

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/deal.ii.html

...
-- Include /build/1st/deal.ii-8.4.2/cmake/configure/configure_2_trilinos.cmake
CMake Error at /usr/lib/x86_64-linux-gnu/cmake/ROL/ROLConfig.cmake:174 
(INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/ROL/../MiniTensor/MiniTensorConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Piro/PiroConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Error at /usr/lib/x86_64-linux-gnu/cmake/Piro/PiroConfig.cmake:145 
(INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/Piro/../Tempus/TempusConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Error at /usr/lib/x86_64-linux-gnu/cmake/Piro/PiroConfig.cmake:181 
(INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/Piro/../MiniTensor/MiniTensorConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Warning at 
/usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:156 (MESSAGE):
  Component "Tempus" NOT found.
Call Stack (most recent call first):
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Warning at 
/usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:156 (MESSAGE):
  Component "Domi" NOT found.
Call Stack (most recent call first):
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Warning at 
/usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:156 (MESSAGE):
  Component "MiniTensor" NOT found.
Call Stack (most recent call first):
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 

Bug#889539: pandas FTBFS: test failures

[Adrian Bunk]

Source: pandas
Version: 0.20.3-11
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pandas.html

...
=== FAILURES ===
 TestDataFramePlots.test_boxplot_legacy 

self = 

@slow
def test_boxplot_legacy(self):
df = DataFrame(randn(6, 4),
   index=list(string.ascii_letters[:6]),
   columns=['one', 'two', 'three', 'four'])
df['indic'] = ['foo', 'bar'] * 3
df['indic2'] = ['foo', 'bar', 'foo'] * 2

_check_plot_works(df.boxplot, return_type='dict')
_check_plot_works(df.boxplot, column=[
  'one', 'two'], return_type='dict')
# _check_plot_works adds an ax so catch warning. see GH #13188
with tm.assert_produces_warning(UserWarning):
_check_plot_works(df.boxplot, column=['one', 'two'],
  by='indic')
_check_plot_works(df.boxplot, column='one', by=['indic', 'indic2'])
with tm.assert_produces_warning(UserWarning):
_check_plot_works(df.boxplot, by='indic')
with tm.assert_produces_warning(UserWarning):
>   _check_plot_works(df.boxplot, by=['indic', 'indic2'])

../debian/tmp/usr/lib/python2.7/dist-packages/pandas/tests/plotting/test_boxplot_method.py:57:
 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/usr/lib/python2.7/contextlib.py:24: in __exit__
self.gen.next()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

expected_warning = , filter_level = 'always'
clear = None, check_stacklevel = True

@contextmanager
def assert_produces_warning(expected_warning=Warning, filter_level="always",
clear=None, check_stacklevel=True):
"""
Context manager for running code that expects to raise (or not raise)
warnings.  Checks that code raises the expected warning and only the
expected warning. Pass ``False`` or ``None`` to check that it does *not*
raise a warning. Defaults to ``exception.Warning``, baseclass of all
Warnings. (basically a wrapper around ``warnings.catch_warnings``).

>>> import warnings
>>> with assert_produces_warning():
... warnings.warn(UserWarning())
...
>>> with assert_produces_warning(False):
... warnings.warn(RuntimeWarning())
...
Traceback (most recent call last):
...
AssertionError: Caused unexpected warning(s): ['RuntimeWarning'].
>>> with assert_produces_warning(UserWarning):
... warnings.warn(RuntimeWarning())
Traceback (most recent call last):
...
AssertionError: Did not see expected warning of class 'UserWarning'.

..warn:: This is *not* thread-safe.
"""
with warnings.catch_warnings(record=True) as w:

if clear is not None:
# make sure that we are clearning these warnings
# if they have happened before
# to guarantee that we will catch them
if not is_list_like(clear):
clear = [clear]
for m in clear:
try:
m.__warningregistry__.clear()
except:
pass

saw_warning = False
warnings.simplefilter(filter_level)
yield w
extra_warnings = []

for actual_warning in w:
if (expected_warning and issubclass(actual_warning.category,
expected_warning)):
saw_warning = True

if check_stacklevel and issubclass(actual_warning.category,
   (FutureWarning,
DeprecationWarning)):
from inspect import getframeinfo, stack
caller = getframeinfo(stack()[2][0])
msg = ("Warning not set with correct stacklevel. "
   "File where warning is raised: {0} != {1}. "
   "Warning message: {2}".format(
   actual_warning.filename, caller.filename,
   actual_warning.message))
assert actual_warning.filename == caller.filename, msg
else:
extra_warnings.append(actual_warning.category.__name__)
if expected_warning:
assert saw_warning, ("Did not see expected warning of class %r."
 % expected_warning.__name__)
assert not extra_warnings, ("Caused unexpected warning(s): %r."
>   

Bug#889189: inventor-doc is empty

[Adrian Bunk]

Package: inventor-doc
Version: 2.1.5-10-21
Severity: grave

$ dpkg -L inventor-doc 
/.
/usr
/usr/share
/usr/share/doc
/usr/share/doc/inventor-doc
/usr/share/doc/inventor-doc/changelog.Debian.gz
/usr/share/doc/inventor-doc/copyright
$ 

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#889183: pyfai FTBFS: RuntimeError: Fail to generate 'check_calib' man documentation

[Adrian Bunk]

Source: pyfai
Version: 0.15.0+dfsg-1
Severity: serious

https://buildd.debian.org/status/package.php?p=pyfai=sid

...
I: pybuild base:184: 
PYTHONPATH=/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build 
xvfb-run -a --server-args="-screen 0 1024x768x24" python3.6 setup.py build_man
INFO:root:Generating grammar tables from /usr/lib/python3.6/lib2to3/Grammar.txt
INFO:root:Generating grammar tables from 
/usr/lib/python3.6/lib2to3/PatternGrammar.txt
INFO:pyFAI.setup:Use setuptools
running build_man
INFO:pyFAI.setup:Build man for entry-point target 'check_calib'
help2man: can't get `--help' info from /tmp/check_calib_59xexrun
Try `--no-discard-stderr' if option outputs to stderr
INFO:pyFAI.setup:b'Traceback (most recent call last):\n  File 
"/tmp/check_calib_59xexrun", line 2, in \nimport 
pyFAI.app.check_calib as app\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/__init__.py",
 line 56, in \nfrom .detectors import Detector\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/detectors.py",
 line 51, in \nfrom . import io\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/io.py", 
line 67, in \nfrom .utils import StringTypes, 
fully_qualified_name\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/utils/__init__.py",
 line 54, in \nfrom ..third_party import six\nModuleNotFoundError: 
No module named \'pyFAI.third_party\'\n'
INFO:pyFAI.setup:b'Traceback (most recent call last):\n  File 
"/tmp/check_calib_59xexrun", line 2, in \nimport 
pyFAI.app.check_calib as app\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/__init__.py",
 line 56, in \nfrom .detectors import Detector\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/detectors.py",
 line 51, in \nfrom . import io\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/io.py", 
line 67, in \nfrom .utils import StringTypes, 
fully_qualified_name\n  File 
"/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build/pyFAI/utils/__init__.py",
 line 54, in \nfrom ..third_party import six\nModuleNotFoundError: 
No module named \'pyFAI.third_party\'\n'
Traceback (most recent call last):
  File "setup.py", line 868, in 
setup_package()
  File "setup.py", line 865, in setup_package
setup(**setup_kwargs)
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 129, in 
setup
return distutils.core.setup(**attrs)
  File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
  File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
  File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
  File "setup.py", line 248, in run
raise RuntimeError("Fail to generate '%s' man documentation" % target_name)
RuntimeError: Fail to generate 'check_calib' man documentation
E: pybuild pybuild:283: build: plugin custom failed with: exit code=1: 
PYTHONPATH=/<>/pyfai-0.15.0+dfsg/.pybuild/pythonX.Y_3.6/build 
xvfb-run -a --server-args="-screen 0 1024x768x24" python3.6 setup.py build_man
dh_auto_build: pybuild --build -i python{version} -p 3.6 returned exit code 13
debian/rules:20: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#888879: rheolef FTBFS on several architectures: test runs forever

[Adrian Bunk]

Source: rheolef
Version: 6.7-5
Severity: serious

https://buildd.debian.org/status/package.php?p=rheolef=sid

...
  mpirun -np 1 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 
left >/dev/null 2>/dev/null
  mpirun -np 2 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 
left >/dev/null 2>/dev/null
  mpirun -np 3 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 
left >/dev/null 2>/dev/null
  mpirun -np 1 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 
right >/dev/null 2>/dev/null
  mpirun -np 2 ./form_mass_bdr_tst -app P2 -weight yz -I my_cube_TP-5-v2 
right >/dev/null 2>/dev/null
E: Build killed with signal TERM after 150 minutes of inactivity


I've reproduced this on i386, two processes are running
forever (aborted after 6 hours on a fast CPU) with 100% CPU.

Backtraces:

Thread 3 (Thread 0xf50ffb40 (LWP 29032)):
#0  0xf7ed6db9 in __kernel_vsyscall ()
#1  0xf70fabd3 in __GI___poll (fds=0xf47005d0, nfds=2, timeout=360) at 
../sysdeps/unix/sysv/linux/poll.c:29
#2  0xf5caed4a in poll (__timeout=360, __nfds=2, __fds=0xf47005d0) at 
/usr/include/i386-linux-gnu/bits/poll2.h:46
#3  poll_dispatch (base=0x578eb9c0, tv=0xf50f9bfc) at poll.c:165
#4  0xf5ca59e9 in opal_libevent2022_event_base_loop (base=, 
flags=) at event.c:1630
#5  0xf5c6b3bd in progress_engine (obj=0x578eb950) at 
runtime/opal_progress_threads.c:105
#6  0xf5df6316 in start_thread (arg=0xf50ffb40) at pthread_create.c:465
#7  0xf7105296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108

Thread 2 (Thread 0xf5ac5b40 (LWP 29031)):
#0  0xf7ed6db9 in __kernel_vsyscall ()
#1  0xf71053fa in __GI_epoll_pwait (epfd=7, events=0x578ea930, maxevents=32, 
timeout=-1, set=0x0)
at ../sysdeps/unix/sysv/linux/epoll_pwait.c:42
#2  0xf710569a in epoll_wait (epfd=7, events=0x578ea930, maxevents=32, 
timeout=-1)
at ../sysdeps/unix/sysv/linux/epoll_wait.c:30
#3  0xf5ca199a in epoll_dispatch (base=0x578ea7a0, tv=0x0) at epoll.c:407
#4  0xf5ca59e9 in opal_libevent2022_event_base_loop (base=, 
flags=) at event.c:1630
#5  0xf5af23eb in progress_engine (obj=0x578ea7a0) at 
src/util/progress_threads.c:52
#6  0xf5df6316 in start_thread (arg=0xf5ac5b40) at pthread_create.c:465
#7  0xf7105296 in clone () at ../sysdeps/unix/sysv/linux/i386/clone.S:108

Thread 1 (Thread 0xf5b4fe00 (LWP 29002)):
#0  0xf7ed67f5 in ?? ()
#1  0xf7ed6b43 in __vdso_clock_gettime ()
#2  0xf7112961 in __GI___clock_gettime (clock_id=1, tp=0xffb74194) at 
../sysdeps/unix/clock_gettime.c:115
#3  0xf5cc3297 in opal_timer_linux_get_usec_clock_gettime () at 
timer_linux_component.c:197
#4  0xf5c669c3 in opal_progress () at runtime/opal_progress.c:197
#5  0xf74b5e05 in sync_wait_st (sync=) at 
../opal/threads/wait_sync.h:80
#6  ompi_request_default_wait_all (count=2, requests=0xffb742e4, statuses=0x0) 
at request/req_wait.c:221
#7  0xf750640d in ompi_coll_base_allreduce_intra_recursivedoubling 
(sbuf=0x57951030, rbuf=0x57a9b400, count=2, 
dtype=0xf7565140 , op=0xf7573e60 , 
comm=0xf7569520 , 
module=0x57976fa0) at base/coll_base_allreduce.c:225
#8  0xe991f640 in ompi_coll_tuned_allreduce_intra_dec_fixed (sbuf=0x57951030, 
rbuf=0x57a9b400, count=2, 
dtype=0xf7565140 , op=0xf7573e60 , 
comm=0xf7569520 , 
module=0x57976fa0) at coll_tuned_decision_fixed.c:66
#9  0xf74c5b77 in PMPI_Allreduce (sendbuf=0x57951030, recvbuf=0x57a9b400, 
count=2, 
datatype=0xf7565140 , op=0xf7573e60 , 
comm=0xf7569520 )
at pallreduce.c:107
#10 0xf7b476cf in boost::mpi::detail::all_reduce_impl > (comm=..., 
in_values=0x57951030, n=n@entry=2, out_values=0x57a9b400) at 
/usr/include/boost/mpi/collectives/all_reduce.hpp:36
#11 0xf7b58fc0 in boost::mpi::all_reduce 
> (out_values=, n=2, 
in_values=, comm=..., op=...) at 
/usr/include/boost/mpi/collectives/all_reduce.hpp:93
#12 rheolef::mpi_assembly_begin >, rheolef::disarray_rep::message_type, 
rheolef::apply_iterator, rheolef::first_op > > (stash=..., first_stash_idx=..., 
last_stash_idx=..., ownership=..., receive=..., send=...) at 
../../include/rheolef/mpi_assembly_begin.h:113
#13 0xf7b5a346 in rheolef::disarray_rep::dis_entry_assembly_begin 
(this=0x57acab70, my_set_op=...)
at ../../include/rheolef/disarray_mpi.icc:223
#14 rheolef::disarray::dis_entry_assembly_begin (this=) at ../../include/rheolef/disarray.h:592
#15 rheolef::disarray::dis_entry_assembly (this=) 
at ../../include/rheolef/disarray.h:594
#16 rheolef::geo_rep::set_element_side_index 
(this=, 
side_dim=) at geo_mpi_get.cc:461
#17 0xf7b5f25a in rheolef::geo_rep::get 
(this=, 

Bug#888733: hyantesite FTBFS on most architectures: test failures

[Adrian Bunk]

Source: hyantesite
Version: 1.3.0-2
Severity: serious

hyantesite FTBFS on most architectures with varying test failures:

https://buildd.debian.org/status/package.php?p=hyantesite

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#888177: pytables FBFS with sphinx 1.6.6-1

[Adrian Bunk]

Source: pytables
Version: 3.4.2-2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pytables.html

...
! LaTeX Error: There's no line here to end.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H   for immediate help.
 ...  
  
l.21844 \\
  
? 
! Emergency stop.
 ...  
  
l.21844 \\
  
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on usersguide-3.4.2.log.
Latexmk: Index file 'usersguide-3.4.2.idx' was written
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs of latex/pdflatex.
Latexmk: Errors, so I did not complete making targets
Makefile:33: recipe for target 'usersguide-3.4.2.pdf' failed
make[3]: *** [usersguide-3.4.2.pdf] Error 12


11:19 < mitya57> bunk: It is a raw latex block, which starts with \\ even 
though it does not know what is before those lines. So looks like a pytables 
 bug, even if it's triggered by sphinx update.
11:19 < mitya57> See 
https://sources.debian.org/src/pytables/3.4.2-2/doc/source/usersguide/optimization.rst/#L1040

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887931: gazebo FTBFS with libtinyxml2-dev 6.0.0+dfsg-1

[Adrian Bunk]

Source: gazebo
Version: 7.8.1+dfsg-4
Severity: serious

https://buildd.debian.org/status/package.php?p=gazebo=sid

...
/<>/gazebo-7.8.1+dfsg/gazebo/util/LogPlay.cc: In member function 
'void gazebo::util::LogPlay::Open(const string&)':
/<>/gazebo-7.8.1+dfsg/gazebo/util/LogPlay.cc:121:51: error: 'class 
tinyxml2::XMLDocument' has no member named 'GetErrorStr1'; did you mean 
'ErrorStr'?
 const char *errorStr1 = this->dataPtr->xmlDoc.GetErrorStr1();
   ^~~~
   ErrorStr
/<>/gazebo-7.8.1+dfsg/gazebo/util/LogPlay.cc:122:51: error: 'class 
tinyxml2::XMLDocument' has no member named 'GetErrorStr2'; did you mean 
'ErrorStr'?
 const char *errorStr2 = this->dataPtr->xmlDoc.GetErrorStr2();
   ^~~~
   ErrorStr
gazebo/util/CMakeFiles/gazebo_util.dir/build.make:89: recipe for target 
'gazebo/util/CMakeFiles/gazebo_util.dir/LogPlay.cc.o' failed
make[3]: *** [gazebo/util/CMakeFiles/gazebo_util.dir/LogPlay.cc.o] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887760: graywolf FTBFS with glibc 2.26

[Adrian Bunk]

Source: graywolf
Version: 0.1.4+20170307gite1bf319-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/graywolf.html

...
/build/1st/graywolf-0.1.4+20170307gite1bf319/src/Ylib/okmalloc.c: In function 
'Ysafe_cfree':
/build/1st/graywolf-0.1.4+20170307gite1bf319/src/Ylib/okmalloc.c:904:5: 
warning: implicit declaration of function 'cfree'; did you mean 'free'? 
[-Wimplicit-function-declaration]
 cfree(ptr);
 ^
...
[ 53%] Linking C executable TimberWolfMC
cd /build/1st/graywolf-0.1.4+20170307gite1bf319/obj-x86_64-linux-gnu/src/twmc 
&& /usr/bin/cmake -E cmake_link_script CMakeFiles/TimberWolfMC.dir/link.txt 
--verbose=1
/usr/bin/cc -g -O2 
-fdebug-prefix-map=/build/1st/graywolf-0.1.4+20170307gite1bf319=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2  -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -rdynamic 
CMakeFiles/TimberWolfMC.dir/acceptt.c.o CMakeFiles/TimberWolfMC.dir/analyze.c.o 
CMakeFiles/TimberWolfMC.dir/compact.c.o CMakeFiles/TimberWolfMC.dir/config1.c.o 
CMakeFiles/TimberWolfMC.dir/config2.c.o 
CMakeFiles/TimberWolfMC.dir/configpads.c.o 
CMakeFiles/TimberWolfMC.dir/debug.c.o CMakeFiles/TimberWolfMC.dir/finalout.c.o 
CMakeFiles/TimberWolfMC.dir/finalpin.c.o CMakeFiles/TimberWolfMC.dir/gmain.c.o 
CMakeFiles/TimberWolfMC.dir/findcheck.c.o 
CMakeFiles/TimberWolfMC.dir/findcost.c.o 
CMakeFiles/TimberWolfMC.dir/findloc.c.o 
CMakeFiles/TimberWolfMC.dir/findside.c.o 
CMakeFiles/TimberWolfMC.dir/fixcell.c.o 
CMakeFiles/TimberWolfMC.dir/genorient.c.o 
CMakeFiles/TimberWolfMC.dir/graphics.c.o 
CMakeFiles/TimberWolfMC.dir/initialize.c.o 
CMakeFiles/TimberWolfMC.dir/initnets.c.o 
 CMakeFiles/TimberWolfMC.dir/loadbins.c.o CMakeFiles/TimberWolfMC.dir/main.c.o 
CMakeFiles/TimberWolfMC.dir/makebins.c.o 
CMakeFiles/TimberWolfMC.dir/makesite.c.o 
CMakeFiles/TimberWolfMC.dir/mergecell.c.o 
CMakeFiles/TimberWolfMC.dir/neworient.c.o 
CMakeFiles/TimberWolfMC.dir/newtemp.c.o CMakeFiles/TimberWolfMC.dir/outgeo.c.o 
CMakeFiles/TimberWolfMC.dir/outpin.c.o CMakeFiles/TimberWolfMC.dir/output.c.o 
CMakeFiles/TimberWolfMC.dir/overlap.c.o CMakeFiles/TimberWolfMC.dir/paths.c.o 
CMakeFiles/TimberWolfMC.dir/partition.c.o 
CMakeFiles/TimberWolfMC.dir/penalties.c.o 
CMakeFiles/TimberWolfMC.dir/perimeter.c.o 
CMakeFiles/TimberWolfMC.dir/placepads.c.o 
CMakeFiles/TimberWolfMC.dir/placepin.c.o 
CMakeFiles/TimberWolfMC.dir/prboard.c.o 
CMakeFiles/TimberWolfMC.dir/readcells.c.o 
CMakeFiles/TimberWolfMC.dir/readnets.c.o CMakeFiles/TimberWolfMC.dir/rmain.c.o 
CMakeFiles/TimberWolfMC.dir/readpar.c.o 
CMakeFiles/TimberWolfMC.dir/reconfig.c.o 
CMakeFiles/TimberWolfMC.dir/savewolf.c.o CMakeFiles/TimberWolfMC.di
 r/scrapnet.c.o CMakeFiles/TimberWolfMC.dir/sortpin.c.o 
CMakeFiles/TimberWolfMC.dir/selectpin.c.o 
CMakeFiles/TimberWolfMC.dir/setpwates.c.o 
CMakeFiles/TimberWolfMC.dir/sortpad.c.o CMakeFiles/TimberWolfMC.dir/twstats.c.o 
CMakeFiles/TimberWolfMC.dir/uaspect.c.o CMakeFiles/TimberWolfMC.dir/uloop.c.o 
CMakeFiles/TimberWolfMC.dir/unbust.c.o CMakeFiles/TimberWolfMC.dir/uinst.c.o 
CMakeFiles/TimberWolfMC.dir/unet.c.o CMakeFiles/TimberWolfMC.dir/upin.c.o 
CMakeFiles/TimberWolfMC.dir/upinswap.c.o CMakeFiles/TimberWolfMC.dir/usite1.c.o 
CMakeFiles/TimberWolfMC.dir/usite2.c.o 
CMakeFiles/TimberWolfMC.dir/usoftmove.c.o CMakeFiles/TimberWolfMC.dir/utemp.c.o 
CMakeFiles/TimberWolfMC.dir/watesides.c.o 
CMakeFiles/TimberWolfMC.dir/window.c.o 
CMakeFiles/TimberWolfMC.dir/wirecosts.c.o 
CMakeFiles/TimberWolfMC.dir/wireest.c.o 
CMakeFiles/TimberWolfMC.dir/wireratio.c.o 
CMakeFiles/TimberWolfMC.dir/__/date/date.c.o  -o TimberWolfMC  
-L/build/1st/graywolf-0.1.4+20170307gite1bf319/obj-x86_64-linux-gnu/src/Ylib 
-Wl,-
 
rpath,/build/1st/graywolf-0.1.4+20170307gite1bf319/obj-x86_64-linux-gnu/src/Ylib:
 -lycadgraywolf -lX11 -lm -lgsl -lgslcblas -lm -lgsl -lgslcblas 
/build/1st/graywolf-0.1.4+20170307gite1bf319/obj-x86_64-linux-gnu/src/Ylib/libycadgraywolf.so:
 undefined reference to `cfree'
collect2: error: ld returned 1 exit status
src/twmc/CMakeFiles/TimberWolfMC.dir/build.make:1788: recipe for target 
'src/twmc/TimberWolfMC' failed
make[3]: *** [src/twmc/TimberWolfMC] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887757: heaptrack FTBFS with glibc 2.26

[Adrian Bunk]

Source: heaptrack
Version: 1.0.1~20170503.git4da8c45-3
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/heaptrack.html

...
/build/1st/heaptrack-1.0.1~20170503.git4da8c45/tests/manual/test.cpp: In 
function 'int main()':
/build/1st/heaptrack-1.0.1~20170503.git4da8c45/tests/manual/test.cpp:85:5: 
error: 'cfree' was not declared in this scope
 cfree(buf);
 ^

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887749: pymca FTBFS with glibc 2.26

[Adrian Bunk]

Source: pymca
Version: 5.2.2+dfsg-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pymca.html

...
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes 
-fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/1st/pymca-5.2.2+dfsg=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -D_GNU_SOURCE=1 -IPyMca5/PyMcaIO/specfile/include 
-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 
-c PyMca5/PyMcaIO/specfile/src/locale_management.c -o 
build/temp.linux-amd64-2.7/PyMca5/PyMcaIO/specfile/src/locale_management.o
PyMca5/PyMcaIO/specfile/src/locale_management.c:27:10: fatal error: xlocale.h: 
No such file or directory
 #include 
  ^~~
compilation terminated.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887693: ipe FTBFS with glibc 2.26

[Adrian Bunk]

Source: ipe
Version: 7.2.7-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ipe.html

...
Compiling ipeplatform.cpp...
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fPIC 
-Wall -Wno-sign-conversion -Wno-inconsistent-missing-override -g -O2 -fPIC 
-Wdate-time -D_FORTIFY_SOURCE=2 -DIPEUI_QT -fPIC -std=c++11 -I../include 
-I/usr/include/libpng16  -c -o ../../build/obj/ipelib/ipeplatform.o 
ipeplatform.cpp
ipeplatform.cpp:41:10: fatal error: xlocale.h: No such file or directory
 #include 
  ^~~
compilation terminated.
../common.mak:246: recipe for target '../../build/obj/ipelib/ipeplatform.o' 
failed
make[3]: *** [../../build/obj/ipelib/ipeplatform.o] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#887646: spass FTBFS with glibc 2.26

[Adrian Bunk]

Source: spass
Version: 3.7-4
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/spass.html

...
In file included from ./SPASS/strings.h:49:0,
 from /usr/include/string.h:431,
 from SPASS/misc.h:52,
 from SPASS/memory.h:49,
 from SPASS/description.h:27,
 from SPASS/description.c:21:
./SPASS/list.h:57:3: error: unknown type name 'POINTER'
   POINTER   car;
   ^~~


The root problem is that SPASS/strings.h gets included
instead of /usr/include/strings.h.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#886669: RM: pyfai [armel hurd-i386 mips mips64el mipsel powerpc ppc64el s390x] -- RoQA; new build dependency python-pyopencl not available on these architectures

[Adrian Bunk]

Package: ftp.debian.org
Severity: normal

pyfai >= 0.14.2+dfsg-1 got direct and indirect (through python{,3}-silx)
build dependencies on python{,3}-pyopencl that is not available on
all architectures.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#886361: apertium: frequent parallel FTBFS

[Adrian Bunk]

Source: apertium
Version: 3.4.2~r68466-3
Severity: serious
Tags: patch

https://tests.reproducible-builds.org/debian/history/apertium.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/apertium.html
https://buildd.debian.org/status/package.php?p=apertium=sid

...
/bin/bash ../libtool  --tag=CXX   --mode=link g++  -Wall -Wextra -g -O2 
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
-Werror=format-security  -Wl,-z,relro -Wl,-z,now -o apertium-filter-ambiguity 
apertium_filter_ambiguity.o -llttoolbox3 -lxml2 -lpcre -lapertium3 -lpcreposix 
-lpcre -lpcrecpp -llttoolbox3 -lxml2 -lpcre
libtool: link: g++ -Wall -Wextra -g -O2 "-fdebug-prefix-map=/<>=." 
-fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro 
-Wl,-z -Wl,now -o apertium-filter-ambiguity apertium_filter_ambiguity.o  
-lapertium3 -lpcreposix -lpcrecpp -llttoolbox3 -lxml2 -lpcre
/usr/bin/ld: cannot find -lapertium3
collect2: error: ld returned 1 exit status
Makefile:1056: recipe for target 'apertium-filter-ambiguity' failed
make[3]: *** [apertium-filter-ambiguity] Error 1


This was triggered by dh comat >= 10 defaulting to parallel building.

Fix attached.
Description: Fix parallel FTBFS
 Tell automake that libapertium3 is a self-built library
 so that proper dependencies are added.
Author: Adrian Bunk <b...@debian.org>

--- apertium-3.4.2~r68466.orig/apertium/Makefile.am
+++ apertium-3.4.2~r68466/apertium/Makefile.am
@@ -226,7 +226,7 @@ apertium_DATA = deformat.xsl reformat.xs
 
 apertium_pretransfer_SOURCES = apertium_pretransfer.cc
 apertium_multiple_translations_SOURCES = apertium-multiple-translations.cc
-apertium_multiple_translations_LDADD = $(APERTIUM_LIBS) 
-lapertium$(GENERIC_MAJOR_VERSION)
+apertium_multiple_translations_LDADD = $(APERTIUM_LIBS) libapertium3.la
 apertium_destxt_SOURCES = apertium_destxt.cc
 apertium_retxt_SOURCES = apertium_retxt.cc
 apertium_deshtml_SOURCES = apertium_deshtml.cc
@@ -249,55 +249,55 @@ apertium_repptx_SOURCES = apertium_reppt
 apertium_desmediawiki_SOURCES = apertium_desmediawiki.cc
 apertium_remediawiki_SOURCES = apertium_remediawiki.cc
 apertium_prelatex_SOURCES = apertium_prelatex.cc
-apertium_prelatex_LDADD= $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_prelatex_LDADD= $(APERTIUM_LIBS) libapertium3.la
 apertium_postlatex_SOURCES = apertium_postlatex.cc
-apertium_postlatex_LDADD= $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_postlatex_LDADD= $(APERTIUM_LIBS) libapertium3.la
 apertium_postlatex_raw_SOURCES = apertium_postlatex_raw.cc
-apertium_postlatex_raw_LDADD= $(APERTIUM_LIBS) 
-lapertium$(GENERIC_MAJOR_VERSION)
+apertium_postlatex_raw_LDADD= $(APERTIUM_LIBS) libapertium3.la
 
 apertium_tagger_SOURCES = apertium_tagger.cc
-apertium_tagger_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_tagger_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_tmxbuild_SOURCES = apertium_tmxbuild.cc
-apertium_tmxbuild_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_tmxbuild_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_preprocess_transfer_SOURCES = transferpp.cc
 apertium_preprocess_transfer_LDADD = $(APERTIUM_LIBS) \
- -lapertium$(GENERIC_MAJOR_VERSION)
+ libapertium3.la
 
 apertium_filter_ambiguity_SOURCES = apertium_filter_ambiguity.cc
 apertium_filter_ambiguity_LDADD = $(APERTIUM_LIBS) \
-  -lapertium$(GENERIC_MAJOR_VERSION)
+  libapertium3.la
 
 apertium_transfer_SOURCES = apertium_transfer.cc
-apertium_transfer_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_transfer_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_interchunk_SOURCES = apertium_interchunk.cc
-apertium_interchunk_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_interchunk_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_postchunk_SOURCES = apertium_postchunk.cc
-apertium_postchunk_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+apertium_postchunk_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 ###apertium_lextor_SOURCES = apertium_lextor.cc
-###apertium_lextor_LDADD = $(APERTIUM_LIBS) -lapertium$(GENERIC_MAJOR_VERSION)
+###apertium_lextor_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 #apertium_lextor_eval_SOURCES = apertium-lextor-eval.C
-#apertium_lextor_eval_LDADD = $(APERTIUM_LIBS) 
-lapertium$(GENERIC_MAJOR_VERSION)
+#apertium_lextor_eval_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_tagger_apply_new_rules_SOURCES = apertium_tagger_apply_new_rules.cc
-apertium_tagger_apply_new_rules_LDADD = $(APERTIUM_LIBS) 
-lapertium$(GENERIC_MAJOR_VERSION)
+apertium_tagger_apply_new_rules_LDADD = $(APERTIUM_LIBS) libapertium3.la
 
 apertium_tagger_readwords_SOURCES = apertium_tagger_readwords.cc
-apertium_tagger_readwords_LDADD = $(APERTIUM_LIBS) 
-lapertium$(GENERIC_MAJOR_VERSION)
+

Bug#833144: mpich: MPICH compiled with BCLR causes problems with valgrind

[Adrian Bunk]

Control: block 876908 by -1

On Mon, Aug 01, 2016 at 06:09:47PM +0200, Anton Gladky wrote:
>...
> thanks for bugreport. We will consider to drop blcr-support in
> Debian-builds.
>...

Any updates on this?

As explained in #876908, the kernel part blcr does not even compile with
the kernels in jessie and later.

> Best regards
> 
> Anton

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#884535: sciscipy FTBFS with scilab 6.0.0-1

[Adrian Bunk]

Source: sciscipy
Version: 1.0.1-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/sciscipy.html

...
   dh_auto_build
dh_auto_build: Compatibility levels before 9 are deprecated (level 5 in use)
pyversions: missing X(S)-Python-Version in control file, fall back to 
debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
python setup.py build --force
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
copying scilab.py -> build/lib.linux-x86_64-2.7
running build_ext
building 'sciscipy' extension
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall 
-Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g 
-fdebug-prefix-map=/build/python2.7-j9xj4T/python2.7-2.7.14=. 
-fstack-protector-strong -Wformat -Werror=format-security -fPIC

creating build/temp.linux-x86_64-2.7
compile options: '-DSCI="/usr/local/share/scilab" -DSCIDEBUG=0 -DNUMPY=1 
-I/usr/include/scilab -I/usr/include/scilab/core 
-I/usr/include/scilab/call_scilab 
-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 
-c'
x86_64-linux-gnu-gcc: deallocator.c
In file included from 
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
 from 
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
 from 
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
 from deallocator.h:7,
 from deallocator.c:7:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
 warning: #warning "Using deprecated NumPy API, disable it by " "#defining 
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^~~
In file included from 
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
 from 
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
 from deallocator.h:7,
 from deallocator.c:7:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1453:1:
 warning: '_import_array' defined but not used [-Wunused-function]
 _import_array(void)
 ^
x86_64-linux-gnu-gcc: util.c
In file included from /usr/include/scilab/api_scilab.h:36:0,
 from util.h:8,
 from util.c:2:
/usr/include/scilab/api_stack_common.h:486:1: warning: function declaration 
isn't a prototype [-Wstrict-prototypes]
 SciErr sciErrInit();
 ^~
util.c: In function 'read_sci_type':
util.c:27:38: error: 'pvApiCtx' undeclared (first use in this function); did 
you mean 'pStrCtx'?
 sciErr = readNamedMatrixOfDouble(pvApiCtx, "_tmp_value_", , , NULL);
  ^~~~
  pStrCtx
util.c:27:38: note: each undeclared identifier is reported only once for each 
function it appears in
util.c: In function 'is_real':
util.c:55:31: error: 'pvApiCtx' undeclared (first use in this function); did 
you mean 'pStrCtx'?
 return !isNamedVarComplex(pvApiCtx, name);
   ^~~~
   pStrCtx
util.c:56:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
In file included from /usr/include/scilab/api_scilab.h:36:0,
 from util.h:8,
 from util.c:2:
/usr/include/scilab/api_stack_common.h:486:1: warning: function declaration 
isn't a prototype [-Wstrict-prototypes]
 SciErr sciErrInit();
 ^~
util.c: In function 'read_sci_type':
util.c:27:38: error: 'pvApiCtx' undeclared (first use in this function); did 
you mean 'pStrCtx'?
 sciErr = readNamedMatrixOfDouble(pvApiCtx, "_tmp_value_", , , NULL);
  ^~~~
  pStrCtx
util.c:27:38: note: each undeclared identifier is reported only once for each 
function it appears in
util.c: In function 'is_real':
util.c:55:31: error: 'pvApiCtx' undeclared (first use in this function); did 
you mean 'pStrCtx'?
 return !isNamedVarComplex(pvApiCtx, name);
   ^~~~
   pStrCtx
util.c:56:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
error: Command "x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall 
-Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g 
-fdebug-prefix-map=/build/python2.7-j9xj4T/python2.7-2.7.14=. 
-fstack-protector-strong -Wformat -Werror=format-security -fPIC 
-DSCI="/usr/local/share/scilab" -DSCIDEBUG=0 -DNUMPY=1 -I/usr/include/scilab 
-I/usr/include/scilab/core -I/usr/include/scilab/call_scilab 
-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 
-c util.c -o build/temp.linux-x86_64-2.7/util.o" failed with exit status 1

Bug#884407: wslay FTBFS with nettle-dev 3.4-1

[Adrian Bunk]

Source: wslay
Version: 1.0.1~39-g6abacc1-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/wslay.html

...
/build/1st/wslay-1.0.1~39-g6abacc1/examples/echoserv.cc: In function 
'std::__cxx11::string base64(const string&)':
/build/1st/wslay-1.0.1~39-g6abacc1/examples/echoserv.cc:126:83: error: invalid 
conversion from 'uint8_t* {aka unsigned char*}' to 'char*' [-fpermissive]
   base64_encode_raw(dst, src.size(), reinterpret_cast(src.c_str()));

   ^
In file included from 
/build/1st/wslay-1.0.1~39-g6abacc1/examples/echoserv.cc:52:0:
/usr/include/nettle/base64.h:117:1: note:   initializing argument 1 of 'void 
nettle_base64_encode_raw(char*, size_t, const uint8_t*)'
 base64_encode_raw(char *dst, size_t length, const uint8_t *src);
 ^
/build/1st/wslay-1.0.1~39-g6abacc1/examples/testclient.cc: In function 
'std::__cxx11::string base64(const string&)':
/build/1st/wslay-1.0.1~39-g6abacc1/examples/testclient.cc:118:66: error: 
invalid conversion from 'uint8_t* {aka unsigned char*}' to 'char*' 
[-fpermissive]
 reinterpret_cast(src.c_str()));
  ^
In file included from 
/build/1st/wslay-1.0.1~39-g6abacc1/examples/testclient.cc:51:0:
/usr/include/nettle/base64.h:117:1: note:   initializing argument 1 of 'void 
nettle_base64_encode_raw(char*, size_t, const uint8_t*)'
 base64_encode_raw(char *dst, size_t length, const uint8_t *src);
 ^
examples/CMakeFiles/echoserv.dir/build.make:65: recipe for target 
'examples/CMakeFiles/echoserv.dir/echoserv.cc.o' failed
make[4]: *** [examples/CMakeFiles/echoserv.dir/echoserv.cc.o] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#882451: ovito: FTBFS on armel: QOpenGLFunctions_* does not name a type

[Adrian Bunk]

On Wed, Nov 22, 2017 at 10:37:36PM -0500, Aaron M. Ucko wrote:
> Source: ovito
> Version: 2.9.0+dfsg1-5
> Severity: important
> Tags: upstream
> Justification: fails to build from source
> User: debian-...@lists.debian.org
> Usertags: armel
> 
> Builds of ovito for armel have been failing lately as detailed in
> https://buildd.debian.org/status/fetch.php?pkg=ovito=armel=2.9.0%2Bdfsg1-5=1511236739=0
> with a cascade of errors starting with
> 
>   
> /<>/ovito-2.9.0+dfsg1/src/opengl_renderer/OpenGLSceneRenderer.h:255:2:
>  error: 'QOpenGLFunctions_2_0' does not name a type; did you mean 
> 'QOpenGLFunctions'?
> 
> IIRC, Qt uses GLES rather than traditional OpenGL here.
>...

Ideally it should be made working to build when Qt is using
OpenGL ES, bug if that is not possible it would be better to
avoid the FTBFS by changing the build dependency from
libqt5opengl5-dev to libqt5opengl5-desktop-dev.


cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#804218: libqglviewer FTBFS on armel and armhf

[Adrian Bunk]

On Fri, Nov 06, 2015 at 10:34:45AM +, Peter Michael Green wrote:
>...
> The qt5 build is suffering from the fact that Debian builds qt5 on
> armel/armhf against opengl es. libqglviewer includes regular opengl headers
> leading to conflicting declarations. I tried patching it to include opengl
> es headers instead but I then ran into a load of stuff that only exists in
> desktop opengl. This needs the attention of an opengl expert if it's fixable
> at all.
>...

If that is not possible it would be better to avoid the FTBFS
by changing the build dependency from libqt5opengl5-dev to 
libqt5opengl5-desktop-dev.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#884294: pandas FTBFS: test failure

[Adrian Bunk]

Source: pandas
Version: 0.20.3-10
Severity: serious

Some recent change in unstable makes pandas FTBFS:

https://tests.reproducible-builds.org/debian/history/pandas.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pandas.html

...
=== FAILURES ===
_ TestSafeSort.test_unsortable _

self = 

def test_unsortable(self):
# GH 13714
arr = np.array([1, 2, datetime.now(), 0, 3], dtype=object)
if compat.PY2 and not pd._np_version_under1p10:
# RuntimeWarning: tp_compare didn't return -1 or -2 for exception
with tm.assert_produces_warning(RuntimeWarning):
>   pytest.raises(TypeError, algos.safe_sort, arr)

../debian/tmp/usr/lib/python2.7/dist-packages/pandas/tests/test_algos.py:131: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/usr/lib/python2.7/contextlib.py:24: in __exit__
self.gen.next()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

expected_warning = , filter_level = 'always'
clear = None, check_stacklevel = True

@contextmanager
def assert_produces_warning(expected_warning=Warning, filter_level="always",
clear=None, check_stacklevel=True):
"""
Context manager for running code that expects to raise (or not raise)
warnings.  Checks that code raises the expected warning and only the
expected warning. Pass ``False`` or ``None`` to check that it does *not*
raise a warning. Defaults to ``exception.Warning``, baseclass of all
Warnings. (basically a wrapper around ``warnings.catch_warnings``).

>>> import warnings
>>> with assert_produces_warning():
... warnings.warn(UserWarning())
...
>>> with assert_produces_warning(False):
... warnings.warn(RuntimeWarning())
...
Traceback (most recent call last):
...
AssertionError: Caused unexpected warning(s): ['RuntimeWarning'].
>>> with assert_produces_warning(UserWarning):
... warnings.warn(RuntimeWarning())
Traceback (most recent call last):
...
AssertionError: Did not see expected warning of class 'UserWarning'.

..warn:: This is *not* thread-safe.
"""
with warnings.catch_warnings(record=True) as w:

if clear is not None:
# make sure that we are clearning these warnings
# if they have happened before
# to guarantee that we will catch them
if not is_list_like(clear):
clear = [clear]
for m in clear:
try:
m.__warningregistry__.clear()
except:
pass

saw_warning = False
warnings.simplefilter(filter_level)
yield w
extra_warnings = []

for actual_warning in w:
if (expected_warning and issubclass(actual_warning.category,
expected_warning)):
saw_warning = True

if check_stacklevel and issubclass(actual_warning.category,
   (FutureWarning,
DeprecationWarning)):
from inspect import getframeinfo, stack
caller = getframeinfo(stack()[2][0])
msg = ("Warning not set with correct stacklevel. "
   "File where warning is raised: {0} != {1}. "
   "Warning message: {2}".format(
   actual_warning.filename, caller.filename,
   actual_warning.message))
assert actual_warning.filename == caller.filename, msg
else:
extra_warnings.append(actual_warning.category.__name__)
if expected_warning:
assert saw_warning, ("Did not see expected warning of class %r."
>% expected_warning.__name__)
E   AssertionError: Did not see expected warning of class 
'RuntimeWarning'.

../debian/tmp/usr/lib/python2.7/dist-packages/pandas/util/testing.py:2655: 
AssertionError
=== warnings summary ===
debian/tmp/usr/lib/python2.7/dist-packages/pandas/tests/dtypes/test_missing.py::test_array_equivalent_compat
  /usr/lib/python2.7/dist-packages/numpy/core/numeric.py:2604: FutureWarning: 
elementwise == comparison failed and returning scalar instead; this will raise 
an error or perform elementwise comparison in the future.
return 

Bug#884033: scilab segfaults building scilab-{ann,celestlab,plotlib}

[Adrian Bunk]

Package: scilab
Version: 6.0.0-1
Severity: serious
Control: affects -1 src:scilab-ann src:scilab-celestlab src:scilab-plotlib

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/scilab-ann.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/scilab-celestlab.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/scilab-plotlib.html

...
SCI_DISABLE_TK=1 SCI_JAVA_ENABLE_HEADLESS=1 /usr/bin/scilab -nw -f builder.sce  
A fatal error has been detected by Scilab.
Please check your user-defined functions (or external module ones) should they 
appear in the stack trace.
Otherwise you can report a bug on http://bugzilla.scilab.org/ with:
 * a sample code which reproduces the issue
 * the result of [a, b] = getdebuginfo()
 * the following information:
[profitbricks-build11-amd64:15107] Signal: Segmentation fault (11)
[profitbricks-build11-amd64:15107] Signal code: Address not mapped (1)
[profitbricks-build11-amd64:15107] Failing at address: (nil)
 
Call stack:
   1: 0x9bc60   
(/lib/x86_64-linux-gnu/libc.so.6)
   2: 0x9bc1e   
(/lib/x86_64-linux-gnu/libc.so.6)
   3: 0x46da76  
(/usr/lib/scilab/libsciast.so.6)
   4: 0x46e042  
(/usr/lib/scilab/libsciast.so.6)
   5: 0x3b9c17 (/usr/lib/scilab/libsciast.so.6)
   6: 0x3b9d61   (/usr/lib/scilab/libsciast.so.6)
   7: 0x3ba9ce  (/usr/lib/scilab/libsciast.so.6)
   8: 0x192d05   
(/usr/lib/scilab/libscilab-cli.so.6)
   9: 0x1a23  (/usr/bin/scilab-bin)
  10: 0x20561  <__libc_start_main>  
(/lib/x86_64-linux-gnu/libc.so.6)
  11: 0x247a   < >  (/usr/bin/scilab-bin)
End of stack



debian/rules:8: recipe for target 'build/scilab-ann' failed
make: *** [build/scilab-ann] Error 51

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#882591: gazebo FTBFS: /usr/include/boost/predef/language/stdc.h:52: Parse error at "defined"

[Adrian Bunk]

Source: gazebo
Version: 7.8.1+dfsg-2
Severity: serious

Some recent change in unstable makes gazebo FTBFS:

https://tests.reproducible-builds.org/debian/history/gazebo.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/gazebo.html

...
/usr/include/boost/predef/language/stdc.h:52: Parse error at "defined"
gazebo/gui/CMakeFiles/gazebo_gui.dir/build.make:75: recipe for target 
'gazebo/gui/moc_ApplyWrenchDialog.cxx' failed
make[3]: *** [gazebo/gui/moc_ApplyWrenchDialog.cxx] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#882312: segyio FTBFS on 32bit: segy_ftell: Assertion `sizeof( long ) == sizeof( long long )' failed

[Adrian Bunk]

Source: segyio
Version: 1.3.3-1
Severity: important

https://buildd.debian.org/status/package.php?p=segyio=sid

...
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:184: dh_auto_test --buildsystem=cmake 
--builddirectory="/<>/.pybuild/pythonX.Y_3.6/build" -- 
cd .pybuild/pythonX.Y_3.6/build && make -j4 test ARGS\+=-j4
make[1]: Entering directory '/<>/.pybuild/pythonX.Y_3.6/build'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<>/.pybuild/pythonX.Y_3.6/build
  Start  1: c.segy
  Start  2: c.utils
  Start  3: python.segy
  Start  4: python.h.segy
 1/17 Test  #1: c.segy ...***Exception: Other  0.22 sec
testsegy: /<>/lib/src/segy.c:409: segy_ftell: Assertion `sizeof( 
long ) == sizeof( long long )' failed.
starting
interpret file
read inline 4
read inline 22
mod traceh
mod texth
test traceh
test readsubtr(mmap)
test readsubtr(no-mmap)
test writesubtr(no-mmap)
test scan headers(mmap)
test scan headers(no-mmap)

  Start  5: python.enum.segy
 2/17 Test  #2: c.utils ..   Passed0.84 sec
 3/17 Test  #4: python.h.segy    Passed1.01 sec
  Start  6: python.tools
  Start  7: python.context
 4/17 Test  #5: python.enum.segy .   Passed0.94 sec
  Start  8: python.example.about
 5/17 Test  #7: python.context ...   Passed0.50 sec
  Start  9: python.example.write
 6/17 Test  #6: python.tools .   Passed1.03 sec
  Start 10: python.example.makefile
 7/17 Test  #3: python.segy ..   Passed2.09 sec
  Start 11: python.example.makepsfile
 8/17 Test  #8: python.example.about .   Passed1.13 sec
  Start 12: python.example.subcube
 9/17 Test  #9: python.example.write .   Passed1.17 sec
  Start 13: python.example.rotate
10/17 Test #10: python.example.makefile ..   Passed1.25 sec
  Start 14: python.example.scan_min_max
11/17 Test #11: python.example.makepsfile    Passed0.93 sec
  Start 15: applications.catr
12/17 Test #12: python.example.subcube ...   Passed0.92 sec
  Start 16: applications.catb
13/17 Test #13: python.example.rotate    Passed1.07 sec
14/17 Test #15: applications.catr    Passed0.59 sec
  Start 17: applications.cath
15/17 Test #14: python.example.scan_min_max ..   Passed1.11 sec
16/17 Test #16: applications.catb    Passed0.70 sec
17/17 Test #17: applications.cath    Passed0.57 sec

94% tests passed, 1 tests failed out of 17

Total Test time (real) =   4.79 sec

The following tests FAILED:
  1 - c.segy (OTHER_FAULT)
Errors while running CTest
Makefile:120: recipe for target 'test' failed
make[1]: *** [test] Error 8

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#882298: trilinos: missing dependencies on libtrilinos-trilinosss-dev

[Adrian Bunk]

Source: trilinos
Version: 12.12.1-2
Severity: serious
Control: affects -1 src:deal.ii

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/deal.ii.html

...
-- Include /build/1st/deal.ii-8.4.2/cmake/configure/configure_2_trilinos.cmake
CMake Error at /usr/lib/x86_64-linux-gnu/cmake/Amesos/AmesosConfig.cmake:144 
(INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/Amesos/../TrilinosSS/TrilinosSSConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Ifpack/IfpackConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/ML/MLConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stratimikos/StratimikosConfig.cmake:144 
(INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Teko/TekoConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/MueLu/MueLuConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stokhos/StokhosConfig.cmake:143 (INCLUDE)
  
/usr/lib/x86_64-linux-gnu/cmake/TrilinosCouplings/TrilinosCouplingsConfig.cmake:143
 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)

CMake Error at /usr/lib/x86_64-linux-gnu/cmake/Ifpack/IfpackConfig.cmake:146 
(INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/Ifpack/../TrilinosSS/TrilinosSSConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/ML/MLConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stratimikos/StratimikosConfig.cmake:144 
(INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Teko/TekoConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/MueLu/MueLuConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stokhos/StokhosConfig.cmake:143 (INCLUDE)
  
/usr/lib/x86_64-linux-gnu/cmake/TrilinosCouplings/TrilinosCouplingsConfig.cmake:143
 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Error at /usr/lib/x86_64-linux-gnu/cmake/ML/MLConfig.cmake:155 (INCLUDE):
  INCLUDE could not find load file:

/usr/lib/x86_64-linux-gnu/cmake/ML/../TrilinosSS/TrilinosSSConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Stratimikos/StratimikosConfig.cmake:144 
(INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Teko/TekoConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/MueLu/MueLuConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stokhos/StokhosConfig.cmake:143 (INCLUDE)
  
/usr/lib/x86_64-linux-gnu/cmake/TrilinosCouplings/TrilinosCouplingsConfig.cmake:143
 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake:146 (INCLUDE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/modules/FindTRILINOS.cmake:40 (FIND_PACKAGE)
  cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
  cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
  obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
  cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
  cmake/macros/macro_configure_feature.cmake:240 (RUN_COMMAND)
  cmake/configure/configure_2_trilinos.cmake:220 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:119 (VERBOSE_INCLUDE)


CMake Error at 
/usr/lib/x86_64-linux-gnu/cmake/Stratimikos/StratimikosConfig.cmake:157 
(INCLUDE):
  INCLUDE could not find load file:


/usr/lib/x86_64-linux-gnu/cmake/Stratimikos/../TrilinosSS/TrilinosSSConfig.cmake
Call Stack (most recent call first):
  /usr/lib/x86_64-linux-gnu/cmake/Teko/TekoConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/MueLu/MueLuConfig.cmake:143 (INCLUDE)
  /usr/lib/x86_64-linux-gnu/cmake/Stokhos/StokhosConfig.cmake:143 (INCLUDE)
  

Bug#882167: solvespace FTBFS with glibc 2.25

[Adrian Bunk]

Source: solvespace
Version: 2.3+repack1-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/solvespace.html

...
In file included from 
/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/limits.h:194:0,
 from 
/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/syslimits.h:7,
 from /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed/limits.h:34,
 from /build/1st/solvespace-2.3+repack1/src/solvespace.h:18,
 from 
/build/1st/solvespace-2.3+repack1/src/unix/unixutil.cpp:12:
/build/1st/solvespace-2.3+repack1/src/ui.h:30:9: error: expected identifier 
before numeric constant
 CHAR_WIDTH = 9,
 ^


This is caused by glibc >= 2.25 having a CHAR_WIDTH
define in /usr/include/limits.h

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#882026: qtiplot FTBFS: fatal error: sipAPIqti.h: No such file or directory

[Adrian Bunk]

Source: qtiplot
Version: 0.9.8.9-16
Severity: serious

Some recent change in unstable makes qtiplot FTBFS:

https://tests.reproducible-builds.org/debian/history/qtiplot.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/qtiplot.html

...
src/scripting/PythonScripting.cpp:61:10: fatal error: sipAPIqti.h: No such file 
or directory
 #include "sipAPIqti.h"
  ^

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#881950: cctz FTBFS on mips/mipsel: time_zone_lookup_test fails

[Adrian Bunk]

Source: cctz
Version: 2.1~git~a59b930afc8+dfsg1-1
Severity: important

https://buildd.debian.org/status/package.php?p=cctz=sid

...
   dh_auto_test -a -O--buildsystem=cmake
cd obj-mips-linux-gnu && make -j4 test ARGS\+=-j4
make[1]: Entering directory 
'/<>/cctz-2.1~git~a59b930afc8+dfsg1/obj-mips-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<>/cctz-2.1~git~a59b930afc8+dfsg1/obj-mips-linux-gnu
Start 1: civil_time_test
Start 2: time_zone_lookup_test
Start 3: time_zone_format_test
Start 4: benchmarks
1/4 Test #1: civil_time_test ..   Passed0.02 sec
2/4 Test #2: time_zone_lookup_test ***Exception: Other  0.05 sec
Running main() from gtest_main.cc
[==] Running 31 tests from 7 test cases.
[--] Global test environment set-up.
[--] 1 test from TimeZones
[ RUN  ] TimeZones.LoadZonesConcurrently
terminate called without an active exception

3/4 Test #3: time_zone_format_test    Passed1.86 sec
4/4 Test #4: benchmarks ...   Passed   33.86 sec

75% tests passed, 1 tests failed out of 4

Total Test time (real) =  33.88 sec

The following tests FAILED:
  2 - time_zone_lookup_test (OTHER_FAULT)
Errors while running CTest
Makefile:121: recipe for target 'test' failed
make[1]: *** [test] Error 8

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#881223: gnuplot binary-all FTBFS: dh_install: Cannot find (any matches for) "debian/tmp/QT/usr/share/texmf/tex/"

[Adrian Bunk]

Source: gnuplot
Version: 5.2.2+dfsg1-1
Severity: serious

https://buildd.debian.org/status/fetch.php?pkg=gnuplot=all=5.2.2%2Bdfsg1-1=1510179219=0

...
   dh_install -i
dh_install: Cannot find (any matches for) "debian/tmp/QT/usr/share/texmf/tex/" 
(tried in ., debian/tmp)

dh_install: gnuplot-data missing files: debian/tmp/QT/usr/share/texmf/tex/
dh_install: missing files, aborting
debian/rules:4: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#880792: yade FTBFS on x86: fatal error: CGAL/Exact_predicates_inexact_constructions_kernel.h: No such file or directory

[Adrian Bunk]

Source: yade
Version: 2017.01a-10
Severity: serious

https://buildd.debian.org/status/package.php?p=yade=sid

...
In file included from /<>/lib/triangulation/Tesselation.h:9:0,
 from /<>/lib/triangulation/Network.hpp:11,
 from 
/<>/lib/triangulation/FlowBoundingSphere.hpp:13,
 from 
/<>/debian/build/pkg/pfv/FlowEngine_FlowEngineT.hpp:39,
 from /<>/pkg/dem/TriaxialStressController.cpp:22:
/<>/lib/triangulation/RegularTriangulation.h:11:10: fatal error: 
CGAL/Exact_predicates_inexact_constructions_kernel.h: No such file or directory
 #include 

  ^~
compilation terminated.
CMakeFiles/yade.dir/build.make:2753: recipe for target 
'CMakeFiles/yade.dir/pkg/dem/TriaxialStressController.cpp.o' failed
make[3]: *** [CMakeFiles/yade.dir/pkg/dem/TriaxialStressController.cpp.o] Error 
1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#880781: sagemath build depends on removed libgd2*-dev provides

[Adrian Bunk]

Source: sagemath
Version: 8.0-8
Severity: serious

The following packages have unmet dependencies:
 builddeps:sagemath : Depends: libgd2-noxpm-dev but it is not installable or
   libgd2-xpm-dev but it is not installable


Please update the build dependency to libgd-dev.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#878937: visp: port baseline violation on i386+amd64 (also causes FTBFS on amd64)

[Adrian Bunk]

Source: visp
Version: 3.0.1-2
Severity: serious

https://buildd.debian.org/status/fetch.php?pkg=visp=i386=3.0.1-2=1487064152=0

...
-- Performing Test HAVE_CXX_MSSE2
-- Performing Test HAVE_CXX_MSSE2 - Success
-- Performing Test HAVE_C_MSSE2
-- Performing Test HAVE_C_MSSE2 - Success
-- Performing Test HAVE_CXX_MSSE3
-- Performing Test HAVE_CXX_MSSE3 - Success
-- Performing Test HAVE_C_MSSE3
-- Performing Test HAVE_C_MSSE3 - Success
-- Performing Test HAVE_CXX_MSSSE3
-- Performing Test HAVE_CXX_MSSSE3 - Success
-- Performing Test HAVE_C_MSSSE3
-- Performing Test HAVE_C_MSSSE3 - Success
...
-- C++ flags (Release): -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. 
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra -fopenmp 
-fvisibility=hidden -msse2 -msse3 -mssse3 -fPIC -g -O2 
-fdebug-prefix-map=/«PKGBUILDDIR»=. -specs=/usr/share/dpkg/no-pie-compile.specs 
-fstack-protector-strong -Wformat -Werror=format-security
-- C++ flags (Debug):   -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. 
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra -fopenmp 
-fvisibility=hidden -msse2 -msse3 -mssse3 -fPIC -g
-- C Compiler:  /usr/bin/cc
-- C flags (Release):   -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. 
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra -fopenmp 
-fvisibility=hidden -msse2 -msse3 -mssse3 -fPIC -g -O2 
-fdebug-prefix-map=/«PKGBUILDDIR»=. -specs=/usr/share/dpkg/no-pie-compile.specs 
-fstack-protector-strong -Wformat -Werror=format-security
-- C flags (Debug): -g -O2 -fdebug-prefix-map=/«PKGBUILDDIR»=. 
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra -fopenmp 
-fvisibility=hidden -msse2 -msse3 -mssse3 -fPIC -g
...
The following tests FAILED:
  2 - testConversion (ILLEGAL)
  4 - testCropAdvanced (ILLEGAL)
 14 - testIoPPM (ILLEGAL)
 16 - testReadImage (ILLEGAL)
 37 - testHistogram (ILLEGAL)
 71 - testKeyPoint-5 (ILLEGAL)
 72 - testKeyPoint-6 (ILLEGAL)
 73 - testKeyPoint-7 (ILLEGAL)
100 - imageDiskRW (ILLEGAL)
Errors while running CTest
Makefile:107: recipe for target 'test' failed
make[2]: *** [test] Error 8


The baseline of the amd64 port includes nothing higher than SSE2.

The baseline of the i386 port includes no SSE (not even MMX).
-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876739: pyfai FTBFS: help2man: can't get `--help' info from /tmp/check_calib_0hk8odnh

[Adrian Bunk]

Control: reopen -1

On Sun, Oct 15, 2017 at 06:23:35AM +, PICCA Frederic-Emmanuel wrote:
> This problem was due to this  
> 
> python-fabio (0.5.0+dfsg-2) unstable; urgency=medium
> 
>   * d/control
> - python-qt4 -> python3-pyqt4-dbg (Closes: #876288)
> 
> Now that python-fabio was solved, it is ok to close this bug

Still FTBFS with python-fabio 0.5.0+dfsg-2:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pyfai.html

> thanks
> 
> Frederic

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#878496: python-escript FTBFS on 32bit with gcc 7

[Adrian Bunk]

Source: python-escript
Version: 5.0-4
Severity: serious

https://buildd.debian.org/status/package.php?p=python-escript=sid

...
escriptcore/src/DataFactory.cpp: In function 'escript::Data 
escript::VectorFromObj(boost::python::api::object, const 
escript::FunctionSpace&, bool)':
escriptcore/src/DataFactory.cpp:49:41: error: '*((void*)& +12)' may 
be used uninitialized in this function [-Werror=maybe-uninitialized]
 double v = bp::extract(o);
 ^
escriptcore/src/DataFactory.cpp: In function 'escript::Data 
escript::TensorFromObj(boost::python::api::object, const 
escript::FunctionSpace&, bool)':
escriptcore/src/DataFactory.cpp:75:41: error: '*((void*)& +12)' may 
be used uninitialized in this function [-Werror=maybe-uninitialized]
 double v = bp::extract(o);
 ^
escriptcore/src/DataFactory.cpp: In function 'escript::Data 
escript::Tensor3FromObj(boost::python::api::object, const 
escript::FunctionSpace&, bool)':
escriptcore/src/DataFactory.cpp:99:41: error: '*((void*)& +12)' may 
be used uninitialized in this function [-Werror=maybe-uninitialized]
 double v = bp::extract(o);
 ^
escriptcore/src/DataFactory.cpp: In function 'escript::Data 
escript::Tensor4FromObj(boost::python::api::object, const 
escript::FunctionSpace&, bool)':
escriptcore/src/DataFactory.cpp:123:41: error: '*((void*)& +12)' may 
be used uninitialized in this function [-Werror=maybe-uninitialized]
 double v = bp::extract(o);
 ^
cc1plus: all warnings being treated as errors
scons: *** [debian/tmp2/posix/escriptcore/src/DataFactory.os] Error 1
scons: building terminated because of errors.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877109: pybtex FTBFS with Sphinx 1.6.4-1

[Adrian Bunk]

On Tue, Oct 10, 2017 at 12:08:29AM +0100, Ghislain Vaillant wrote:
> On 09/10/17 23:06, Adrian Bunk wrote:
> > On Mon, Oct 09, 2017 at 12:28:22PM +0100, Ghislain Vaillant wrote:
> > > ...
> > > I was complaining about the insufficiencies behind this RC, more than the
> > > situation with Sphinx. No offense to Adrian, but getting an RC bug 
> > > reported
> > > without much context to work with is just plain frustrating. Without your
> > > intervention, this RC could have dragged for a long time.
> > 
> > Ghis, I do consider our repeated attempts to blame me for not fixing a bug 
> > in
> > your package VERY offensive.
> 
> I don't recall saying anywhere in this thread that I expected *you* to
> provide a patch for this. I complained about the lack of context of the
> initial bug report, albeit too bluntly to your taste.
>...

Your repeated "without much context to work with" are just fancy words 
for blaming me for not having debugged a FTBFS in your package.

I did tell you everything I knew (including providing the email address 
of the person causing the FTBFS in the initial bug report), and it is 
not my job to debug a FTBFS in your package.

You were even lucky that I was able to point you at what broke it,
there are more than 200 open RC bugs for FTBFS I reported [1] and
in many cases the error message is all I can provide.

> Ghis

cu
Adrian

[1] https://bugs.debian.org/cgi-bin/pkgreport.cgi?submitter=bunk%40debian.org

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877109: pybtex FTBFS with Sphinx 1.6.4-1

[Adrian Bunk]

On Mon, Oct 09, 2017 at 12:28:22PM +0100, Ghislain Vaillant wrote:
>...
> I was complaining about the insufficiencies behind this RC, more than the
> situation with Sphinx. No offense to Adrian, but getting an RC bug reported
> without much context to work with is just plain frustrating. Without your
> intervention, this RC could have dragged for a long time.

Ghis, I do consider our repeated attempts to blame me for not fixing a bug in 
your package VERY offensive.

I did not break it, I am not the maintainer of the package that broke,
and I have zero knowledge about either package.

And the fact that I even did the extra work of finding the exact change
that broke your package makes it even more insulting - for a large part
of the FTBFS I report I do not even have a clue what broke it.

The only thing I regret is that I tried to be helpful after your initial 
email, and I am seriously considering giving you a permanent entry in my 
killfile so that I won't have to read another email from you for the rest
of my life.

> Ghis

Adrian

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877109: pybtex FTBFS with Sphinx 1.6.4-1

[Adrian Bunk]

On Sat, Sep 30, 2017 at 10:40:52AM +0100, Ghislain Vaillant wrote:
> > sphinx (1.6.4-1) unstable; urgency=medium
> > ...
> >   * dh_sphinxdoc: Turn warning about missing SOURCELINK_SUFFIX to an error.
> > ...
> >  -- Dmitry Shachnev   Tue, 26 Sep 2017 17:47:54 +0300
> 
> And what the hell am I supposed to do with this?!
> 
> Nice of you to report the issue but, without further context, I can't take
> further actions.

00:26 < mitya57> bunk: if you find more bugs caused by this, can you please add 
an explanation that without SOURCELINK_SUFFIX, search 
 will not work with Sphinx 1.5+?
00:27 < mitya57> Like I wrote in #876544.
00:27 -zwiebelbot:#debian-python- Debian#876544: isso: FTBFS: 
DOCUMENTATION_OPTIONS does not define SOURCELINK_SUFFIX - 
  https://bugs.debian.org/876544


> Isn't it the Dmitry's responsibility to at least communicate on the change
> and suggest solutions for it to people impacted by RCs? If he did, please
> point me to the announcement in case I missed it.

00:22 < mitya57> Oh, that my SOURCELINK_SUFFIX change causes too many FTBFSes, 
I did not expect that :(


> This is really frustrating.
> 
> Ghis

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877210: normaliz FTBFS on i386/armhf: Some error in the normaliz input data detected: Error while reading grading (a 1x2 matrix) !

[Adrian Bunk]

Source: normaliz
Version: 3.1.1+ds-1
Severity: serious
Tags: buster sid

Some recent change in unstable makes normaliz FTBFS on i386/armhf
(could be on all 32bit architectures):

https://tests.reproducible-builds.org/debian/history/normaliz.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/i386/normaliz.html

...
/usr/bin/make -C test NORMALIZ=/build/1st/normaliz-3.1.1+ds/_build/normaliz
make[2]: Entering directory '/build/1st/normaliz-3.1.1+ds/test'
/build/1st/normaliz-3.1.1+ds/_build/normaliz  -s test-s/23
Some error in the normaliz input data detected: Error while reading grading (a 
1x2 matrix) !
BadInputException caught... exiting.
Makefile:54: recipe for target 'test-s/23.out' failed
make[2]: *** [test-s/23.out] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877150: python-h5netcdf FTBFS: OSError: Can't read data (no appropriate function for conversion path)

[Adrian Bunk]

Source: python-h5netcdf
Version: 0.3.1-1
Severity: serious

Some recent change in unstable makes python-h5netcdf FTBFS
and fail in Debci:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-h5netcdf.html
https://ci.debian.net/packages/p/python-h5netcdf/unstable/amd64/

...
Testing with python3.6:
= test session starts ==
platform linux -- Python 3.6.3rc1, pytest-3.2.1, py-1.4.34, pluggy-0.4.0
rootdir: /tmp/autopkgtest-virt-lxc.shared.yugb8pcz/downtmp/autopkgtest_tmp, 
inifile:
collected 17 items

tests/test_h5netcdf.py ..F...F..

=== FAILURES ===
__ test_write_netCDF4_read_legacyapi ___

tmp_netcdf = 
'/tmp/pytest-of-debci/pytest-0/test_write_netCDF4_read_legacy0/testfile.nc'

def test_write_netCDF4_read_legacyapi(tmp_netcdf):
>   roundtrip_legacy_netcdf(tmp_netcdf, legacyapi, netCDF4)

tests/test_h5netcdf.py:341: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/test_h5netcdf.py:329: in roundtrip_legacy_netcdf
read_legacy_netcdf(tmp_netcdf, read_module, write_module)
tests/test_h5netcdf.py:191: in read_legacy_netcdf
if is_h5py_char_working(tmp_netcdf, 'z'):
tests/test_h5netcdf.py:52: in is_h5py_char_working
assert array_equal(v, _char_array)
tests/test_h5netcdf.py:32: in array_equal
a, b = map(np.array, (a[...], b[...]))
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
/usr/lib/python3/dist-packages/h5py/_hl/dataset.py:496: in __getitem__
self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
h5py/h5d.pyx:181: in h5py.h5d.DatasetID.read
???
h5py/_proxy.pyx:130: in h5py._proxy.dset_rw
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   OSError: Can't read data (no appropriate function for conversion path)

h5py/_proxy.pyx:84: OSError
___ test_write_netCDF4_read_h5netcdf ___

tmp_netcdf = 
'/tmp/pytest-of-debci/pytest-0/test_write_netCDF4_read_h5netc0/testfile.nc'

def test_write_netCDF4_read_h5netcdf(tmp_netcdf):
write_legacy_netcdf(tmp_netcdf, netCDF4)
>   read_h5netcdf(tmp_netcdf, netCDF4)

tests/test_h5netcdf.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/test_h5netcdf.py:279: in read_h5netcdf
if is_h5py_char_working(tmp_netcdf, 'z'):
tests/test_h5netcdf.py:52: in is_h5py_char_working
assert array_equal(v, _char_array)
tests/test_h5netcdf.py:32: in array_equal
a, b = map(np.array, (a[...], b[...]))
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
/usr/lib/python3/dist-packages/h5py/_hl/dataset.py:496: in __getitem__
self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)
h5py/_objects.pyx:54: in h5py._objects.with_phil.wrapper
???
h5py/_objects.pyx:55: in h5py._objects.with_phil.wrapper
???
h5py/h5d.pyx:181: in h5py.h5d.DatasetID.read
???
h5py/_proxy.pyx:130: in h5py._proxy.dset_rw
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   OSError: Can't read data (no appropriate function for conversion path)

h5py/_proxy.pyx:84: OSError

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877109: pybtex FTBFS with Sphinx 1.6.4-1: dh_sphinxdoc: DOCUMENTATION_OPTIONS does not define SOURCELINK_SUFFIX

[Adrian Bunk]

Source: pybtex
Version: 0.21-2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pybtex.html

...
   dh_sphinxdoc -O--buildsystem=pybuild
dh_sphinxdoc: DOCUMENTATION_OPTIONS does not define SOURCELINK_SUFFIX
debian/rules:18: recipe for target 'binary' failed
make: *** [binary] Error 255


sphinx (1.6.4-1) unstable; urgency=medium
...
  * dh_sphinxdoc: Turn warning about missing SOURCELINK_SUFFIX to an error.
...
 -- Dmitry Shachnev   Tue, 26 Sep 2017 17:47:54 +0300

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877065: alglib FTBFS on i386 with gcc 7

[Adrian Bunk]

Source: alglib
Version: 3.11.0-1
Severity: serious
Tags: patch

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/i386/alglib.html

...
   dh_auto_test
cd obj-i686-linux-gnu && make -j18 test ARGS\+=-j18
make[1]: Entering directory '/build/1st/alglib-3.11.0/obj-i686-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j18
Test project /build/1st/alglib-3.11.0/obj-i686-linux-gnu
Start 1: test_c
Start 2: test_i
1/2 Test #2: test_i ...   Passed0.82 sec
2/2 Test #1: test_c ...***Failed  176.26 sec
SEED: 1506088789
COMPILER: GCC
HARDWARE: 32-bit
HARDWARE: little-endian
CPU:   unknown
CORES: 1 (serial version)
LIBS:  
CPUID: 
OS: unknown
TESTING MODE: single core
tsortOK
nearestneighbor  OK
hqrndOK
odesolverOK
sparse   OK
reflections  OK
creflections OK
matgen   OK
ablasOK
trfacOK
trlinsolve   OK
safesolveOK
rcondOK
matinv   OK
hblasOK
sblasOK
ortfac   OK
fbls OK
cqmodels OK
bdsvdOK
blas OK
svd  OK
optserv  OK
snnlsOK
sactivesets  OK
linmin   OK
minlbfgs OK
xblasOK
densesolver  OK
normestimatorOK
linlsqr  FAILED
mincgOK
minbleic OK
minqpOK
minnlc   OK
minbcOK
minnsOK
evd  OK
basestat OK
pca  OK
bdss OK
mlpbase  OK
lda  OK
gammafuncOK
linreg   OK
filters  OK
mcpd OK
mlpe OK
mlptrain OK
clustering   OK
dforest  OK
gq   OK
gkq  OK
autogk   OK
fft  OK
fht  OK
conv OK
corr OK
idwint   OK
ratint   OK
spline1d OK
parametric   OK
spline3d OK
polint   OK
lsfitOK
nsfitOK
spline2d OK
rbf  OK
hermite  OK
laguerre OK
legendre OK
chebyshevOK
wsr  OK
stestOK
studentttestsOK
mannwhitneyu OK
schurOK
spdgevd  OK
inverseupdateOK
polynomialsolver OK
nleq OK
lincgOK
alglibbasics OK
Done in 176 seconds


50% tests passed, 1 tests failed out of 2

Total Test time (real) = 176.26 sec

The following tests FAILED:
  1 - test_c (Failed)
Errors while running CTest
Makefile:121: recipe for target 'test' failed
make[1]: *** [test] Error 8


If the exact result is required here, the following fixes it:

--- debian/rules.old2017-09-28 10:00:01.0 +
+++ debian/rules2017-09-28 10:00:34.0 +
@@ -2,6 +2,13 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
+ 
+ifneq (,$(findstring $(DEB_HOST_ARCH), i386))
+export DEB_CFLAGS_MAINT_APPEND = -ffloat-store
+export DEB_CXXFLAGS_MAINT_APPEND = -ffloat-store
+endif
+
 %:
dh $@
 

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877063: libitpp FTBFS on i386 with gcc 7

[Adrian Bunk]

Source: libitpp
Version: 4.3.1-7
Severity: serious
Tags: patch

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/i386/libitpp.html

...
[--] 1 test from Rand
[ RUN  ] Rand.All
libitpp_4.3.1-7/gtests/rand_test.cpp:277: Failure
The difference between 2.9631003166431262 and ric_rng() is 
8.8817841970012523e-16, which exceeds eps, where
2.9631003166431262 evaluates to 2.9631003166431262,
ric_rng() evaluates to 2.9631003166431253, and
eps evaluates to 4.4408920985006262e-16.
[  FAILED  ] Rand.All (1 ms)
[--] 1 test from Rand (1 ms total)
...
[  PASSED  ] 77 tests.
[  FAILED  ] 1 test, listed below:
[  FAILED  ] Rand.All

 1 FAILED TEST
debian/rules:16: recipe for target 'override_dh_auto_build-arch' failed
make[1]: *** [override_dh_auto_build-arch] Error 1


If the exact result is required here, the following fixes it:

--- debian/rules.old2017-09-28 09:37:10.0 +
+++ debian/rules2017-09-28 09:37:58.0 +
@@ -1,7 +1,13 @@
 #!/usr/bin/make -f
 
+DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
 DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 
+ifneq (,$(findstring $(DEB_HOST_ARCH), i386))
+export DEB_CFLAGS_MAINT_APPEND = -ffloat-store
+export DEB_CXXFLAGS_MAINT_APPEND = -ffloat-store
+endif
+
 DEBUG_PACKAGE = $(shell awk '/^Package/ && /-dbg *$$/ { print $$2 }' 
debian/control)
 %:
VERBOSE=1 dh $@ --parallel --builddirectory=build

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877061: p4est: missing build dependency on gfortran

[Adrian Bunk]

Source: p4est
Version: 1.1-4
Severity: serious
Tags: buster sid

It seems something was until recently pulling in gfortran,
but not anymore - exposing the missing build dependency:

https://tests.reproducible-builds.org/debian/history/p4est.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/p4est.html

...
configure: F77 set to mpif77
configure:  FC set to mpif90
configure:  CC set to mpicc
configure: CXX set to mpicxx
checking whether the Fortran 77 compiler works... no
configure: error: in `/build/1st/p4est-1.1':
configure: error: Fortran 77 compiler cannot create executables

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#877054: hypre FTBFS with multiarch blas

[Adrian Bunk]

Source: hypre
Version: 2.11.1-4
Severity: serious
Tags: patch

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/hypre.html

...
Building libHYPRE_DistributedMatrixPilutSolver.so ... 
mpiCC -shared -o libHYPRE_DistributedMatrixPilutSolver-2.11.1.so comm.o debug.o 
distributed_qsort.o distributed_qsort_si.o HYPRE_DistributedMatrixPilutSolver.o 
ilut.o parilut.o parutil.o pblas1.o serilut.o trifactor.o util.o 
../../utilities/libHYPRE_utilities.so 
../../distributed_matrix/libHYPRE_DistributedMatrix.so -lmpi -lm null -lblas 
-Wl,-soname,libHYPRE_DistributedMatrixPilutSolver-2.11.1.so -Wl,-z,defs
g++: error: null: No such file or directory
Makefile:88: recipe for target 'libHYPRE_DistributedMatrixPilutSolver.so' failed
make[4]: *** [libHYPRE_DistributedMatrixPilutSolver.so] Error 1


Fix attached.
Description: Don't keep BLASLIBDIRS as "null"
 The linker already knows where to find the libraries,
 so AC_HYPRE_FIND_BLAS not finding then is not a problem.
 .
 But keeping BLASLIBDIRS="null" was a problem,
 since this passed the string "null" to the compiler.
Author: Adrian Bunk <b...@debian.org>

--- hypre-2.11.1.orig/src/config/hypre_blas_macros.m4
+++ hypre-2.11.1/src/config/hypre_blas_macros.m4
@@ -127,6 +127,8 @@ AC_DEFUN([AC_HYPRE_FIND_BLAS],
 
   if test "$BLASLIBDIRS" != "null"; then
  BLASLIBDIRS="-L$BLASLIBDIRS"
+  else
+ BLASLIBDIRS=""
   fi
 
 #***
-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876908: Is blcr completely useless?

[Adrian Bunk]

Source: blcr
Version: 0.8.5-2.1
Severity: serious
Tags: buster sid

As far as I can see:
1. blcr is dead upstream since 2013.
2. blcr requires both userspace and kernel parts.
3. The -dkms package is removed in unstable.
4. The beta version in experimental has an RC bug against
   the -dkms package that the module does not build
   with the jessie (sic) kernel.

mpich is linked with the userspace library,
but does that make any sense without the kernel part?

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876890: scalapack FTBFS on arm64: test failures

[Adrian Bunk]

Source: scalapack
Version: 2.0.2-3
Severity: serious

Some recent change in unstable makes scalapack FTBFS on arm64:

https://tests.reproducible-builds.org/debian/history/scalapack.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/scalapack.html

...
The following tests FAILED:
  1 - xCbtest (Failed)
  2 - xFbtest (Failed)
 75 - xssvd (Failed)
 76 - xdsvd (Failed)
 77 - xssep (Failed)
 78 - xdsep (Failed)
 79 - xcsep (Failed)
 80 - xzsep (Failed)
 81 - xsgsep (Failed)
 82 - xdgsep (Failed)
 83 - xcgsep (Failed)
 84 - xzgsep (Failed)
 91 - xssyevr (Failed)
 92 - xdsyevr (Failed)
 93 - xcheevr (Failed)
 94 - xzheevr (Failed)
Errors while running CTest
Makefile:143: recipe for target 'test' failed
make[2]: *** [test] Error 8

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876870: apertium-en-es FTBFS with apertium 3.4.2~r68466-2: test failure

[Adrian Bunk]

Source: apertium-en-es
Version: 0.8.0~r57502-2
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/apertium-en-es.html

...
   dh_auto_test -O--fail-missing
make -j1 test VERBOSE=1
make[1]: Entering directory '/build/1st/apertium-en-es-0.8.0~r57502'
echo  "Fue un malentendido."  | apertium -d . es-en | tee .test-mt
It went a misunderstanding.
1c1
< It was a misunderstanding.
---
> It went a misunderstanding.
Makefile:784: recipe for target 'test' failed
make[1]: *** [test] Error 1

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876776: fityk FTBFS: FAIL: tests/psvoigt

[Adrian Bunk]

Source: fityk
Version: 1.3.1-1
Severity: serious
Tags: patch

https://buildd.debian.org/status/fetch.php?pkg=fityk=i386=1.3.1-2=1506310354=0
https://tests.reproducible-builds.org/debian/rb-pkg/buster/i386/fityk.html

...
make  check-TESTS
make[3]: Entering directory '/<>'
make[4]: Entering directory '/<>'
PASS: tests/num
PASS: tests/guess
PASS: tests/gradient
PASS: tests/lua
FAIL: tests/psvoigt
===
   fityk 1.3.1: ./test-suite.log
===

# TOTAL: 5
# PASS:  4
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: tests/psvoigt
===


~~~
psvoigt is a Catch v1.10.0 host application.
Run with -? for options

---
pseudo-voigt
---
tests/psvoigt.cpp:25
...

tests/psvoigt.cpp:50: FAILED:
  REQUIRE( ib == area/height )
with expansion:
  8.2712875192 == 8.2712875192
with message:
  Testing PseudoVoigt

===
test cases:  6 |  5 passed | 1 failed
assertions: 34 | 33 passed | 1 failed

FAIL tests/psvoigt (exit status: 1)


Testsuite summary for fityk 1.3.1

# TOTAL: 5
# PASS:  4
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

See ./test-suite.log

Makefile:1441: recipe for target 'test-suite.log' failed
make[4]: *** [test-suite.log] Error 1


Fix:

--- debian/rules.old2017-09-25 18:45:49.0 +
+++ debian/rules2017-09-25 18:50:19.0 +
@@ -2,6 +2,10 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+ifneq (,$(filter $(DEB_HOST_ARCH), i386))
+export DEB_CXXFLAGS_MAINT_APPEND=-ffloat-store
+endif
+
 %:
dh $@ --buildsystem=autoconf --parallel --with sphinxdoc
 

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876739: pyfai FTBFS: help2man: can't get `--help' info from /tmp/check_calib_0hk8odnh

[Adrian Bunk]

Source: pyfai
Version: 0.14.2+dfsg-1
Severity: serious

https://buildd.debian.org/status/package.php?p=pyfai=sid

...
running build_man
INFO:pyFAI.setup:Build man for entry-point target 'check_calib'
INFO:pyFAI.setup:Build man for entry-point target 'detector2nexus'
INFO:pyFAI.setup:Build man for entry-point target 'diff_map'
INFO:pyFAI.setup:Build man for entry-point target 'diff_tomo'
INFO:pyFAI.setup:Build man for entry-point target 'eiger-mask'
INFO:pyFAI.setup:Build man for entry-point target 'MX-calibrate'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-average'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-benchmark'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-calib'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-calib2'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-drawmask'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-integrate'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-recalib'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-saxs'
INFO:pyFAI.setup:Build man for entry-point target 'pyFAI-waxs'
[298091 refs]
I: pybuild base:184: 
PYTHONPATH=/<>/pyfai-0.14.2+dfsg/.pybuild/pythonX.Y_3.6/build 
xvfb-run -a --server-args="-screen 0 1024x768x24" python3.6 setup.py build_man
INFO:root:Generating grammar tables from /usr/lib/python3.6/lib2to3/Grammar.txt
INFO:root:Generating grammar tables from 
/usr/lib/python3.6/lib2to3/PatternGrammar.txt
INFO:pyFAI.setup:Use setuptools
running build_man
INFO:pyFAI.setup:Build man for entry-point target 'check_calib'
help2man: can't get `--help' info from /tmp/check_calib_0hk8odnh
Try `--no-discard-stderr' if option outputs to stderr
Traceback (most recent call last):
  File "setup.py", line 868, in 
setup_package()
  File "setup.py", line 865, in setup_package
setup(**setup_kwargs)
  File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
  File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
  File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
  File "setup.py", line 248, in run
raise RuntimeError("Fail to generate '%s' man documentation" % target_name)
RuntimeError: Fail to generate 'check_calib' man documentation
E: pybuild pybuild:283: build: plugin custom failed with: exit code=1: 
PYTHONPATH=/<>/pyfai-0.14.2+dfsg/.pybuild/pythonX.Y_3.6/build 
xvfb-run -a --server-args="-screen 0 1024x768x24" python3.6 setup.py build_man
dh_auto_build: pybuild --build -i python{version} -p "3.6 3.5" returned exit 
code 13
debian/rules:18: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876631: libroscpp-dev: node_handle.h includes steady_timer.h but it isn't included in the package

[Adrian Bunk]

Package: libroscpp-dev
Version: 1.13.2+ds1-1
Severity: serious
Control: affects -1 src:ros-actionlib

https://buildd.debian.org/status/package.php?p=ros-actionlib=sid

...
/usr/bin/c++  -DROSCONSOLE_BACKEND_LOG4CXX -DROS_PACKAGE_NAME=\"actionlib\" 
-Dactionlib_EXPORTS -I/<>/build/devel/include 
-I/<>/include 
-I/usr/share/xmlrpcpp/cmake/../../../include/xmlrpcpp  -g -O2 
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC   -o 
CMakeFiles/actionlib.dir/src/goal_id_generator.cpp.o -c 
/<>/src/goal_id_generator.cpp
In file included from /usr/include/ros/ros.h:45:0,
 from /<>/src/goal_id_generator.cpp:35:
/usr/include/ros/node_handle.h:39:10: fatal error: ros/steady_timer.h: No such 
file or directory
 #include "ros/steady_timer.h"
  ^~~~
compilation terminated.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#876620: 3depict: missing build dependency on rename

[Adrian Bunk]

Source: 3depict
Version: 0.0.19-1
Severity: serious
Tags: buster sid

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/3depict.html

...
# convert installed 3Depict.mo files to lowercase   
find /build/1st/3depict-0.0.19/debian/3depict/usr/share/locale/ -name 
3Depict.mo | xargs rename 's/3Depict.mo/3depict.mo/'
xargs: rename: No such file or directory
debian/rules:25: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 127

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#873512: statsmodels FTBFS with Cython 0.26

[Adrian Bunk]

Source: statsmodels
Version: 0.8.0-3
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/statsmodels.html

...
==
ERROR: statsmodels.tsa.statespace.tests.test_save.test_sarimax
--
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/tsa/statespace/tests/test_save.py",
 line 22, in test_sarimax
res.save('test_save_sarimax.p')
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/base/wrapper.py",
 line 72, in save
save_pickle(self, fname)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/iolib/smpickle.py",
 line 15, in save_pickle
cPickle.dump(obj, fout, protocol=-1)
  File "stringsource", line 2, in 
statsmodels.tsa.statespace._statespace.zStatespace.__reduce_cython__
TypeError: 
self._design,self._initial_state,self._initial_state_cov,self._obs,self._obs_cov,self._obs_intercept,self._selected_state_cov,self._selection,self._state_cov,self._state_intercept,self._transition
 cannot be converted to a Python object for pickling

==
ERROR: statsmodels.tsa.statespace.tests.test_save.test_structural
--
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/tsa/statespace/tests/test_save.py",
 line 35, in test_structural
res.save('test_save_structural.p')
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/base/wrapper.py",
 line 72, in save
save_pickle(self, fname)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/iolib/smpickle.py",
 line 15, in save_pickle
cPickle.dump(obj, fout, protocol=-1)
  File "stringsource", line 2, in 
statsmodels.tsa.statespace._statespace.zStatespace.__reduce_cython__
TypeError: 
self._design,self._initial_state,self._initial_state_cov,self._obs,self._obs_cov,self._obs_intercept,self._selected_state_cov,self._selection,self._state_cov,self._state_intercept,self._transition
 cannot be converted to a Python object for pickling

==
ERROR: statsmodels.tsa.statespace.tests.test_save.test_dynamic_factor
--
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/tsa/statespace/tests/test_save.py",
 line 50, in test_dynamic_factor
res.save('test_save_dynamic_factor.p')
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/base/wrapper.py",
 line 72, in save
save_pickle(self, fname)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/iolib/smpickle.py",
 line 15, in save_pickle
cPickle.dump(obj, fout, protocol=-1)
  File "stringsource", line 2, in 
statsmodels.tsa.statespace._statespace.zStatespace.__reduce_cython__
TypeError: 
self._design,self._initial_state,self._initial_state_cov,self._obs,self._obs_cov,self._obs_intercept,self._selected_state_cov,self._selection,self._state_cov,self._state_intercept,self._transition
 cannot be converted to a Python object for pickling

==
ERROR: statsmodels.tsa.statespace.tests.test_save.test_varmax
--
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/tsa/statespace/tests/test_save.py",
 line 65, in test_varmax
res.save('test_save_varmax.p')
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/base/wrapper.py",
 line 72, in save
save_pickle(self, fname)
  File 
"/build/1st/statsmodels-0.8.0/debian/python-statsmodels/usr/lib/python2.7/dist-packages/statsmodels/iolib/smpickle.py",
 line 15, in save_pickle
cPickle.dump(obj, fout, protocol=-1)
  File "stringsource", line 2, in 

Bug#873509: python-admesh FTBFS with Cython 0.26

[Adrian Bunk]

Source: python-admesh
Version: 0.98.7-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-admesh.html

...
   dh_auto_build -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build 
running build
running build_ext
generating cadmesh.pxd and admesh.pyx
found /usr/include/admesh/stl.h
cythoning admesh.pyx to admesh.c

Error compiling Cython file:

...

def write_edge(self, edge, label='admesh'):
"""stl_write_edge"""

by_label = label.encode('UTF-8')
stl_write_edge(_c_stl_file, by_label, edge)
   ^


admesh.pyx:224:56: Cannot convert Python object to 'stl_hash_edge'
building 'admesh' extension
creating build
creating build/temp.linux-amd64-2.7
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes 
-fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 
-I/usr/include/python2.7 -c admesh.c -o build/temp.linux-amd64-2.7/admesh.o
admesh.c:1:2: error: #error Do not use this file, it is the result of a failed 
Cython compilation.
 #error Do not use this file, it is the result of a failed Cython compilation.
  ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: 
/usr/bin/python setup.py build 
dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13
debian/rules:6: recipe for target 'build' failed
make: *** [build] Error 25

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#873426: frobby: frequent parallel FTBFS

[Adrian Bunk]

Source: frobby
Version: 0.9.0-4
Severity: serious

Example:

https://buildd.debian.org/status/fetch.php?pkg=frobby=i386=0.9.0-4=1503827903=0

...
Transcript written on bin/doc//manual.log.
cd bin; dvips doc/manual.dvi
rm -rf bin/doc
mkdir bin/doc
for i in 1 2 3; do pdflatex -output-directory=bin/doc/ doc/manual.tex; done
This is dvips(k) 5.997 Copyright 2017 Radical Eye Software (www.radicaleye.com)
dvips: DVI file can't be opened: doc/manual.dvi: No such file or directory
Makefile:253: recipe for target 'docPs' failed
make[2]: *** [docPs] Error 1
make[2]: *** Waiting for unfinished jobs
...


dh compat 10 defaults to parallel building, if this cannot easily
be fixed then calling dh with --no-parallel brings gives what was
previously the default.

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#873008: hfst FTBFS on big endian: FAIL: test

[Adrian Bunk]

Source: hfst
Version: 3.12.2~r3289-1
Severity: serious

https://buildd.debian.org/status/package.php?p=hfst=sid

...
Making check in tools
make[3]: Entering directory '/<>/tools'
Making check in src
make[4]: Entering directory '/<>/tools/src'
Making check in hfst-proc
make[5]: Entering directory '/<>/tools/src/hfst-proc'
make[5]: Nothing to be done for 'check'.
make[5]: Leaving directory '/<>/tools/src/hfst-proc'
Making check in hfst-twolc
make[5]: Entering directory '/<>/tools/src/hfst-twolc'
Making check in src
make[6]: Entering directory '/<>/tools/src/hfst-twolc/src'
make[6]: Nothing to be done for 'check'.
make[6]: Leaving directory '/<>/tools/src/hfst-twolc/src'
Making check in test
make[6]: Entering directory '/<>/tools/src/hfst-twolc/test'
/usr/bin/make  test1 test1.txt_fst test10 test10.txt_fst test11 test11.txt_fst 
test12 test12.txt_fst test13 test13.txt_fst test14 test14.txt_fst test15 
test15.txt_fst test16 test16.txt_fst test17 test17.txt_fst test18 
test18.txt_fst test19 test19.txt_fst test2 test2.txt_fst test20 test20.txt_fst 
test21 test21.txt_fst test22 test22.txt_fst test23 test23.txt_fst test24 
test24.txt_fst test25 test25.txt_fst test26 test26.txt_fst test27 
test27.txt_fst test28 test28.txt_fst test29 test29.txt_fst test3 test3.txt_fst 
test30 test30.txt_fst test31 test31.txt_fst test32 test32.txt_fst test33 
test33.txt_fst test34 test34.txt_fst test35 test35.txt_fst test36 
test36.txt_fst test37 test37.txt_fst test38 test38.txt_fst test39 
test39.txt_fst test4 test4.txt_fst test40 test40.txt_fst test41 test41.txt_fst 
test42 test42.txt_fst test43 test43.txt_fst test44 test44.txt_fst test45 
test45.txt_fst test46 test46.txt_fst test47 test47.txt_fst test48 
test48.txt_fst test49 test49.txt_fst test5 test5.txt_fst tes
 t51 test51.txt_fst test52 test52.txt_fst test53 test53.txt_fst test54 
test54.txt_fst test55 test55.txt_fst test56 test56.txt_fst test57 
test57.txt_fst test58 test58.txt_fst test59 test59.txt_fst test6 test6.txt_fst 
test60 test60.txt_fst test61 test61.txt_fst test62 test62.txt_fst test7 
test7.txt_fst test8 test8.txt_fst test9 test9.txt_fst
make[7]: Entering directory '/<>/tools/src/hfst-twolc/test'
make[7]: Nothing to be done for 'test1'.
make[7]: Nothing to be done for 'test1.txt_fst'.
make[7]: Nothing to be done for 'test10'.
make[7]: Nothing to be done for 'test10.txt_fst'.
make[7]: Nothing to be done for 'test11'.
make[7]: Nothing to be done for 'test11.txt_fst'.
make[7]: Nothing to be done for 'test12'.
make[7]: Nothing to be done for 'test12.txt_fst'.
make[7]: Nothing to be done for 'test13'.
make[7]: Nothing to be done for 'test13.txt_fst'.
make[7]: Nothing to be done for 'test14'.
make[7]: Nothing to be done for 'test14.txt_fst'.
make[7]: Nothing to be done for 'test15'.
make[7]: Nothing to be done for 'test15.txt_fst'.
make[7]: Nothing to be done for 'test16'.
make[7]: Nothing to be done for 'test16.txt_fst'.
make[7]: Nothing to be done for 'test17'.
make[7]: Nothing to be done for 'test17.txt_fst'.
make[7]: Nothing to be done for 'test18'.
make[7]: Nothing to be done for 'test18.txt_fst'.
make[7]: Nothing to be done for 'test19'.
make[7]: Nothing to be done for 'test19.txt_fst'.
make[7]: Nothing to be done for 'test2'.
make[7]: Nothing to be done for 'test2.txt_fst'.
make[7]: Nothing to be done for 'test20'.
make[7]: Nothing to be done for 'test20.txt_fst'.
make[7]: Nothing to be done for 'test21'.
make[7]: Nothing to be done for 'test21.txt_fst'.
make[7]: Nothing to be done for 'test22'.
make[7]: Nothing to be done for 'test22.txt_fst'.
make[7]: Nothing to be done for 'test23'.
make[7]: Nothing to be done for 'test23.txt_fst'.
make[7]: Nothing to be done for 'test24'.
make[7]: Nothing to be done for 'test24.txt_fst'.
make[7]: Nothing to be done for 'test25'.
make[7]: Nothing to be done for 'test25.txt_fst'.
make[7]: Nothing to be done for 'test26'.
make[7]: Nothing to be done for 'test26.txt_fst'.
make[7]: Nothing to be done for 'test27'.
make[7]: Nothing to be done for 'test27.txt_fst'.
make[7]: Nothing to be done for 'test28'.
make[7]: Nothing to be done for 'test28.txt_fst'.
make[7]: Nothing to be done for 'test29'.
make[7]: Nothing to be done for 'test29.txt_fst'.
make[7]: Nothing to be done for 'test3'.
make[7]: Nothing to be done for 'test3.txt_fst'.
make[7]: Nothing to be done for 'test30'.
make[7]: Nothing to be done for 'test30.txt_fst'.
make[7]: Nothing to be done for 'test31'.
make[7]: Nothing to be done for 'test31.txt_fst'.
make[7]: Nothing to be done for 'test32'.
make[7]: Nothing to be done for 'test32.txt_fst'.
make[7]: Nothing to be done for 'test33'.
make[7]: Nothing to be done for 'test33.txt_fst'.
make[7]: Nothing to be done for 'test34'.
make[7]: Nothing to be done for 'test34.txt_fst'.
make[7]: Nothing to be done for 'test35'.
make[7]: Nothing to be done for 'test35.txt_fst'.
make[7]: Nothing to be done for 'test36'.
make[7]: Nothing to be done for 'test36.txt_fst'.
make[7]: Nothing to be done for 'test37'.
make[7]: Nothing to be 

Bug#872918: sketch: parallel FTBFS

[Adrian Bunk]

Source: sketch
Version: 1:0.3.7-5
Severity: serious
Tags: patch

dh compat 10 enables paralles building,
which sometimes runs into the following bug:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/sketch.html

...
dh_auto_build
make -j15
make[2]: Entering directory '/build/1st/sketch-0.3.7'
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o bsp.o bsp.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o cmdline.o 
cmdline.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o emit.o 
emit.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o error.o 
error.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o expr.o 
expr.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o geometry.o 
geometry.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o geomio.o 
geomio.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o global.o 
global.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o langver.o 
langver.c
bison --defines --debug --report=all --yacc sketch.y
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o main.o 
main.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o memutil.o 
memutil.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o opts.o 
opts.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o scene.o 
scene.c
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o symbol.o 
symbol.c
expr.c: In function 'to_integer':
expr.c:374:12: warning: variable 'frac_part' set but not used 
[-Wunused-but-set-variable]
 double frac_part, int_part;
^
bison --defines --debug --report=all --yacc sketch.y
gcc -O1 -g -Wall -Wall -g -O2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o lex.yy.o 
lex.yy.c
sketch.l: In function 'yylex':
sketch.l:86:3: error: 'yylval' undeclared (first use in this function); did you 
mean 'yylex'?
   yylval.str = safe_malloc(yyleng + 1 - 2);
   ^~
   yylex
...


Note how bison is running twice, with an output file already being
used while the second bison regenerates it again resulting in an
incomplete file being used.

Fix attached.
Description: Fix parallel FTBFS
 Don't run bison twice, with a generated file already being used
 while the second bison is still running.
Author: Adrian Bunk <b...@debian.org>

--- sketch-0.3.7.orig/makefile
+++ sketch-0.3.7/makefile
@@ -43,7 +43,9 @@ HEADERS=bsp.h cmdline.h dynarray.h emit.
 $(EXE) : $(OBJECTS)
$(CC) -o $(EXE) $(OBJECTS) -lm
 
-y.tab.c y.tab.h : sketch.y
+y.tab.c : y.tab.h
+
+y.tab.h : sketch.y
$(YACC) $<
 
 lex.yy.c : sketch.l
-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Bug#872860: csound FTBFS with libgmm++-dev 5.2+dfsg1-5

[Adrian Bunk]

Source: csound
Version: 1:6.09.1~dfsg-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/csound.html

...
/build/1st/csound-6.09.1~dfsg/Opcodes/linear_algebra.cpp: In member function 
'int la_i_print_vr_t::init(CSOUND*)':
/build/1st/csound-6.09.1~dfsg/Opcodes/linear_algebra.cpp:633:12: error: no 
match for 'operator<<' (operand types are 'std::ostringstream {aka 
std::__cxx11::basic_ostringstream}' and 'std::vector')
 stream << array->vr << std::endl;
 ~~~^~~~
In file included from /usr/include/c++/7/istream:39:0,
 from /usr/include/c++/7/sstream:38,
 from /usr/include/c++/7/complex:45,
 from 
/build/1st/csound-6.09.1~dfsg/Opcodes/linear_algebra.cpp:345:
/usr/include/c++/7/ostream:108:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, 
_Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ostream_type& 
(*)(std::basic_ostream<_CharT, _Traits>::__ostream_type&)) [with _CharT = char; 
_Traits = std::char_traits; std::basic_ostream<_CharT, 
_Traits>::__ostream_type = std::basic_ostream]
   operator<<(__ostream_type& (*__pf)(__ostream_type&))
   ^~~~
/usr/include/c++/7/ostream:108:7: note:   no known conversion for argument 1 
from 'std::vector' to 'std::basic_ostream::__ostream_type& 
(*)(std::basic_ostream::__ostream_type&) {aka std::basic_ostream& 
(*)(std::basic_ostream&)}'
/usr/include/c++/7/ostream:117:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, 
_Traits>::operator<<(std::basic_ostream<_CharT, _Traits>::__ios_type& 
(*)(std::basic_ostream<_CharT, _Traits>::__ios_type&)) [with _CharT = char; 
_Traits = std::char_traits; std::basic_ostream<_CharT, 
_Traits>::__ostream_type = std::basic_ostream; std::basic_ostream<_CharT, 
_Traits>::__ios_type = std::basic_ios]
   operator<<(__ios_type& (*__pf)(__ios_type&))
   ^~~~
/usr/include/c++/7/ostream:117:7: note:   no known conversion for argument 1 
from 'std::vector' to 'std::basic_ostream::__ios_type& 
(*)(std::basic_ostream::__ios_type&) {aka std::basic_ios& 
(*)(std::basic_ios&)}'
/usr/include/c++/7/ostream:127:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, 
_Traits>::operator<<(std::ios_base& (*)(std::ios_base&)) [with _CharT = char; 
_Traits = std::char_traits; std::basic_ostream<_CharT, 
_Traits>::__ostream_type = std::basic_ostream]
   operator<<(ios_base& (*__pf) (ios_base&))
   ^~~~
/usr/include/c++/7/ostream:127:7: note:   no known conversion for argument 1 
from 'std::vector' to 'std::ios_base& (*)(std::ios_base&)'
/usr/include/c++/7/ostream:166:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long 
int) [with _CharT = char; _Traits = std::char_traits; 
std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream]
   operator<<(long __n)
   ^~~~
/usr/include/c++/7/ostream:166:7: note:   no known conversion for argument 1 
from 'std::vector' to 'long int'
/usr/include/c++/7/ostream:170:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long 
unsigned int) [with _CharT = char; _Traits = std::char_traits; 
std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream]
   operator<<(unsigned long __n)
   ^~~~
/usr/include/c++/7/ostream:170:7: note:   no known conversion for argument 1 
from 'std::vector' to 'long unsigned int'
/usr/include/c++/7/ostream:174:7: note: candidate: std::basic_ostream<_CharT, 
_Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(bool) 
[with _CharT = char; _Traits = std::char_traits; 
std::basic_ostream<_CharT, _Traits>::__ostream_type = std::basic_ostream]
   operator<<(bool __n)
   ^~~~
/usr/include/c++/7/ostream:174:7: note:   no known conversion for argument 1 
from 'std::vector' to 'bool'
In file included from /usr/include/c++/7/ostream:693:0,
 from /usr/include/c++/7/istream:39,
 from /usr/include/c++/7/sstream:38,
 from /usr/include/c++/7/complex:45,
 from 
/build/1st/csound-6.09.1~dfsg/Opcodes/linear_algebra.cpp:345:
/usr/include/c++/7/bits/ostream.tcc:91:5: note: candidate: 
std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, 
_Traits>::operator<<(short int) [with _CharT = char; _Traits = 
std::char_traits]
 basic_ostream<_CharT, _Traits>::
 ^~
/usr/include/c++/7/bits/ostream.tcc:91:5: note:   no known conversion for 
argument 1 from 'std::vector' to 'short int'
In file included from /usr/include/c++/7/istream:39:0,
 from /usr/include/c++/7/sstream:38,
 from /usr/include/c++/7/complex:45,
 from 

Bug#872670: libgmm++-dev requires header that is shipped in libgetfem++-dev

[Adrian Bunk]

Package: libgmm++-dev
Version: 5.2+dfsg1-4
Severity: serious
Control: affects -1 src:csound

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/csound.html

...
-- Looking for C++ include gmm/gmm.h
-- Looking for C++ include gmm/gmm.h - not found
...
CMake Error at CMakeLists.txt:108 (message):
  BUILD_LINEAR_ALGEBRA_OPCODES is enabled, but GMM_HEADER=""
...
In file included from /usr/include/gmm/gmm_except.h:42:0,
 from /usr/include/gmm/gmm_ref.h:46,
 from /usr/include/gmm/gmm_def.h:40,
 from /usr/include/gmm/gmm_kernel.h:41,
 from /usr/include/gmm/gmm.h:40,
 from 
/build/1st/csound-6.09.1~dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx:1:
/usr/include/gmm/gmm_std.h:41:10: fatal error: getfem/getfem_arch_config.h: No 
such file or directory
 #include 
  ^

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers