Bug#894905: fflas-ffpack: missing Depends: libgivaro-dev (>= 4.0.3)

[Andreas Beckmann]

Package: fflas-ffpack
Version: 2.3.2-1~exp1
Severity: serious

Hi,

noticed this while rebuilding linbox/experimental in sid+experimental:

...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for FFLAS_FFPACK... no
configure: error: Package requirements (fflas-ffpack >= 2.3.0) were not met:

Package 'fflas-ffpack' requires 'givaro >= 4.0.3' but version of givaro is 4.0.2
You may find new versions of Givaro at http://givaro.forge.imag.fr

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables FFLAS_FFPACK_CFLAGS
and FFLAS_FFPACK_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
...


The pkg-config file contains:

/-- fflas-ffpack.pc 
prefix=/usr
exec_prefix=/usr
libdir=/usr/lib
includedir=/usr/include

Name: fflas-ffpack
Description: Finite Field Linear Algebra Suroutines/Package
URL: http://github.com/linbox-team/fflas-ffpack
Version: 2.3.2
Requires: givaro >= 4.0.3
Libs: -fopenmp  -lblas -llapack
Cflags: -I${prefix}/include-fopenmp   -fabi-version=6
\---


Andreas

-- 
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#892971: libignition-fuel-tools1-{1, dev}: both ship /usr/lib/ruby/ignition/cmdfuel1.rb

[Andreas Beckmann]

Package: libignition-fuel-tools1-dev,libignition-fuel-tools1-1
Version: 1.0.0+dfsg4-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package failed to install
because it tries to overwrite other packages files.

  Selecting previously unselected package libignition-fuel-tools1-dev:amd64.
  Preparing to unpack 
.../35-libignition-fuel-tools1-dev_1.0.0+dfsg4-3_amd64.deb ...
  Unpacking libignition-fuel-tools1-dev:amd64 (1.0.0+dfsg4-3) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-ADbRwA/35-libignition-fuel-tools1-dev_1.0.0+dfsg4-3_amd64.deb
 (--unpack):
   trying to overwrite '/usr/lib/ruby/ignition/cmdfuel1.rb', which is also in 
package libignition-fuel-tools1-1:amd64 1.0.0+dfsg4-3
  Errors were encountered while processing:
   
/tmp/apt-dpkg-install-ADbRwA/35-libignition-fuel-tools1-dev_1.0.0+dfsg4-3_amd64.deb


cheers,

Andreas

-- 
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#892874: libmatio-doc: fails to upgrade from 'stable' to 'sid' - trying to overwrite /usr/share/doc/libmatio-dev/NEWS.gz

[Andreas Beckmann]

Package: libmatio-doc
Version: 1.5.12-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'stable'.
It installed fine in 'stable', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces

This test intentionally skipped 'testing' to find file overwrite
problems before packages migrate from 'unstable' to 'testing'.

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libmatio-doc.
  Preparing to unpack .../libmatio-doc_1.5.12-1_all.deb ...
  Unpacking libmatio-doc (1.5.12-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libmatio-doc_1.5.12-1_all.deb (--unpack):
   trying to overwrite '/usr/share/doc/libmatio-dev/NEWS.gz', which is also in 
package libmatio-dev:amd64 1.5.9-1+b1
  dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libmatio-doc_1.5.12-1_all.deb


cheers,

Andreas


libmatio-dev=1.5.9-1+b1_libmatio-doc=1.5.12-1.log.gz
Description: application/gzip
-- 
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#892139: eclib: FTBFS on i386: tests fail: reference solution precision mismatch

[Andreas Beckmann]

Source: eclib
Version: 20171219-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

eclib/experimental FTBFS on i386:
https://buildd.debian.org/status/fetch.php?pkg=eclib=i386=20171219-1=1519985150=0

make check_procs check_qcurves check_qrank check_g0n
make[3]: Entering directory '/<>/tests'
Running procs checks...
for prog in smattest comptest rattest bigrattest ptest mptest tbessel mvectest 
mmattest mspace thilbert tp2points tilll vectest1 vectest2 mattest1 mattest2 
space1 space2 svectest1 svectest2 tcon2 tlegcert timing threading; do echo 
"Testing ${prog}..."; ./${prog} < ./in_ntl/${prog}.in > ${prog}.testout 
2>/dev/null && diff ${prog}.testout ./out_ntl/${prog}.out || exit $?; done
Testing smattest...
Testing comptest...
5c5
< AGM((3.125,4.25),(1,0)) = (2.07831617217326684,1.5633615899065958201)
---
> AGM((3.125,4.25),(1,0)) = (2.07831617217326684003,1.56336158990659582007)
7c7
< AGM((1,1),(2,1)) = (1.471349362864653566,1.0200541263376600196)
---
> AGM((1,1),(2,1)) = (1.47134936286465356604,1.02005412633766001965)
11,16c11,16
< Enter a real or complex: Main cube root = 
(1.6289371459221758752,0.52017450230454583955)
< whose cube is(3,4)
< Next cube root = (-1.2649529063577516597,1.1506136983844504996)
< whose cube is(3,4)
< Next cube root = (-0.36398423956442421551,-1.6707882006889963392)
< whose cube is(3,4)
---
> Enter a real or complex: Main cube root = 
> (1.62893714592217587521,0.520174502304545839545)
> whose cube is(2.,3.)
> Next cube root = (-1.2649529063577516597,1.15061369838445049961)
> whose cube is(2.,4.0001)
> Next cube root = (-0.363984239564424215513,-1.67078820068899633915)
> whose cube is(3.0001,3.)
18,21c18,21
< (-1.2878154795576479889,-0.85789675832849028642)
< (-1.2878154795576479889,0.85789675832849028642)
< (0.28781547955764798887,1.4160930801719079387)
< (0.28781547955764798887,-1.4160930801719079387)
---
> (-1.28781547955764798887,-0.857896758328490286416)
> (-1.28781547955764798887,0.857896758328490286416)
> (0.287815479557647988873,1.41609308017190793872)
> (0.287815479557647988873,-1.41609308017190793872)
Makefile:1285: recipe for target 'check_procs' failed
make[3]: *** [check_procs] Error 1

make[3]: Entering directory '/<>/tests'
Running qrank checks...
for prog in tmrank tequiv d2; do echo "Testing ${prog}..."; ./${prog} < 
./in_ntl/${prog}.in > ${prog}.testout 2>/dev/null && diff ${prog}.testout 
./out_ntl/${prog}.out || exit $?; done
Testing tmrank...
Testing tequiv...
Testing d2...
14c14
< height = 13.565420700285587132
---
> height = 13.5654207002855871318
16c16
< height = 27.130841400571174263
---
> height = 27.1308414005711742635
Makefile:1297: recipe for target 'check_qrank' failed
make[3]: *** [check_qrank] Error 1


Looks like there is now one more digit in the output ...


Andreas

-- 
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#892047: libvlfeat-doc: fails to upgrade from 'testing' - trying to overwrite /usr/share/doc/libvlfeat-dev/examples/aib.c

[Andreas Beckmann]

Package: libvlfeat-doc
Version: 0.9.21+dfsg0-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libvlfeat-doc.
  Preparing to unpack .../libvlfeat-doc_0.9.21+dfsg0-1_all.deb ...
  Unpacking libvlfeat-doc (0.9.21+dfsg0-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libvlfeat-doc_0.9.21+dfsg0-1_all.deb (--unpack):
   trying to overwrite '/usr/share/doc/libvlfeat-dev/examples/aib.c', which is 
also in package libvlfeat-dev:amd64 0.9.20+dfsg0-2
  Errors were encountered while processing:
   /var/cache/apt/archives/libvlfeat-doc_0.9.21+dfsg0-1_all.deb


cheers,

Andreas

-- 
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#891993: syrthes: Build-Depends on Qt4-only python-qwt5-qt4

[Andreas Beckmann]

Source: syrthes
Version: 4.3.0-dfsg1-2
Severity: serious
Tags: sid buster
Justification: blocks python-qwt5-qt4 removal
Control: block 886779 with -1

Hi,

src:syrthes Build-Depends on python-qwt5-qt4 which is scheduled for
removal (#886779). Please switch to a Qt5 solution or drop the
(Build-)Dependency altogether.


Andreas

-- 
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#891992: thepeg: Build-Depends on hepmc which is scheduled for removal

[Andreas Beckmann]

Source: thepeg
Version: 1.8.0-3
Severity: serious
Control: block 885180 with -1

Hi,

src:hepmc is scheduled for removal (#885180). Please remove the
Build-Depends and Depends on packages from src:hepmc. If src:thepeg
cannot be built without hepmc, please get it removed as well.


Andreas

-- 
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#891991: rivet: Build-Depends on hepmc which is scheduled for removal

[Andreas Beckmann]

Source: rivet
Version: 1.8.3-2
Severity: serious
Control: block 885180 with -1

Hi,

src:hepmc is scheduled for removal (#885180). Please remove the
Build-Depends and Depends on packages from src:hepmc. If src:rivet
cannot be built without hepmc, please get it removed as well.


Andreas

-- 
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#891990: pythia8: Build-Depends on hepmc which is scheduled for removal

[Andreas Beckmann]

Source: pythia8
Version: 8.1.86-1.2
Severity: serious
Justification: fails to build from source (but built successfully in the past)
Control: block 885180 with -1

Hi,

src:hepmc is scheduled for removal (#885180). Please remove the
Build-Depends and Depends on packages from src:hepmc. If src:pythia8
cannot be built without hepmc, please get it removed as well.


Andreas

-- 
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#891367: libsimbody-dev: broken symlink: /usr/share/doc/simbody/examples/bin -> ../../../../lib/x86_64-linux-gnu/simbody/examples

[Andreas Beckmann]

Package: libsimbody-dev
Version: 3.5.4+dfsg2-1
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m30.1s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/simbody/examples/bin -> 
../../../../lib/x86_64-linux-gnu/simbody/examples


cheers,

Andreas


libsimbody-dev_3.5.4+dfsg2-1.log.gz
Description: application/gzip
-- 
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#891348: mpich: broken symlink: /usr/lib/TRIPLET/mpich/include -> ../../../include/TRIPLET/mpich

[Andreas Beckmann]

Package: mpich
Version: 3.3~b1-4
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m32.0s ERROR: FAIL: Broken symlinks:
  /usr/lib/TRIPLET/mpich/include -> ../../../include/TRIPLET/mpich


Some placeholders were not substituted ...


cheers,

Andreas


mpich_3.3~b1-4.log.gz
Description: application/gzip
-- 
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#891029: dxf2gcode: overly generic python module name: /usr/lib/python3/dist-packages/core/__init__.py

[Andreas Beckmann]

Package: dxf2gcode
Version: 20170925-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package uses a very generic
python module name that now clashes with other packages:

/usr/lib/python3/dist-packages/core/__init__.py


Andreas

-- 
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#891023: python-tables-doc: fails to upgrade from 'stretch' - trying to overwrite /usr/share/doc/python-tables/README.rst.gz

[Andreas Beckmann]

Package: python-tables-doc
Version: 3.4.2-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'stretch'.
It installed fine in 'stretch', then the upgrade to 'buster' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package python-tables-doc.
  Preparing to unpack .../11-python-tables-doc_3.4.2-3_all.deb ...
  Unpacking python-tables-doc (3.4.2-3) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-nbbJmI/11-python-tables-doc_3.4.2-3_all.deb (--unpack):
   trying to overwrite '/usr/share/doc/python-tables/README.rst.gz', which is 
also in package python-tables 3.3.0-5
  Errors were encountered while processing:
   /tmp/apt-dpkg-install-nbbJmI/11-python-tables-doc_3.4.2-3_all.deb

This is probably caused by a behavior change of dh_installdocs in
debhelper compat level 11.


cheers,

Andreas


python-tables=3.3.0-5_python-tables-doc=3.4.2-3.log.gz
Description: application/gzip
-- 
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#889502: cypari2: FTBFS on several architectures

[Andreas Beckmann]

Source: cypari2
Version: 1.1.3-3
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

cypari2/experimental FTBFS on several architectures:
https://buildd.debian.org/status/package.php?p=cypari2=experimental

I can reproduce this in pbuilder on i386, but not on amd64 (where it
also built successfully on the buildd).

Excerpt from
https://buildd.debian.org/status/fetch.php?pkg=cypari2=i386=1.1.3-3=1516945955=0

make[2]: Entering directory '/<>/docs'
Running Sphinx v1.6.6
making output directory...
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 6 source files that are out of date
updating environment: 6 added, 0 changed, 0 removed
reading sources... [ 16%] closure
reading sources... [ 33%] convert
reading sources... [ 50%] gen
reading sources... [ 66%] handle_error
reading sources... [ 83%] index
reading sources... [100%] pari_instance

/<>/docs/source/closure.rst:1: WARNING: autodoc: failed to import 
module u'cypari2.closure'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 658, in 
import_object
__import__(self.modname)
ImportError: No module named cypari2.closure
/<>/docs/source/convert.rst:1: WARNING: autodoc: failed to import 
module u'cypari2.convert'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 658, in 
import_object
__import__(self.modname)
ImportError: No module named cypari2.convert
/<>/docs/source/gen.rst:1: WARNING: autodoc: failed to import 
module u'cypari2.gen'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 658, in 
import_object
__import__(self.modname)
ImportError: No module named cypari2.gen
/<>/docs/source/handle_error.rst:1: WARNING: autodoc: failed to 
import module u'cypari2.handle_error'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 658, in 
import_object
__import__(self.modname)
ImportError: No module named cypari2.handle_error
/<>/docs/source/pari_instance.rst:1: WARNING: autodoc: failed to 
import module u'cypari2.pari_instance'; the following exception was raised:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line 658, in 
import_object
__import__(self.modname)
ImportError: No module named cypari2.pari_instance
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done


Andreas

-- 
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#888556: libetsf-io-doc: fails to upgrade from 'testing' - trying to overwrite /usr/share/doc/libetsf-io-dev/AUTHORS

[Andreas Beckmann]

Package: libetsf-io-doc
Version: 1.0.4-2
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libetsf-io-doc.
  Preparing to unpack .../libetsf-io-doc_1.0.4-2_all.deb ...
  Unpacking libetsf-io-doc (1.0.4-2) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libetsf-io-doc_1.0.4-2_all.deb (--unpack):
   trying to overwrite '/usr/share/doc/libetsf-io-dev/AUTHORS', which is also 
in package libetsf-io-dev 1.0.4-1.1+b3
  dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libetsf-io-doc_1.0.4-2_all.deb

This is probably caused by a dh_installdocs behavior change in
debhelper compat level 11.


cheers,

Andreas


libetsf-io-dev=1.0.4-1.1+b3_libetsf-io-doc=1.0.4-2.log.gz
Description: application/gzip
-- 
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#888558: python-backports.tempfile: ships file with generic name: /usr/lib/python2.7/dist-packages/backports/__init__.py

[Andreas Beckmann]

Package: python-backports.tempfile
Version: 1.0-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'stable'.
It installed fine in 'stable', then the upgrade to 'sid' fails
because it tries to overwrite other packages files.

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package python-backports.tempfile.
  Preparing to unpack .../python-backports.tempfile_1.0-1_all.deb ...
  Unpacking python-backports.tempfile (1.0-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/python-backports.tempfile_1.0-1_all.deb (--unpack):
   trying to overwrite 
'/usr/lib/python2.7/dist-packages/backports/__init__.py', which is also in 
package python-backports-shutil-get-terminal-size 1.0.0-3
  Errors were encountered while processing:
   /var/cache/apt/archives/python-backports.tempfile_1.0-1_all.deb

I don't think Breaks+Replaces is the correct approach to handle this very
generic file name.


cheers,

Andreas


python-backports-shutil-get-terminal-size=1.0.0-3_python-backports.tempfile=1.0-1.log.gz
Description: application/gzip
-- 
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#887618: libgetfem++-dev: needs Depends: libgmm++-dev (= ${source:Version})

[Andreas Beckmann]

Package: libgetfem++-dev
Version: 5.2+dfsg1-5
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package is no longer
installable.
Since libgmm++-dev is an arch:all package, the (= ${binary:Version}) is
incorrect and no longer satisfiable after the recent binNMU.

Andreas

-- 
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#887614: libmpich-dev: fails to upgrade from 'sid': update-alternatives: error: alternative mpicc can't be slave of mpi-x86_64-linux-gnu: it is a slave of mpi

[Andreas Beckmann]

Package: libmpich-dev
Version: 3.3~a3-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails.

>From the attached log (scroll to the bottom...):

  Setting up libmpich-dev (3.3~a3-1) ...
  update-alternatives: error: alternative mpicc can't be slave of 
mpi-x86_64-linux-gnu: it is a slave of mpi
  dpkg: error processing package libmpich-dev (--configure):
   installed libmpich-dev package post-installation script subprocess returned 
error exit status 2
  Processing triggers for libc-bin (2.26-4) ...
  Errors were encountered while processing:
   libmpich-dev


cheers,

Andreas


libmpich-dev_3.3~a3-1.log.gz
Description: application/gzip
-- 
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#887570: libsuitesparse-dev: missing Depends: libgraphblas1 (= ${binary:Version})

[Andreas Beckmann]

Package: libsuitesparse-dev
Version: 1:5.1.2-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m26.2s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libgraphblas.so -> libgraphblas.so.1


cheers,

Andreas


libsuitesparse-dev_1:5.1.2-1.log.gz
Description: application/gzip
-- 
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#887568: cb2bib: broken symlink: /usr/share/doc/man/man1/c2bimport.1 -> cb2bib.1

[Andreas Beckmann]

Package: cb2bib
Version: 1.9.7-1
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m54.2s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/man/man1/c2bimport.1 -> cb2bib.1

That should probably have been c2bimport.1.gz -> cb2bib.1.gz


cheers,

Andreas


cb2bib_1.9.7-1.log.gz
Description: application/gzip
-- 
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#887005: openturns: FTBFS on arm64, i386, ppc64el, s390x

[Andreas Beckmann]

Source: openturns
Version: 1.10-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

openturns/experimental FTBFS on several architectures where it built on
sid:

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

There are always some (but not neccessarily the same) tests failing.


Andreas

-- 
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#880885: caffe-contrib: B-D on obsolete compiler gcc-5 not available in testing

[Andreas Beckmann]

Followup-For: Bug #880885

Hi lumin,

I missed to put you in the loop, but the CUDA 9.0 transition has now
started, so you can switch to gcc-6 (the best version supported by
CUDA so far).


Andreas

-- 
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#886698: sollya-doc: fails to upgrade from 'stretch' - trying to overwrite /usr/share/doc/sollya/AUTHORS

[Andreas Beckmann]

Package: sollya-doc
Version: 6.0+ds-4
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'stretch'.
It installed fine in 'stretch', then the upgrade to 'buster' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/#overwriting-files-and-replacing-packages-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package sollya-doc.
  Preparing to unpack .../sollya-doc_6.0+ds-4_all.deb ...
  Unpacking sollya-doc (6.0+ds-4) ...
  dpkg: error processing archive 
/var/cache/apt/archives/sollya-doc_6.0+ds-4_all.deb (--unpack):
   trying to overwrite '/usr/share/doc/sollya/AUTHORS', which is also in 
package sollya 6.0+ds-1
  Errors were encountered while processing:
   /var/cache/apt/archives/sollya-doc_6.0+ds-4_all.deb


cheers,

Andreas


sollya=6.0+ds-1_sollya-doc=6.0+ds-4.log.gz
Description: application/gzip
-- 
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#884564: suitesparse: FTBFS on i386: out of memory

[Andreas Beckmann]

Source: suitesparse
Version: 1:5.1.0-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)

suitesparse/experimental FTBFS on i386 (and any-i386, x32 and
some ports), but succeeds on all other 32-bit release architectures:

https://buildd.debian.org/status/fetch.php?pkg=suitesparse=i386=1%3A5.1.0-1=1512882884=0

cc1: out of memory allocating 65536 bytes after a total of 3464364032 bytes
CMakeFiles/graphblas.dir/build.make:65: recipe for target 
'CMakeFiles/graphblas.dir/Source/GB_AxB_builtin.c.o' failed



Andreas

-- 
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#883987: rheolef: FTBFS error: partial specialization ... after instantiation ...

[Andreas Beckmann]

On 2017-12-12 20:26, Graham Inggs wrote:
> Would you please quote the bug number?  I failed to find your bug report.
> 
> I think the thing to do here is reassign this bug to src:boost1.62 and
> mark that it affects src:rheolef.

just saw these (against cgal) in my buster RC udd query: #884184 #884185


Andreas

-- 
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#883987: rheolef: FTBFS error: partial specialization ... after instantiation ...

[Andreas Beckmann]

Source: rheolef
Version: 6.7-4
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

rheolef did FTBFS during the binNMU against the new cgal:

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

>From the amd64 log:

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../config -I../../util/qd 
-I../../include -I/usr/include/openmpi -Wdate-time -D_FORTIFY_SOURCE=2 -g 
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 
-Werror=format-security -std=c++11 -Wall -Wno-unused -Wno-strict-aliasing 
-Wno-literal-suffix -Wno-deprecated-declarations -O3 -MT point_predicate.lo -MD 
-MP -MF .deps/point_predicate.Tpo -c point_predicate.cc  -fPIC -DPIC -o 
.libs/point_predicate.o
In file included from /usr/include/boost/container/detail/flat_tree.hpp:29:0,
 from /usr/include/boost/container/flat_map.hpp:29,
 from /usr/include/CGAL/config.h:123,
 from /usr/include/CGAL/basic.h:29,
 from /usr/include/CGAL/Cartesian/Cartesian_base.h:28,
 from /usr/include/CGAL/Cartesian.h:28,
 from ../../include/rheolef/cgal_kernel.h:42,
 from ../../include/rheolef/cgal_traits.h:24,
 from point_predicate.cc:34:
/usr/include/boost/container/detail/pair.hpp:433:8: error: partial 
specialization of 'struct boost::is_enum >' after 
instantiation of 'struct boost::is_enum >' [-fpermissive]
 struct is_enum< ::std::pair >
^~~~
Makefile:1130: recipe for target 'point_predicate.lo' failed
make[4]: *** [point_predicate.lo] Error 1


Andreas

-- 
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#883824: scotch: broken symlinks: /usr/share/man/man1/{scotch_gbase, mcv, amk_grf}-{long, int64, int32}.1.gz -> {scotch_gbase, mcv, amk_grf}.1.gz

[Andreas Beckmann]

Package: scotch
Version: 6.0.4.dfsg1-7
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
broken symlinks.

>From the attached log (scroll to the bottom...):

0m27.2s ERROR: FAIL: Broken symlinks:
  /usr/share/man/man1/scotch_gbase-long.1.gz -> scotch_gbase.1.gz
  /usr/share/man/man1/scotch_gbase-int64.1.gz -> scotch_gbase.1.gz
  /usr/share/man/man1/scotch_gbase-int32.1.gz -> scotch_gbase.1.gz
  /usr/share/man/man1/mcv-long.1.gz -> mcv.1.gz
  /usr/share/man/man1/mcv-int64.1.gz -> mcv.1.gz
  /usr/share/man/man1/mcv-int32.1.gz -> mcv.1.gz
  /usr/share/man/man1/amk_grf-long.1.gz -> amk_grf.1.gz
  /usr/share/man/man1/amk_grf-int64.1.gz -> amk_grf.1.gz
  /usr/share/man/man1/amk_grf-int32.1.gz -> amk_grf.1.gz

The targeted manpages do not seem to exist in any package.


cheers,

Andreas


scotch_6.0.4.dfsg1-7.log.gz
Description: application/gzip
-- 
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#883820: scilab-cli: broken symlink: /usr/share/man/man1/scilab-cli.1.gz -> scilab.1.gz

[Andreas Beckmann]

Package: scilab-cli
Version: 6.0.0-1
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m39.7s ERROR: FAIL: Broken symlinks:
  /usr/share/man/man1/scilab-cli.1.gz -> scilab.1.gz

Is scilab-cli missing a Depends/Recommends/Suggests: scilab ?


cheers,

Andreas


scilab-cli_6.0.0-1.log.gz
Description: application/gzip
-- 
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#883817: libqhull-dev: missing Depends: libqhull-r7 (= ${binary:Version})

[Andreas Beckmann]

Package: libqhull-dev
Version: 2015.2-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

1m17.9s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libqhull_r.so -> libqhull_r.so.7


cheers,

Andreas


libqhull-dev_2015.2-3.log.gz
Description: application/gzip
-- 
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#881883: libnormaliz-dev-common: fails to upgrade from 'testing' - trying to overwrite /usr/include/libnormaliz/HilbertSeries.h

[Andreas Beckmann]

Package: libnormaliz-dev-common
Version: 3.4.1+ds-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libnormaliz-dev-common.
  Preparing to unpack .../libnormaliz-dev-common_3.4.1+ds-1_all.deb ...
  Unpacking libnormaliz-dev-common (3.4.1+ds-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libnormaliz-dev-common_3.4.1+ds-1_all.deb (--unpack):
   trying to overwrite '/usr/include/libnormaliz/HilbertSeries.h', which is 
also in package libnormaliz0-dev-common 3.1.1+ds-1
  Errors were encountered while processing:
   /var/cache/apt/archives/libnormaliz-dev-common_3.4.1+ds-1_all.deb


cheers,

Andreas


libnormaliz0-dev-common=3.1.1+ds-1_libnormaliz-dev-common=3.4.1+ds-1.log.gz
Description: application/gzip
-- 
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#881881: libtrilinos-kokkos-kernels-dev: fails to upgrade from 'testing' - trying to overwrite /usr/include/trilinos/Kokkos_ArithTraits.hpp

[Andreas Beckmann]

Package: libtrilinos-kokkos-kernels-dev
Version: 12.12.1-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libtrilinos-kokkos-kernels-dev:amd64.
  Preparing to unpack .../libtrilinos-kokkos-kernels-dev_12.12.1-1_amd64.deb ...
  Unpacking libtrilinos-kokkos-kernels-dev:amd64 (12.12.1-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libtrilinos-kokkos-kernels-dev_12.12.1-1_amd64.deb 
(--unpack):
   trying to overwrite '/usr/include/trilinos/Kokkos_ArithTraits.hpp', which is 
also in package libtrilinos-tpetra-dev 12.10.1-4+b1
  dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libtrilinos-kokkos-kernels-dev_12.12.1-1_amd64.deb


cheers,

Andreas


libtrilinos-tpetra-dev=12.10.1-4+b1_libtrilinos-kokkos-kernels-dev=12.12.1-1.log.gz
Description: application/gzip
-- 
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#881706: openturns: FTBFS against python3.6

[Andreas Beckmann]

Source: openturns
Version: 1.7-3
Severity: serious
Tags: sid buster
Justification: fails to build from source (but built successfully in the past)

Hi,

openturns/sid FTBFS with python3.6 as the default python3 version:

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

These tests failed on amd64:

The following tests FAILED:
429 - pyinstallcheck_Matrix_std (Failed)
432 - pyinstallcheck_SquareMatrix_std (Failed)
433 - pyinstallcheck_TriangularMatrix_std (Failed)
434 - pyinstallcheck_SymmetricMatrix_std (Failed)
442 - pyinstallcheck_ComplexMatrix_std (Failed)
443 - pyinstallcheck_SquareComplexMatrix_std (Failed)
444 - pyinstallcheck_HermitianMatrix_std (Failed)
445 - pyinstallcheck_TriangularComplexMatrix_std (Failed)
447 - pyinstallcheck_Matrix_operators (Failed)
502 - pyinstallcheck_NumericalSample_operators (Failed)
505 - pyinstallcheck_CorrelationMatrix_std (Failed)
579 - pyinstallcheck_ARMACoefficients_std (Failed)
732 - pyinstallcheck_Distribution_arithmetic (Failed)
Errors while running CTest


Andreas

-- 
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#880921: libopencv-dev: removal of libopencv-dev makes files disappear from libhighgui-dev

[Andreas Beckmann]

On 11/08/2017 04:08 PM, Mattia Rizzolo wrote:
> libhighgui-dev has been removed altogether.  Therefore, I wonder if an
> acceptable solution would be to remove the version restriction in the
> Conflicts.
> Seemingly, I'd remove the version from the libcv-dev, libcvaux-dev
> Conflicts as well

Sounds like a sensible approach to get cruft deinstalled.

> (they are in the same situation, probably if you test
> them you will find the same bug).
> Are the other binaries that are affected by a similar situation?

Didn't see similar problems in other packages, but if the dependency
chain is not trivial, it may take more crafting to get a reproducible
buggy path ...

Andreas

-- 
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#857393: closed by Jochen Sprickerhof <jspri...@debian.org> (Bug#857393: fixed in gazebo 7.8.1+dfsg-2)

[Andreas Beckmann]

On 10/16/2017 09:21 AM, Debian Bug Tracking System wrote:
>  gazebo (7.8.1+dfsg-2) unstable; urgency=medium
>* Fix fonts dependencies (Closes: #878595, #857393, #857393)

For consistency, the fonts-liberation dependency should rather be moved
to gazebo7-common (which contains the font symlinks)


Andreas

-- 
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#880921: libopencv-dev: removal of libopencv-dev makes files disappear from libhighgui-dev

[Andreas Beckmann]

Package: libopencv-dev
Version: 3.2.0+dfsg-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts replaces-without-breaks

Hi,

during a test with piuparts and DOSE tools I noticed your package causes
removal of files that also belong to another package.
This is caused by using Replaces without corresponding Breaks.

The installation sequence to reproduce this problem is

  apt-get install libhighgui-dev/stretch
  # (1)
  apt-get install libopencv-dev/buster
  apt-get remove libopencv-dev
  # (2)

The list of installed files at points (1) and (2) should be identical,
but the following files have disappeared:

  /usr/include/opencv/highgui.h

This is a serious bug violating policy 7.6, see
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces
and also see the footnote that describes this incorrect behavior
https://www.debian.org/doc/debian-policy/footnotes.html#f53

The libopencv-dev package has the following relationships with libhighgui-dev:

  Conflicts: libhighgui-dev (<= 2.4.9.1+dfsg-2.1)
  Breaks:
  Replaces:  libhighgui-dev

* The Conflicts version obviously predates the moving around of highgui.h
* The Replaces should be versioned identical to the corresponding Breaks (or 
Conflicts)
* Breaks is preferred over Conflicts for moving files between packages since it 
makes apt's job easier
* There are more unversioned Replaces with versioned Conflicts, these should be 
made versioned, too


>From the attached log (scroll to the bottom...):

5m57.4s DEBUG: Modified(user, group, mode, size, target): 
/var/lib/dpkg/info/libhighgui-dev:amd64.list expected(root, root, - 100644, 
261, None) != found(root, root, - 100644, 231, None)
5m57.4s INFO: Warning: Package purging left files on system:
  /etc/fonts/conf.d/10-hinting-slight.conf -> 
/usr/share/fontconfig/conf.avail/10-hinting-slight.confnot owned

5m57.4s ERROR: FAIL: After purging files have disappeared:
  /usr/include/opencv/highgui.h  owned by: libopencv-dev

5m57.4s ERROR: FAIL: After purging files have been modified:
  /var/lib/dpkg/info/libhighgui-dev:amd64.list   not owned


cheers,

Andreas


libopencv3.2-java=3.2.0+dfsg-3_libopencv3.3-java=3.3.0+dfsg-1~exp0.log.gz
Description: application/gzip
-- 
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#880885: caffe-contrib: B-D on obsolete compiler gcc-5 not available in testing

[Andreas Beckmann]

Source: caffe-contrib
Version: 1.0.0-4
Severity: serious
Justification: fails to build from source

caffe-contrib cannot be rebuilt in testing since gcc-5 is not available
in testing (and won't return there).


Andreas

-- 
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#880214: libjava-gmsh3: fails to upgrade from 'testing' - trying to overwrite /usr/lib/x86_64-linux-gnu/libjava-gmsh.so

[Andreas Beckmann]

Package: libjava-gmsh3
Version: 3.0.5+dfsg1-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libjava-gmsh3.
  Preparing to unpack .../libjava-gmsh3_3.0.5+dfsg1-1_amd64.deb ...
  Unpacking libjava-gmsh3 (3.0.5+dfsg1-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libjava-gmsh3_3.0.5+dfsg1-1_amd64.deb (--unpack):
   trying to overwrite '/usr/lib/x86_64-linux-gnu/libjava-gmsh.so', which is 
also in package libjava-gmsh2 2.15.0+dfsg1-3+b2
  dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /var/cache/apt/archives/libjava-gmsh3_3.0.5+dfsg1-1_amd64.deb


cheers,

Andreas


libjava-gmsh2=2.15.0+dfsg1-3+b2_libjava-gmsh3=3.0.5+dfsg1-1.log.gz
Description: application/gzip
-- 
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#880212: libopencv3.3-java: fails to upgrade from 'sid' - trying to overwrite /usr/share/java/opencv.jar

[Andreas Beckmann]

Package: libopencv3.3-java
Version: 3.3.0+dfsg-1~exp0
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'sid' to 'experimental'.
It installed fine in 'sid', then the upgrade to 'experimental' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libopencv3.3-java.
  Preparing to unpack .../29-libopencv3.3-java_3.3.0+dfsg-1~exp0_all.deb ...
  Unpacking libopencv3.3-java (3.3.0+dfsg-1~exp0) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-RPe3bU/29-libopencv3.3-java_3.3.0+dfsg-1~exp0_all.deb 
(--unpack):
   trying to overwrite '/usr/share/java/opencv.jar', which is also in package 
libopencv3.2-java 3.2.0+dfsg-3


cheers,

Andreas


libopencv3.2-java=3.2.0+dfsg-3_libopencv3.3-java=3.3.0+dfsg-1~exp0.log.gz
Description: application/gzip
-- 
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#878010: r-cran-vcdextra: unsatisfiable Depends: r-cran-gnm (>= 1.0.3) but 1.0-8-1+b2 is to be installed

[Andreas Beckmann]

Package: r-cran-vcdextra
Version: 0.7-1-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package is no longer
installable in sid:

The following packages have unmet dependencies:
 r-cran-vcdextra : Depends: r-cran-gnm (>= 1.0.3) but it is not going to be 
installed

r-cran-gnm | 1.0-8-1   | unstable   | source
r-cran-gnm | 1.0-8-1   | unstable-debug | source
r-cran-gnm | 1.0-8-1+b2| unstable   | amd64, arm64, armel, armhf, 
hurd-i386, i386, kfreebsd-amd64, kfreebsd-i386, mips, mips64el, mipsel, 
powerpc, ppc64el, s390x


Cheers,

Andreas

-- 
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#875911: still not completely solved

[Andreas Beckmann]

On 10/05/2017 09:33 AM, Ole Streicher wrote:
> Ping?

Sorry, didn't have time to look into this, yet.

> I don't see a problem with the package, so I would close this bug (and
> let plplot migrate) otherwise.

I could have thought earlier of pointing you there:

https://piuparts.debian.org/testing2sid/installs_over_symlink_error.html
https://piuparts.debian.org/testing2sid/source/p/plplot.html

There are 4 more packages needing the symlink_to_dir transition
There is also one r-dependency of python-plplot that has not been tested
(due to python-plplot failing), but may need this as well. That should
be python-plplot-qt.


Andreas

-- 
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#877460: python-escript-doc: broken symlink /usr/share/doc/python-escript-doc/python_html/_static/doctools.js -> ../../../../sphinx/themes/basic/static/doctools.js

[Andreas Beckmann]

Package: python-escript-doc
Version: 5.0-4
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

4m56.6s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/python-escript-doc/python_html/_static/doctools.js -> 
../../../../sphinx/themes/basic/static/doctools.js

spinx-common only ships a doctools.js_t file at that location ...


cheers,

Andreas


python-escript-doc_5.0-4.log.gz
Description: application/gzip
-- 
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#875911: still not completely solved

[Andreas Beckmann]

Control: reopen -1

that still does not work as planned ... investigating ... trying to
follow up with a patch later ...


Andreas

-- 
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#877277: python-tables-doc: broken symlink: /usr/share/doc/python-tables-doc/html/_static/MathJax.js -> ../../../../javascript/mathjax/MathJax.js

[Andreas Beckmann]

Package: python-tables-doc
Version: 3.4.2-1
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m57.1s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/python-tables-doc/html/_static/MathJax.js -> 
../../../../javascript/mathjax/MathJax.js

Is python-tables-doc missing a dependency on libjs-mathjax?


cheers,

Andreas


python-tables-doc_3.4.2-1.log.gz
Description: application/gzip
-- 
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#877131: lua-torch-image: FTBFS: ./image.lua:156: [read_png] Error during init_io: IDAT: chunk data is too large

[Andreas Beckmann]

Source: lua-torch-image
Version: 0~20170420-g5aa1881-2
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

lua-torch-image FTBFS for me in a sid/experimental amd64 pbuilder chroot
with some test failures:

[...]
luajit: /usr/share/lua/5.1/torch/Tester.lua:363: An error was found while 
running tests!
stack traceback:
[C]: in function 'assert'
/usr/share/lua/5.1/torch/Tester.lua:363: in function 'run'
./image/test.lua:708: in function 'test'
(command line):1: in main chunk
[C]: at 0x5617972f11d0
Completed 74 asserts in 41 tests with ESC[0;32m0 failuresESC[0m and ESC[0;35m2 
errorsESC[0m

LoadPNG
 Function call failed
./image.lua:156: [read_png] Error during init_io: IDAT: chunk data is too large
stack traceback:
[C]: in function 'load'
./image.lua:156: in function 'loader'
./image.lua:388: in function 'load'
./image/test.lua:538: in function 'checkPNG'
./image/test.lua:549: in function <./image/test.lua:546>
[C]: in function 'xpcall'
/usr/share/lua/5.1/torch/Tester.lua:477: in function '_pcall'
/usr/share/lua/5.1/torch/Tester.lua:436: in function '_run'
/usr/share/lua/5.1/torch/Tester.lua:355: in function 'run'
./image/test.lua:708: in function 'test'
(command line):1: in main chunk
[C]: at 0x5617972f11d0


DecompressPNG
 Function call failed
./image.lua:156: [read_png] Error during init_io: IDAT: chunk data is too large
stack traceback:
[C]: in function 'load'
./image.lua:156: in function 'loader'
./image.lua:388: in function 'load'
./image/test.lua:578: in function <./image/test.lua:576>
[C]: in function 'xpcall'
/usr/share/lua/5.1/torch/Tester.lua:477: in function '_pcall'
/usr/share/lua/5.1/torch/Tester.lua:436: in function '_run'
/usr/share/lua/5.1/torch/Tester.lua:355: in function 'run'
./image/test.lua:708: in function 'test'
(command line):1: in main chunk
[C]: at 0x5617972f11d0


debian/rules:14: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1

full log attached


Andreas


lua-torch-image_0~20170420-g5aa1881-2.log.gz
Description: application/gzip
-- 
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#875911: Processed: found 875911 in 5.13.0+dfsg-1~exp3

[Andreas Beckmann]

Control: found -1 5.13.0+dfsg-3
Control: notfixed -1 5.13.0+dfsg-2

On 09/22/2017 04:33 PM, Ole Streicher wrote:
> Hi Andreas,
> 
> On 22.09.2017 16:15, Debian Bug Tracking System wrote:
>> Processing commands for cont...@bugs.debian.org:
>>
>>> found 875911 5.13.0+dfsg-1~exp3
> 
> Could I ask you to explain that a bit more verbose?
> 
> The required install scripts (postinst preinst prerm) are there, so the
> conversion should work.

You shouldn't add duplicate copies of the maintainer scripts, but use
debian/$package.maintscript instead and let debhelper do the
duplication. See dh_installdeb(1) for details.
And you can omit the package name argument if it's the same as $package.

>From commit 26e01b3d20b6 I'm concluding that all the prior-versions you
used are wrong. If 5.13.0+dfsg-1 shipped a wrong version there (and
therefore the transition didn't take place when upgrading from ... to
... to 5.13.0+dfsg-1~exp3 to 5.13.0+dfsg-1), it should have been set to
5.13.0+dfsg-2~ (i.e. not the version that initially brought the change
in the filesystem, but the version that adds the correct
dpkg-maintscript-helper symlink_to_dir call) in the fixing upload of
5.13.0+dfsg-2 (so the conversion would be attempted again while
upgrading to 5.13.0+dfsg-2, but since 5.13.0+dfsg-1~exp2~ is older than
5.13.0+dfsg-1, nothing would be retried and the broken state would be
left in place).

So assuming the next upload will be 5.13.0+dfsg-4, use 5.13.0+dfsg-4~ as
the prior-version in all *.maintscript files (this will ensure the
upgrade path from stable to unstable will do the symlink_to_dir
transition once and correctly, regardless of which intermediate versions
from sid and experimental have been installed).

Reopening again, since this problem also exists in python-plplot,
libplplot-ocaml, plplot-tcl-bin, plplot-tcl-dev (found in testing->sid
and stable->sid upgrade tests). Reusing this bug report instead of
opening a new, since this is still the same issue.
(I initially filed two bugs against the same source package since I
didn't recognize libqsastime* was related to *plplot*.)


Andreas

-- 
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#876708: libtorch-thnn: broken symlink: /usr/lib/x86_64-linux-gnu/lua/5.1/libTHNN.so -> ../../libTHNN.so

[Andreas Beckmann]

Package: libtorch-thnn
Version: 0~20170726-gf613412+dfsg-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m42.3s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/lua/5.1/libTHNN.so -> ../../libTHNN.so

You probably want to target ../../ibTHNN.so.0 instead,
since the .so is only available in the -dev package.


cheers,

Andreas


libtorch-thnn_0~20170726-gf613412+dfsg-1.log.gz
Description: application/gzip
-- 
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#875911: Processed: found 875911 in 5.13.0+dfsg-1~exp3

[Andreas Beckmann]

On 09/22/2017 04:33 PM, Ole Streicher wrote:
>>> found 875911 5.13.0+dfsg-1~exp3
> 
> Could I ask you to explain that a bit more verbose?
> 
> The required install scripts (postinst preinst prerm) are there, so the
> conversion should work.

I'll wait for the new packages uploaded to unstable to be tested and
post new logs.


Andreas

-- 
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#875913: plplot-tcl, libplplot-{java, lua}: unhandled symlink to directory conversion: /usr/share/doc/PACKAGE

[Andreas Beckmann]

Package: plplot-tcl,libplplot-java,libplplot-lua
Version: 5.13.0+dfsg-1~exp1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

an upgrade test with piuparts revealed that your package installs files
over existing symlinks and possibly overwrites files owned by other
packages. This usually means an old version of the package shipped a
symlink but that was later replaced by a real (and non-empty)
directory. This kind of overwriting another package's files cannot be
detected by dpkg.

This was observed on the following upgrade paths:

  sid -> experimental

For /usr/share/doc/PACKAGE this may not be problematic as long as both
packages are installed, ship byte-for-byte identical files and are
upgraded in lockstep. But once one of the involved packages gets
removed, the other one will lose its documentation files, too,
including the copyright file, which is a violation of Policy 12.5:
https://www.debian.org/doc/debian-policy/ch-docs.html#s-copyrightfile

For other overwritten locations anything interesting may happen.

Note that dpkg intentionally does not replace directories with symlinks
and vice versa, you need the maintainer scripts to do this.
See in particular the end of point 4 in
https://www.debian.org/doc/debian-policy/ch-maintainerscripts.html#s-unpackphase

It is recommended to use the dpkg-maintscript-helper commands
'dir_to_symlink' and 'symlink_to_dir' (available since dpkg 1.17.14)
to perform the conversion, ideally using d/$PACKAGE.maintscript.
Do not forget to add 'Pre-Depends: ${misc:Pre-Depends}' in d/control.
See dpkg-maintscript-helper(1) and dh_installdeb(1) for details.


>From the attached log (scroll to the bottom...):

0m18.0s INFO: dirname part contains a symlink:
  /usr/share/doc/plplot-tcl/changelog.Debian.gz (plplot-tcl) != 
/usr/share/doc/libplplot12/changelog.Debian.gz (?)
/usr/share/doc/plplot-tcl -> libplplot12
  /usr/share/doc/plplot-tcl/changelog.gz (plplot-tcl) != 
/usr/share/doc/libplplot12/changelog.gz (?)
/usr/share/doc/plplot-tcl -> libplplot12
  /usr/share/doc/plplot-tcl/copyright (plplot-tcl) != 
/usr/share/doc/libplplot12/copyright (?)
/usr/share/doc/plplot-tcl -> libplplot12

0m15.9s INFO: dirname part contains a symlink:
  /usr/share/doc/libplplot-java/changelog.Debian.gz (libplplot-java) != 
/usr/share/doc/libplplot12/changelog.Debian.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/changelog.gz (libplplot-java) != 
/usr/share/doc/libplplot12/changelog.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/copyright (libplplot-java) != 
/usr/share/doc/libplplot12/copyright (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples (libplplot-java) != 
/usr/share/doc/libplplot12/examples (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/CMakeLists.txt.gz (libplplot-java) != 
/usr/share/doc/libplplot12/examples/CMakeLists.txt.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/Makefile.examples.in (libplplot-java) 
!= /usr/share/doc/libplplot12/examples/Makefile.examples.in (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/README.javademos (libplplot-java) != 
/usr/share/doc/libplplot12/examples/README.javademos (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x00.java (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x00.java (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x01.java.gz (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x01.java.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x02.java.gz (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x02.java.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x03.java (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x03.java (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x04.java.gz (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x04.java.gz (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x05.java (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x05.java (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x06.java (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x06.java (?)
/usr/share/doc/libplplot-java -> libplplot12
  /usr/share/doc/libplplot-java/examples/x07.java (libplplot-java) != 
/usr/share/doc/libplplot12/examples/x07.java (?)
/usr/share/doc/libplplot-java -> libplplot12
...

0m15.4s INFO: dirname part contains a symlink:
  /usr/share/doc/libplplot-lua/changelog.Debian.gz (libplplot-lua:amd64) != 
/usr/share/doc/libplplot12/changelog.Debian.gz (?)

Bug#875911: libqsastime-dev: unhandled symlink to directory conversion: /usr/share/doc/PACKAGE

[Andreas Beckmann]

Package: libqsastime-dev
Version: 5.13.0+dfsg-1~exp1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

an upgrade test with piuparts revealed that your package installs files
over existing symlinks and possibly overwrites files owned by other
packages. This usually means an old version of the package shipped a
symlink but that was later replaced by a real (and non-empty)
directory. This kind of overwriting another package's files cannot be
detected by dpkg.

This was observed on the following upgrade paths:

  sid -> experimental

For /usr/share/doc/PACKAGE this may not be problematic as long as both
packages are installed, ship byte-for-byte identical files and are
upgraded in lockstep. But once one of the involved packages gets
removed, the other one will lose its documentation files, too,
including the copyright file, which is a violation of Policy 12.5:
https://www.debian.org/doc/debian-policy/ch-docs.html#s-copyrightfile

For other overwritten locations anything interesting may happen.

Note that dpkg intentionally does not replace directories with symlinks
and vice versa, you need the maintainer scripts to do this.
See in particular the end of point 4 in
https://www.debian.org/doc/debian-policy/ch-maintainerscripts.html#s-unpackphase

It is recommended to use the dpkg-maintscript-helper commands
'dir_to_symlink' and 'symlink_to_dir' (available since dpkg 1.17.14)
to perform the conversion, ideally using d/$PACKAGE.maintscript.
Do not forget to add 'Pre-Depends: ${misc:Pre-Depends}' in d/control.
See dpkg-maintscript-helper(1) and dh_installdeb(1) for details.


>From the attached log (scroll to the bottom...):

0m14.6s ERROR: FAIL: silently overwrites files via directory symlinks:
  /usr/share/doc/libqsastime-dev/changelog.Debian.gz (libqsastime-dev:amd64) != 
/usr/share/doc/libqsastime0/changelog.Debian.gz (libqsastime0:amd64)
/usr/share/doc/libqsastime-dev -> libqsastime0
  /usr/share/doc/libqsastime-dev/changelog.gz (libqsastime-dev:amd64) != 
/usr/share/doc/libqsastime0/changelog.gz (libqsastime0:amd64)
/usr/share/doc/libqsastime-dev -> libqsastime0
  /usr/share/doc/libqsastime-dev/copyright (libqsastime-dev:amd64) != 
/usr/share/doc/libqsastime0/copyright (libqsastime0:amd64)
/usr/share/doc/libqsastime-dev -> libqsastime0


cheers,

Andreas


libqsastime-dev_5.13.0+dfsg-1~exp1.log.gz
Description: application/gzip
-- 
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#875812: kbibtex-data: fails to upgrade from 'testing' - trying to overwrite /usr/share/icons/hicolor/128x128/apps/kbibtex.png

[Andreas Beckmann]

Package: kbibtex-data
Version: 0.8~20170819git31a77b27e8e83836e-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'testing'.
It installed fine in 'testing', then the upgrade to 'sid' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package kbibtex-data.
  Preparing to unpack 
.../26-kbibtex-data_0.8~20170819git31a77b27e8e83836e-1_all.deb ...
  Unpacking kbibtex-data (0.8~20170819git31a77b27e8e83836e-1) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-Qnbzx9/26-kbibtex-data_0.8~20170819git31a77b27e8e83836e-1_all.deb
 (--unpack):
   trying to overwrite '/usr/share/icons/hicolor/128x128/apps/kbibtex.png', 
which is also in package kbibtex 0.4-4+b2
  dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)


cheers,

Andreas


kbibtex=0.4-4+b2_kbibtex-data=0.8~20170819git31a77b27e8e83836e-1.log.gz
Description: application/gzip
-- 
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#874761: hfst: broken symlink: /usr/share/doc/hfst/README -> README.rst

[Andreas Beckmann]

Package: hfst
Version: 3.12.2~r3289-2
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

5m0.3s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/hfst/README -> README.rst


cheers,

Andreas


hfst_3.12.2~r3289-2.log.gz
Description: application/gzip
-- 
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#874563: apertium-all-dev: please switch dependency from libhfst45-dev to libhfst-dev (or libhfst49-dev)

[Andreas Beckmann]

Package: apertium-all-dev
Version: 3.4.2~r68466-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

src:hfst does no longer build libhfst45-dev, but there is libhfst49-dev
now. Please consider whether you can just depend on the virtual
libhfst-dev package provided by libhfst49-dev, that should ease future
upgrades by not requiring any further changes in apertium-all-dev.


Cheers,

Andreas

-- 
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#874562: python-bloom: python-rosdep was renamed to python-rosdep2

[Andreas Beckmann]

Package: python-bloom
Version: 0.5.26-5
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package is no longer
installable in sid:

python-bloom still depends on python-rosdep, but that was renamed to
python-rosdep2.


Cheers,

Andreas

-- 
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#871232: caffe-contrib: FTBFS with GCC-7: bits/std_abs.h:101:3: error: unknown type name '__float128'

[Andreas Beckmann]

Source: caffe-contrib
Version: 1.0.0-3
Severity: serious
Tags: sid buster
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-7

caffe-contrib FTBFS since GCC-7 was made the default compiler:

[...]
[  0%] Building CXX object 
src/caffe/CMakeFiles/caffeproto.dir/__/__/include/caffe/proto/caffe.pb.cc.o
cd /build/caffe-contrib-1.0.0/caffe_cuda_build/src/caffe && 
/usr/bin/clang++-3.8  -DCAFFE_VERSION=1.0.0 
-I/build/caffe-contrib-1.0.0/caffe_cuda_build/include -I/usr/include/opencv 
-I/build/caffe-contrib-1.0.0/caffe
_cuda_build  -g -O2 -fdebug-prefix-map=/build/caffe-contrib-1.0.0=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wall  -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -Wall -Wno-sign-compare -Wno-uninitialized 
-O3 -DNDEBUG   -o 
CMakeFiles/caffeproto.dir/__/__/include/caffe/proto/caffe.pb.cc.o -c 
/build/caffe-contrib-1.0.0/caffe_cuda_build/include/caffe/proto/caffe.pb.cc
In file included from 
/build/caffe-contrib-1.0.0/caffe_cuda_build/include/caffe/proto/caffe.pb.cc:5:
In file included from 
/build/caffe-contrib-1.0.0/caffe_cuda_build/include/caffe/proto/caffe.pb.h:9:
In file included from /usr/include/google/protobuf/stubs/common.h:40:
In file included from /usr/include/google/protobuf/stubs/port.h:35:
In file included from 
/usr/bin/../lib/gcc/x86_64-linux-gnu/7.1.0/../../../../include/c++/7.1.0/stdlib.h:36:
In file included from 
/usr/bin/../lib/gcc/x86_64-linux-gnu/7.1.0/../../../../include/c++/7.1.0/cstdlib:77:
/usr/bin/../lib/gcc/x86_64-linux-gnu/7.1.0/../../../../include/c++/7.1.0/bits/std_abs.h:101:3:
 error: unknown type name '__float128'
  __float128
  ^
/usr/bin/../lib/gcc/x86_64-linux-gnu/7.1.0/../../../../include/c++/7.1.0/bits/std_abs.h:102:7:
 error: unknown type name '__float128'
  abs(__float128 __x)
  ^
2 errors generated.
src/caffe/CMakeFiles/caffeproto.dir/build.make:77: recipe for target 
'src/caffe/CMakeFiles/caffeproto.dir/__/__/include/caffe/proto/caffe.pb.cc.o' 
failed
make[5]: *** 
[src/caffe/CMakeFiles/caffeproto.dir/__/__/include/caffe/proto/caffe.pb.cc.o] 
Error 1


This looks related to #871011 in clang-3.8 (clang-3.9 is fine).


Cheers,

Andreas


caffe-contrib_1.0.0-3.log.gz
Description: application/gzip
-- 
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#870718: lua-torch-cutorch: FTBFS with linker error: undefined reference to `THLongStorage_calculateExpandGeometry'

[Andreas Beckmann]

Source: lua-torch-cutorch
Version: 0~20170511-g92e9c08-1
Severity: serious

build log ends with

[...]
libtool --silent --tag=CC --mode=link clang-3.8 -g -O2 
-fdebug-prefix-map=/build/lua-torch-cutorch-0~20170511-g92e9c08=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -I/usr//include/lua5.1 
-I/build/lua-torch-cutorch-0~20170511-g92e9c08 -I/usr/include/lua5.1 
-I/build/lua-torch-cutorch-0~20170511-g92e9c08/lib/THC -I/usr/include/TH 
-I/build/lua-torch-cutorch-0~20170511-g92e9c08/THC.build 
-I/build/lua-torch-cutorch-0~20170511-g92e9c08/torch -Wall -Wextra 
-Wl,--no-add-needed \
-o 
/build/lua-torch-cutorch-0~20170511-g92e9c08/5.1-torch-cutorch/app-dynamic -I . 
-I /build/lua-torch-cutorch-0~20170511-g92e9c08/5.1-torch-cutorch/ \
/usr/share/dh-lua/test/5.1/app.c 
/build/lua-torch-cutorch-0~20170511-g92e9c08/5.1-torch-cutorch/liblua5.1-torch-cutorch.la
 \
-Wl,-z,relro -Wl,--as-needed 
-L/build/lua-torch-cutorch-0~20170511-g92e9c08/THC.build -lluaT -lTH -lTHC 
-lcudart -lcublas -lcurand -L/usr//lib/x86_64-linux-gnu -llua5.1
/build/lua-torch-cutorch-0~20170511-g92e9c08/THC.build/libTHC.so: undefined 
reference to `THLongStorage_calculateExpandGeometry'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
/usr/share/dh-lua/make/dh-lua.Makefile.single:460: recipe for target 
'/build/lua-torch-cutorch-0~20170511-g92e9c08/5.1-torch-cutorch/app-dynamic' 
failed
make[2]: *** 
[/build/lua-torch-cutorch-0~20170511-g92e9c08/5.1-torch-cutorch/app-dynamic] 
Error 1
/usr/share/dh-lua/make/dh-lua.Makefile.multiple:12: recipe for target 'test' 
failed
make[1]: *** [test] Error 1
dh_auto_test: make --no-print-directory -f 
/usr/share/dh-lua/make/dh-lua.Makefile.multiple test returned exit code 2
debian/rules:31: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2


Andreas


lua-torch-cutorch_0~20170511-g92e9c08-1.log.gz
Description: application/gzip
-- 
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#870688: sagemath: new upstream release 8.0

[Andreas Beckmann]

Package: sagemath
Version: 7.6-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package is no longer
installable in sid:

sagemath depends on python-cysignals-pari, but the new
python-cysignals-pari in sid has
  Breaks: sagemath (<< 8.0~)


Cheers,

Andreas

-- 
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#870582: libscalapack-openmpi-dev: fails to upgrade from 'sid' - trying to overwrite /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so

[Andreas Beckmann]

Package: libscalapack-openmpi-dev
Version: 2.0.2-1exp3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts
Control: affects -1 + libscalapack-mpi-dev

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'sid' to 'experimental'.
It installed fine in 'sid', then the upgrade to 'experimental' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package libscalapack-openmpi2.0.
  (Reading database ... 
(Reading database ... 7455 files and directories currently installed.)
  Preparing to unpack .../libscalapack-openmpi2.0_2.0.2-1exp3_amd64.deb ...
  Unpacking libscalapack-openmpi2.0 (2.0.2-1exp3) ...
  Selecting previously unselected package libscalapack-openmpi-dev.
  Preparing to unpack .../libscalapack-openmpi-dev_2.0.2-1exp3_amd64.deb ...
  Unpacking libscalapack-openmpi-dev (2.0.2-1exp3) ...
  dpkg: error processing archive 
/var/cache/apt/archives/libscalapack-openmpi-dev_2.0.2-1exp3_amd64.deb 
(--unpack):
   trying to overwrite '/usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so', 
which is also in package libscalapack-mpi-dev 1.8.0-14
  Preparing to unpack .../libscalapack-mpi-dev_2.0.2-1exp3_amd64.deb ...
  Unpacking libscalapack-mpi-dev (2.0.2-1exp3) over (1.8.0-14) ...
  Errors were encountered while processing:
   /var/cache/apt/archives/libscalapack-openmpi-dev_2.0.2-1exp3_amd64.deb

cheers,

Andreas


libscalapack-mpi-dev_2.0.2-1exp3.log.gz
Description: application/gzip
-- 
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#859844: vmtk: Please migrate to openssl1.1 in Buster

[Andreas Beckmann]

Followup-For: Bug #859844
Control: tag -1 serious

currently vmtk (transitively) Build-Depends on both libssl-dev and
libssl1.0-dev which conflict with each other.


Andreas

-- 
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#867454: libvtk6-qt-dev: missing Depends: libvtk6-qt (= ${binary:Version})

[Andreas Beckmann]

Package: libvtk6-qt-dev
Version: 6.3.0+dfsg1-7
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

2m42.4s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libvtkViewsQt-6.3.so -> libvtkViewsQt-6.3.so.6.3
  /usr/lib/x86_64-linux-gnu/libvtkRenderingQt-6.3.so -> 
libvtkRenderingQt-6.3.so.6.3
  /usr/lib/x86_64-linux-gnu/libvtkGUISupportQtWebkit-6.3.so -> 
libvtkGUISupportQtWebkit-6.3.so.6.3
  /usr/lib/x86_64-linux-gnu/libvtkGUISupportQtSQL-6.3.so -> 
libvtkGUISupportQtSQL-6.3.so.6.3
  /usr/lib/x86_64-linux-gnu/libvtkGUISupportQtOpenGL-6.3.so -> 
libvtkGUISupportQtOpenGL-6.3.so.6.3
  /usr/lib/x86_64-linux-gnu/libvtkGUISupportQt-6.3.so -> 
libvtkGUISupportQt-6.3.so.6.3

The targets are in libvtk6-qt ...


cheers,

Andreas


libvtk6-qt-dev_6.3.0+dfsg1-7.log.gz
Description: application/gzip
-- 
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#866925: nexus: switch B-D from libhdf4g-dev to libhdf4-dev

[Andreas Beckmann]

Source: nexus
Version: 4.3.2-svn1921-5
Severity: serious

The transitional libhdf4g-dev package is no longer built. Please switch
to libhdf4-dev.


Andreas

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

Re: vtkdata: do not ship in stretch

[Andreas Beckmann]

On Thu, 8 Jun 2017 21:23:00 +0200 Mathieu Malaterre 
wrote:
> Source: vtkdata
> Version: 5.8.0-1
> Severity: serious
> Tags: stretch sid
> 
> Since #798164 there is basically no point in shipping vtkdata with stretch.

Dear vtk and vtk6 maintainers,

could you gave a status update for the src:vtkdata (5.8.0-1) package?
Should this be removed from the sid (and stretch), or is it still useful
with vtk6?


Andreas

-- 
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#861677: libgfs-dev: broken symlink on i386: /usr/lib/x86_64-linux-gnu/libgfs[23]D-1.3.so -> libgfs[23]D-1.3.so.2.0.0

[Andreas Beckmann]

Package: libgfs-dev
Version: 20131206+dfsg-14
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

1m26.4s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libgfs3D-1.3.so -> libgfs3D-1.3.so.2.0.0
  /usr/lib/x86_64-linux-gnu/libgfs2D-1.3.so -> libgfs2D-1.3.so.2.0.0
   ^^

Since this happens on i386 ... these symlinks seem to be manually
created, while they should rather come from the build system.


cheers,

Andreas


gfsview_20121130+dfsg-4.log.gz
Description: application/gzip
-- 
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#861030: gfsview: broken symlink: /usr/share/gfsview/fonts/Garuda.ttf -> ../../fonts/opentype/tlwg/Garuda.otf

[Andreas Beckmann]

Followup-For: Bug #861030
Control: found -1 20121130+dfsg-3

Hi,

you only updated the Build-Depends, but not the Depends.


Andreas

-- 
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#861498: python-skimage-doc: broken symlinks: /usr/share/doc/python-skimage-doc/html/_static/*/*.* -> ../../../../../twitter-bootstrap/files/*/*.*

[Andreas Beckmann]

Package: python-skimage-doc
Version: 0.12.3-9
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m31.2s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/python-skimage-doc/html/_static/js/bootstrap.min.js -> 
../../../../../twitter-bootstrap/files/js/bootstrap.min.js
  /usr/share/doc/python-skimage-doc/html/_static/css/bootstrap.min.css -> 
../../../../../twitter-bootstrap/files/css/bootstrap.min.css
  /usr/share/doc/python-skimage-doc/html/_static/css/bootstrap-responsive.css 
-> ../../../../../twitter-bootstrap/files/css/bootstrap-responsive.css


Is python-skimage-doc missing a Depends/Recommends/Suggests: 
libjs-twitter-bootstrap ?


cheers,

Andreas


python-skimage-doc_0.12.3-9.log.gz
Description: application/gzip
-- 
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#861030: gfsview: broken symlink: /usr/share/gfsview/fonts/Garuda.ttf -> ../../fonts/opentype/tlwg/Garuda.otf

[Andreas Beckmann]

Package: gfsview
Version: 20121130+dfsg-2
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

1m28.0s ERROR: FAIL: Broken symlinks:
  /usr/share/gfsview/fonts/Garuda.ttf -> ../../fonts/opentype/tlwg/Garuda.otf


gfsview has Depends: fonts-tlwg-garuda, but that is the wrong
package, since it is only a metapackage:

  Package: fonts-tlwg-garuda
  Depends: fonts-tlwg-garuda-ttf | fonts-tlwg-garuda-otf

which is not suitable if you want a specific file to exist.
So depend on fonts-tlwg-garuda-otf instead. (Or switch the symlink
target to the corresponding .ttf and depend on the -ttf package.)


cheers,

Andreas


gfsview_20121130+dfsg-2+b3.log.gz
Description: application/gzip
-- 
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#861028: morse-simulator: abuses Conflicts to circument Policy 10.1 on /usr/bin/morse collision with morse

[Andreas Beckmann]

Package: morse-simulator
Version: 0.5.2-1
Severity: serious

Hi,

both morse and morse-simulator ship /usr/bin/morse

  Package: morse
  Description-en: training program about morse-code for aspiring radio hams

  Package: morse-simulator
  Description-en: Multi-OpenRobot Simulation Engine
  Conflicts: morse

These two packages seem in no way related, so using Conflicts is
incorrect here, hiding a violation of Policy 10.1:

  10.1 Binaries
  Two different packages must not install programs with different
  functionality but with the same filenames.
  [...]
  https://www.debian.org/doc/debian-policy/ch-files.html#s-binaries

Given the long history of this bug (going back to wheezy (at least)),
it's probably OK to ask for {stretch,jessie,wheezy}-ignore.


Andreas

PS: I stomped on this by accident since morse-simulator-doc puts stuff
into /usr/share/doc/morse :-)

-- 
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#861024: gerris: broken symlinks: /usr/lib/gerris/(m4.awk|gfs2tex.py) -> ../../share/gerris/lib/$1

[Andreas Beckmann]

Package: gerris
Version: 20131206+dfsg-13
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

1m52.3s ERROR: FAIL: Broken symlinks:
  /usr/lib/gerris/m4.awk -> ../../share/gerris/lib/m4.awk
  /usr/lib/gerris/gfs2tex.py -> ../../share/gerris/lib/gfs2tex.py

The gerris package ships instead
  /usr/share/gerris/m4.awk
  /usr/share/gerris/gfs2tex.py
which are probably the intended targets.


cheers,

Andreas


gerris_20131206+dfsg-13.log.gz
Description: application/gzip
-- 
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#861023: python-escript-doc: broken symlinks: /usr/share/doc/python-escript-doc/python_html/_static/*

[Andreas Beckmann]

Package: python-escript-doc
Version: 5.0-3
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

6m17.7s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/python-escript-doc/python_html/_static/websupport.js -> 
../../../../sphinx/themes/basic/static/websupport.js
  /usr/share/doc/python-escript-doc/python_html/_static/up.png -> 
../../../../sphinx/themes/basic/static/up.png
  /usr/share/doc/python-escript-doc/python_html/_static/up-pressed.png -> 
../../../../sphinx/themes/basic/static/up-pressed.png
  /usr/share/doc/python-escript-doc/python_html/_static/underscore.js -> 
../../../../sphinx/themes/basic/static/underscore.js
  /usr/share/doc/python-escript-doc/python_html/_static/plus.png -> 
../../../../sphinx/themes/basic/static/plus.png
  /usr/share/doc/python-escript-doc/python_html/_static/minus.png -> 
../../../../sphinx/themes/basic/static/minus.png
  /usr/share/doc/python-escript-doc/python_html/_static/jquery.js -> 
../../../../sphinx/themes/basic/static/jquery.js
  /usr/share/doc/python-escript-doc/python_html/_static/file.png -> 
../../../../sphinx/themes/basic/static/file.png
  /usr/share/doc/python-escript-doc/python_html/_static/down.png -> 
../../../../sphinx/themes/basic/static/down.png
  /usr/share/doc/python-escript-doc/python_html/_static/down-pressed.png -> 
../../../../sphinx/themes/basic/static/down-pressed.png
  /usr/share/doc/python-escript-doc/python_html/_static/doctools.js -> 
../../../../sphinx/themes/basic/static/doctools.js
  /usr/share/doc/python-escript-doc/python_html/_static/comment.png -> 
../../../../sphinx/themes/basic/static/comment.png
  /usr/share/doc/python-escript-doc/python_html/_static/comment-close.png -> 
../../../../sphinx/themes/basic/static/comment-close.png
  /usr/share/doc/python-escript-doc/python_html/_static/comment-bright.png -> 
../../../../sphinx/themes/basic/static/comment-bright.png
  /usr/share/doc/python-escript-doc/python_html/_static/ajax-loader.gif -> 
../../../../sphinx/themes/basic/static/ajax-loader.gif
  /usr/share/doc/python-escript-doc/c++_html/jquery.js -> 
../../../sphinx/themes/basic/static/jquery.js


Looks like despite the package uses dh --with sphinxdoc, the linking and
dependency on libjs-sphinxdoc are done manually.
The symlink targets are actually provided by sphinx-common, so maybe
you need to depend on that instead.


cheers,

Andreas


python-escript-doc_5.0-3.log.gz
Description: application/gzip
-- 
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#859579: python-cvxopt-doc: fails to upgrade from 'sid' - trying to overwrite /usr/share/doc-base/cvxopt

[Andreas Beckmann]

Package: python-cvxopt-doc
Version: 1.1.8+dfsg-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'sid' to 'experimental'.
It installed fine in 'sid', then the upgrade to 'experimental' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package python-cvxopt-doc.
  Preparing to unpack .../10-python-cvxopt-doc_1.1.8+dfsg-1_all.deb ...
  Unpacking python-cvxopt-doc (1.1.8+dfsg-1) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-zhgQWq/10-python-cvxopt-doc_1.1.8+dfsg-1_all.deb 
(--unpack):
   trying to overwrite '/usr/share/doc-base/cvxopt', which is also in package 
python-cvxopt 1.1.4-1.5
  Errors were encountered while processing:
   /tmp/apt-dpkg-install-zhgQWq/10-python-cvxopt-doc_1.1.8+dfsg-1_all.deb


cheers,

Andreas


python-cvxopt=1.1.4-1.5_python-cvxopt-doc=1.1.8+dfsg-1.log.gz
Description: application/gzip
-- 
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#858958: morse-simulator-doc: broken symlink: /usr/share/doc/morse/html/_static/underscore.js -> ../../../../javascript/jquery/underscore.js

[Andreas Beckmann]

Package: morse-simulator-doc
Version: 1.4-2
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts
Control: affects -1 + morse-simulator

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m11.5s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/morse/html/_static/underscore.js -> 
../../../../javascript/jquery/underscore.js

^^

You probably wanted to target /usr/share/javascript/underscore/underscore.js
^^

cheers,

Andreas


morse-simulator-doc_1.4-2.log.gz
Description: application/gzip
-- 
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#715107: libptscotch-5.1: ships libs in /usr/lib/scotch_*/ instead of /usr/lib/scotch-*/

[Andreas Beckmann]

Followup-For: Bug #715107
Control: tag -1 patch pending

Hi,

I prepared a patch fixing several issues in scotch and will upload it to
DELAYED/5. Please let me know if I should delay it longer or reschedule.

Andreas
diff -Nru scotch-5.1.12b.dfsg/debian/changelog scotch-5.1.12b.dfsg/debian/changelog
--- scotch-5.1.12b.dfsg/debian/changelog	2012-07-17 10:51:39.0 +0200
+++ scotch-5.1.12b.dfsg/debian/changelog	2017-03-17 23:23:06.0 +0100
@@ -1,3 +1,16 @@
+scotch (5.1.12b.dfsg-2.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Drop DMUA.
+  * Remove Christophe Prud'homme from Uploaders.  (Closes: #835019)
+  * libptscotch-5.1: Fix library installation path.  (Closes: #715107)
+  * libscotchmetis-dev: Fix libmetis.* -> libscotchmetis.* links.
+  * libscotchparmetis-dev: Fix libparmetis.* -> libptscotchparmetis.* links.
+(Closes: #715112, #816109)
+  * Make package build reproducibly, thanks to Dhole.  (Closes: #787997)
+
+ -- Andreas Beckmann <a...@debian.org>  Fri, 17 Mar 2017 23:23:06 +0100
+
 scotch (5.1.12b.dfsg-2) unstable; urgency=low
 
   [ Christophe Trophime ]
diff -Nru scotch-5.1.12b.dfsg/debian/control scotch-5.1.12b.dfsg/debian/control
--- scotch-5.1.12b.dfsg/debian/control	2012-07-17 10:51:39.0 +0200
+++ scotch-5.1.12b.dfsg/debian/control	2017-03-17 23:23:00.0 +0100
@@ -2,10 +2,9 @@
 Section: math
 Priority: extra
 Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
-Uploaders: Christophe Prud'homme <prudh...@debian.org>,
+Uploaders:
  "Adam C. Powell, IV" <hazel...@debian.org>,
  Andreas Tille <ti...@debian.org>
-DM-Upload-Allowed: yes
 Build-Depends: quilt, debhelper (>= 7), bison, flex, zlib1g-dev, chrpath,
  mpi-default-dev, mpi-default-bin
 Standards-Version: 3.9.3
diff -Nru scotch-5.1.12b.dfsg/debian/libptscotch-5.1.install scotch-5.1.12b.dfsg/debian/libptscotch-5.1.install
--- scotch-5.1.12b.dfsg/debian/libptscotch-5.1.install	2012-07-17 10:51:39.0 +0200
+++ scotch-5.1.12b.dfsg/debian/libptscotch-5.1.install	2017-03-17 20:31:34.0 +0100
@@ -4,20 +4,20 @@
 int/lib/libptscotchparmetis-*.so /usr/lib
 int/lib/libptesmumps-*.so /usr/lib
 
-int32/lib/libptscotch-*.so /usr/lib/scotch_int32
-int32/lib/libptscotcherr-*.so /usr/lib/scotch_int32
-int32/lib/libptscotcherrexit-*.so /usr/lib/scotch_int32
-int32/lib/libptscotchparmetis-*.so /usr/lib/scotch_int32
-int32/lib/libptesmumps-*.so /usr/lib/scotch_int32
+int32/lib/libptscotch-*.so /usr/lib/scotch-int32
+int32/lib/libptscotcherr-*.so /usr/lib/scotch-int32
+int32/lib/libptscotcherrexit-*.so /usr/lib/scotch-int32
+int32/lib/libptscotchparmetis-*.so /usr/lib/scotch-int32
+int32/lib/libptesmumps-*.so /usr/lib/scotch-int32
 
-int64/lib/libptscotch-*.so /usr/lib/scotch_int64
-int64/lib/libptscotcherr-*.so /usr/lib/scotch_int64
-int64/lib/libptscotcherrexit-*.so /usr/lib/scotch_int64
-int64/lib/libptscotchparmetis-*.so /usr/lib/scotch_int64
-int64/lib/libptesmumps-*.so /usr/lib/scotch_int64
+int64/lib/libptscotch-*.so /usr/lib/scotch-int64
+int64/lib/libptscotcherr-*.so /usr/lib/scotch-int64
+int64/lib/libptscotcherrexit-*.so /usr/lib/scotch-int64
+int64/lib/libptscotchparmetis-*.so /usr/lib/scotch-int64
+int64/lib/libptesmumps-*.so /usr/lib/scotch-int64
 
-long/lib/libptscotch-*.so /usr/lib/scotch_long
-long/lib/libptscotcherr-*.so /usr/lib/scotch_long
-long/lib/libptscotcherrexit-*.so /usr/lib/scotch_long
-long/lib/libptscotchparmetis-*.so /usr/lib/scotch_long
-long/lib/libptesmumps-*.so /usr/lib/scotch_long
+long/lib/libptscotch-*.so /usr/lib/scotch-long
+long/lib/libptscotcherr-*.so /usr/lib/scotch-long
+long/lib/libptscotcherrexit-*.so /usr/lib/scotch-long
+long/lib/libptscotchparmetis-*.so /usr/lib/scotch-long
+long/lib/libptesmumps-*.so /usr/lib/scotch-long
diff -Nru scotch-5.1.12b.dfsg/debian/libscotchmetis-dev.install scotch-5.1.12b.dfsg/debian/libscotchmetis-dev.install
--- scotch-5.1.12b.dfsg/debian/libscotchmetis-dev.install	2012-07-17 10:51:39.0 +0200
+++ scotch-5.1.12b.dfsg/debian/libscotchmetis-dev.install	2017-03-17 21:27:37.0 +0100
@@ -3,16 +3,16 @@
 int/lib/libmetis.a /usr/lib
 
 int32/include/metis.h /usr/include/metis-int32
-int32/lib/libmetis.so /usr/lib/metis-int32
-int32/lib/libmetis.a /usr/lib/metis-int32
+#int32/lib/libmetis.so /usr/lib/metis-int32
+#int32/lib/libmetis.a /usr/lib/metis-int32
 
 int64/include/metis.h /usr/include/metis-int64
-int64/lib/libmetis.so /usr/lib/metis-int64
-int64/lib/libmetis.a /usr/lib/metis-int64
+#int64/lib/libmetis.so /usr/lib/metis-int64
+#int64/lib/libmetis.a /usr/lib/metis-int64
 
 long/include/metis.h /usr/include/metis-long
-long/lib/libmetis.so /usr/lib/metis-long
-long/lib/libmetis.a /usr/lib/metis-long
+#long/lib/libmetis.so /usr/lib/metis-long
+#long/lib/libmetis.a /usr/lib/metis-long
 
 doc/CeCILL-C_V1-en.txt /usr/share/doc/libscotchmetis-dev
 doc/CeCILL-C_V1-fr.txt /usr/share/doc/libscotchmetis-dev
diff -Nru scotch-5.

Bug#715107: Broken library symlink detected in libptscotch-dev

[Andreas Beckmann]

Followup-For: Bug #715107
Control: severity -1 serious
Control: reassign -1 libptscotch-5.1 5.1.12b.dfsg-2
Control: retitle -1 libptscotch-5.1: ships libs in /usr/lib/scotch_*/ instead 
of /usr/lib/scotch-*/

libscotch-5.1   ships /usr/lib/scotch-*/libscotch-5.1.so etc.
libscotch-dev   ships /usr/lib/scotch-*/libscotch.so -> libscotch-5.1.so etc.
libptscotch-dev ships /usr/lib/scotch-*/libptscotch.so -> libptscotch-5.1.so 
(BROKEN) etc.
libptscotch-5.1 ships /usr/lib/scotch_*/libptscotch-5.1.so etc.

That '_' instead of '-' looks inconsistent.


Andreas

-- 
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#857393: gazebo7-common: broken symlink: /usr/share/gazebo-7/media/fonts/arial.ttf -> ../../../fonts/truetype/ttf-liberation/LiberationSans-Regular.ttf

[Andreas Beckmann]

Package: gazebo7-common
Version: 7.5.0+dfsg-1
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m35.1s ERROR: FAIL: Broken symlinks:
  /usr/share/gazebo-7/media/fonts/arial.ttf -> 
../../../fonts/truetype/ttf-liberation/LiberationSans-Regular.ttf

gazebo7-common has no Depends/Recommends/Suggests on a package
containing LiberationSans-Regular.ttf

That file is is in package ttf-liberation, but this is a transitional
package that will disappear at some point. Therefore better use
fonts-liberation which ships the file at a different location:
/usr/share/fonts/truetype/ttf-liberation/LiberationSans-Regular.ttf

gazebo7-common Depends on ttf-dejavu-core which is also a transitional
package and should be replaced with fonts-dejavu-core.


cheers,

Andreas


gazebo7-common_7.5.0+dfsg-1.log.gz
Description: application/gzip
-- 
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#857155: scilab-doc: broken symlink: /usr/share/doc/scilab-doc/man -> ../../../lib/scilab/man

[Andreas Beckmann]

Package: scilab-doc
Version: 5.5.2-4
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

2m53.7s ERROR: FAIL: Broken symlinks:
  /usr/share/doc/scilab-doc/man -> ../../../lib/scilab/man

/usr/lib/scilab/man does not seem to exist in any package in unstable.


cheers,

Andreas


scilab_5.5.2-4.log.gz
Description: application/gzip
-- 
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#856949: libgiac-dev: missing Depends: libgiac0 (= ${binary:Version})

[Andreas Beckmann]

Package: libgiac-dev
Version: 1.2.3.25+dfsg1-2
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m26.1s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libgiac.so -> libgiac.so.0.0.0


cheers,

Andreas


libgiac-dev_1.2.3.25+dfsg1-2.log.gz
Description: application/gzip
-- 
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#856937: libslvs1-dev: missing Depends: libslvs1 (= ${binary:Version})

[Andreas Beckmann]

Package: libslvs1-dev
Version: 2.3+repack1-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m21.2s ERROR: FAIL: Broken symlinks:
  /usr/lib/x86_64-linux-gnu/libslvs.so -> libslvs.so.1


cheers,

Andreas


libslvs1-dev_2.3+repack1-1.log.gz
Description: application/gzip
-- 
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#856871: singular-doc: broken symlink: /usr/share/info/singular.info.gz -> singular.hlp.gz

[Andreas Beckmann]

Package: singular-doc
Version: 1:4.0.3-p3+ds-5
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m24.6s ERROR: FAIL: Broken symlinks:
  /usr/share/info/singular.info.gz -> singular.hlp.gz


A file called singular.hlp.gz does not seem to exist in any
package in the Debian archive.


cheers,

Andreas


singular-doc_1:4.0.3-p3+ds-5.log.gz
Description: application/gzip
-- 
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#856866: sagemath-common: broken symlink: /usr/lib/python2.7/dist-packages/sage/misc/docs/common/themes/sage/static/thebe.js -> ../../../../../../local/share/thebe/thebe.js

[Andreas Beckmann]

Package: sagemath-common
Version: 7.4-9
Severity: normal
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package ships (or creates)
a broken symlink.

>From the attached log (scroll to the bottom...):

0m35.3s ERROR: FAIL: Broken symlinks:
  
/usr/lib/python2.7/dist-packages/sage/misc/docs/common/themes/sageref/static/thebe.js
 -> ../../sage/static/thebe.js
  
/usr/lib/python2.7/dist-packages/sage/misc/docs/common/themes/sage/static/thebe.js
 -> ../../../../../../local/share/thebe/thebe.js

A file called thebe.js does not appear to be in any package in the Debian 
archive ...


cheers,

Andreas


sagemath-common_7.4-9.log.gz
Description: application/gzip
-- 
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#855577: numba: FTBFS: several tests fail

[Andreas Beckmann]

Package: numba
Version: 0.30.0-3
Severity: serious
Justification: fails to build from source

Looks like the maintainer upload for amd64 was built without running the
tests, since several tests fail on all platforms on the buildds
(and also if I rebuild it for amd64):

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


Andreas

-- 
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#816699: libga-dev and libarmci-mpi-dev: error when trying to install together

[Andreas Beckmann]

Followup-For: Bug #816699

Neither src:armci-mpi nor src:ga have rdepends or reverse build-depends in
stretch, so removing them both from stetch would be OK if this file
conflict is not solved.


Andreas

-- 
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#852514: libpetsc3.7-dev: leaves alternatives after purge: /usr/lib/petscdir/{3.7, 3.7-real}

[Andreas Beckmann]

Package: libpetsc3.7-dev
Version: 3.7.5+dfsg1-3
Severity: important
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package left unowned files on
the system after purge, which is a violation of policy 6.8:

https://www.debian.org/doc/debian-policy/ch-maintainerscripts.html#s-removedetails

The leftover files are actually alternatives that were installed by the
package but have not been properly removed.

This was observed after a stretch->sid upgrade, the packages in stretch
and sid itself work fine. Therefore I assume you obsoleted some
alternative in the sid package. To clean this up, you should unregister
the obsolete alternative in the postinst script.

>From the attached log (scroll to the bottom...):

2m18.4s INFO: Warning: Package purging left files on system:
  /etc/alternatives/petsc3.7 -> /usr/lib/petscdir/3.7.4/x86_64-linux-gnu-real   
 not owned
  /etc/alternatives/petsc3.7-real -> 
/usr/lib/petscdir/3.7.4/x86_64-linux-gnu-real   not owned
  /usr/lib/petscdir/ owned by: libpetsc3.7.5-dev:amd64, 
libpetsc3.7.4-dev:amd64
  /usr/lib/petscdir/3.7 -> /etc/alternatives/petsc3.7not owned
  /usr/lib/petscdir/3.7-real -> /etc/alternatives/petsc3.7-real  not owned


cheers,

Andreas


libpetsc3.7-dev_3.7.5+dfsg1-3.log.gz
Description: application/gzip
-- 
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#852470: Bug#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

Please continue discussion in this *NEW* bug.

On 2017-01-24 23:25, Maarten van Gompel wrote:
> Hi Andreas, Mattia,
> 
> Quoting Andreas Beckmann (2017-01-24 19:04:24)
>>>
>>> Oops... Well spotted, I just fixed it in git, but it is probably overkill 
>>> to prepare/upload a new release just
>>> for that now I guess?
>>
>> Correct. But let me see what else I found:
>>
>> jessie-> sid upgrades:
>>
>> ucto.maintscript is missing, doing rm_conffile on the conffiles shipped
>> in jessie (use 0.9.6-2~ as prior version, if this gets fixed in -2).
>> If there was a post-jessie version shipping more conffiles in /etc,
>> clean them up as well.
>>
>>   ucto: obsolete-conffile /etc/ucto/exotic-eos.eos
>>   ucto: obsolete-conffile /etc/ucto/nl_afk.abr
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-nl
>>   ucto: obsolete-conffile /etc/ucto/smiley.rule
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-it
>>   ucto: obsolete-conffile /etc/ucto/standard-eos.eos
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-sv
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-fr
>>   ucto: obsolete-conffile /etc/ucto/exotic-quotes.quote
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-nl-twitter
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-es
>>   ucto: obsolete-conffile /etc/ucto/url.rule
>>   ucto: obsolete-conffile /etc/ucto/e-mail.rule
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-nl-sonarchat
>>   ucto: obsolete-conffile /etc/ucto/es.abr
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-fy
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-de
>>   ucto: obsolete-conffile /etc/ucto/tokconfig-en
>>   ucto: obsolete-conffile /etc/ucto/ligatures.filter
>>   ucto: obsolete-conffile /etc/ucto/standard-quotes.quote
> 
> I think I get it. Because these moved to uctodata, which did not exist yet for
> jessie (before the split), the config files are owned by ucto and uctodata 
> can't clean
> it. Hadn't thought of that yet. I added an ucto.maintscript now for 0.9.6-2 
> (in
> git).

Theoretically making uctodata cleaning them up, too, is possible, but
the tasks in uctodata are already "interesting" enough. And ucto is not
going to be removed on the jessie->stretch upgrade.

>> frog looks fine
>>
>> stretch -> sid upgrades:
>>
>>   libucto2:amd64: obsolete-conffile /etc/ucto/textcat.cfg
> 
> added
> 
>>
>>   uctodata: obsolete-conffile /etc/ucto/spa.abr
>>   uctodata: obsolete-conffile /etc/ucto/por.abr
>>   uctodata: obsolete-conffile /etc/ucto/nld_afk.abr
>>
> 
> added
> 
>> frog looks fine, too
>>
>>
>> That's not RC, the upgrades went smooth, but it would still be great to
>> get this cleaned up properly.
> 
> I'm glad it went smooth in spite of this. Hopefully the next releases will
> clean it up for good.
> 
>>
>> But lets take a detailed look what happened here:
>>
>>   Unpacking uctodata (0.4-1) over (0.3.1-1) ...
>>   dpkg: warning: unable to delete old directory '/etc/ucto': Directory
>> not empty
>>   Setting up uctodata (0.4-1) ...
>>   Obsolete conffile /etc/ucto/es.abr has been modified by you.
>>   Saving as /etc/ucto/es.abr.dpkg-bak ...
>>   Removing obsolete conffile /etc/ucto/exotic-eos.eos ...
>>   Removing obsolete conffile /etc/ucto/exotic-quotes.quote ...
>>   Removing obsolete conffile /etc/ucto/ligatures.filter ...
>>   Obsolete conffile /etc/ucto/nl_afk.abr has been modified by you.
>>   Saving as /etc/ucto/nl_afk.abr.dpkg-bak ...
>>   Obsolete conffile /etc/ucto/pt.abr has been modified by you.
>>   Saving as /etc/ucto/pt.abr.dpkg-bak ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-deu ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-eng ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-spa ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-fra ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-fry ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-ita ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-nld ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-nld-sonarchat ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-nld-twitter ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-nld-withplaceholder ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-por ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-rus ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-swe ...
>>   Removing obsolete conffile /etc/ucto/tokconfig-tur ...
>>   Processing triggers for libc-bin (2.24-9) ...
&g

Bug#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-24 23:25, Maarten van Gompel wrote:

I'll reply to 852...@bugs.debian.org


Andreas

-- 
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#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-24 19:30, Mattia Rizzolo wrote:
> Wow, upgrades issues are so full of cases.
> Anyhow, I still don't think we should fix these, if nothing to try to
> have the newer upstream versions and their fairly big diffs into
> stretch.
> 
> I suggest you (Andreas) file a new bug(s) copy-pasting what you wrote
> here, and we (=> Maarten) will possibly deal with it after the current
> testing migrations happen.

#852470

Fixing in git and testing should happen before migration s.t. the
current stretch version is still available for my tests.
(I'll throw the new packages in my piuparts engine.)

See you over there :-)


>> I think you found a bug in dpkg here :-)
> 
> ISTR reading something somewhere that not handling symlinks as conffile
> is a known decision, because it's particuarly hard to do.

#852468

I was more thinking about rm_conffile messing around with something that
is not a conffile.


Andreas

-- 
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#852470: uctodata,libucto2: leftover conffiles after upgrades

[Andreas Beckmann]

Package: uctodata,libucto2
Severity: important
Control: found -1 0.4-1
Control: found -1 0.9.6-1

jessie-> sid upgrades:

ucto.maintscript is missing, doing rm_conffile on the conffiles shipped
in jessie (use 0.9.6-2~ as prior version, if this gets fixed in -2).
If there was a post-jessie version shipping more conffiles in /etc,
clean them up as well.

  ucto: obsolete-conffile /etc/ucto/exotic-eos.eos
  ucto: obsolete-conffile /etc/ucto/nl_afk.abr
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl
  ucto: obsolete-conffile /etc/ucto/smiley.rule
  ucto: obsolete-conffile /etc/ucto/tokconfig-it
  ucto: obsolete-conffile /etc/ucto/standard-eos.eos
  ucto: obsolete-conffile /etc/ucto/tokconfig-sv
  ucto: obsolete-conffile /etc/ucto/tokconfig-fr
  ucto: obsolete-conffile /etc/ucto/exotic-quotes.quote
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl-twitter
  ucto: obsolete-conffile /etc/ucto/tokconfig-es
  ucto: obsolete-conffile /etc/ucto/url.rule
  ucto: obsolete-conffile /etc/ucto/e-mail.rule
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl-sonarchat
  ucto: obsolete-conffile /etc/ucto/es.abr
  ucto: obsolete-conffile /etc/ucto/tokconfig-fy
  ucto: obsolete-conffile /etc/ucto/tokconfig-de
  ucto: obsolete-conffile /etc/ucto/tokconfig-en
  ucto: obsolete-conffile /etc/ucto/ligatures.filter
  ucto: obsolete-conffile /etc/ucto/standard-quotes.quote

frog looks fine

stretch -> sid upgrades:

  libucto2:amd64: obsolete-conffile /etc/ucto/textcat.cfg

  uctodata: obsolete-conffile /etc/ucto/spa.abr
  uctodata: obsolete-conffile /etc/ucto/por.abr
  uctodata: obsolete-conffile /etc/ucto/nld_afk.abr

frog looks fine, too


That's not RC, the upgrades went smooth, but it would still be great to
get this cleaned up properly.

But lets take a detailed look what happened here:

  Unpacking uctodata (0.4-1) over (0.3.1-1) ...
  dpkg: warning: unable to delete old directory '/etc/ucto': Directory
not empty
  Setting up uctodata (0.4-1) ...
  Obsolete conffile /etc/ucto/es.abr has been modified by you.
  Saving as /etc/ucto/es.abr.dpkg-bak ...
  Removing obsolete conffile /etc/ucto/exotic-eos.eos ...
  Removing obsolete conffile /etc/ucto/exotic-quotes.quote ...
  Removing obsolete conffile /etc/ucto/ligatures.filter ...
  Obsolete conffile /etc/ucto/nl_afk.abr has been modified by you.
  Saving as /etc/ucto/nl_afk.abr.dpkg-bak ...
  Obsolete conffile /etc/ucto/pt.abr has been modified by you.
  Saving as /etc/ucto/pt.abr.dpkg-bak ...
  Removing obsolete conffile /etc/ucto/tokconfig-deu ...
  Removing obsolete conffile /etc/ucto/tokconfig-eng ...
  Removing obsolete conffile /etc/ucto/tokconfig-spa ...
  Removing obsolete conffile /etc/ucto/tokconfig-fra ...
  Removing obsolete conffile /etc/ucto/tokconfig-fry ...
  Removing obsolete conffile /etc/ucto/tokconfig-ita ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-sonarchat ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-twitter ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-withplaceholder ...
  Removing obsolete conffile /etc/ucto/tokconfig-por ...
  Removing obsolete conffile /etc/ucto/tokconfig-rus ...
  Removing obsolete conffile /etc/ucto/tokconfig-swe ...
  Removing obsolete conffile /etc/ucto/tokconfig-tur ...
  Processing triggers for libc-bin (2.24-9) ...

You probably shouldn't call rm_conffile on the symlinks owned by
uctodata - these are no conffiles, but you seem to confuse dpkg by doing
this. Removing the conffiles from jessie is better left to
ucto.maintscript.

I think you found a bug in dpkg here :-)
==> #852468


  Preparing to unpack .../libucto2_0.9.6-1_amd64.deb ...
  Unpacking libucto2:amd64 (0.9.6-1) over (0.9.5-1) ...
  dpkg: warning: unable to delete old directory '/etc/ucto': Directory
not empty
  Setting up libgomp1:amd64 (6.3.0-4) ...
  Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ...
  Processing triggers for libc-bin (2.24-9) ...
  Setting up libucto2:amd64 (0.9.6-1) ...
  Removing obsolete conffile /etc/ucto/e-mail.rule ...
  Removing obsolete conffile /etc/ucto/smiley.rule ...
  Removing obsolete conffile /etc/ucto/url.rule ...
  Removing obsolete conffile /etc/ucto/standard-eos.eos ...
  Removing obsolete conffile /etc/ucto/standard-quotes.quote ...
  Removing obsolete conffile /etc/ucto/tokconfig-generic ...
  Processing triggers for libc-bin (2.24-9) ...


libucto2.maintscript is missing this line:

rm_conffile /etc/ucto/tokconfig-generic 0.9.6-2~


Let's prepare these fixed in git s.t. I can test the upgrade paths
(especially testing the stretch->sid path must happen before the sid
version migrates), but let's postpone the upload until after the current
packages migrated to testing.


Andreas

-- 
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#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-24 09:32, Maarten van Gompel wrote:
> Quoting Andreas Beckmann (2017-01-24 02:54:36)
>> On 2017-01-24 02:51, Andreas Beckmann wrote:
>>> spotted a typo (trailing "a") in frogdata.maintscript
>>>
>>> echo "rm_conffile /etc/frog/${subdir}Frog.mbt.1.0.known.dddwfWaw.wgt 
>>> 0.13.7~"a
>>
>> but that's harmless, its still a valid version to achieve your goal
> 
> Oops... Well spotted, I just fixed it in git, but it is probably overkill to 
> prepare/upload a new release just
> for that now I guess?

Correct. But let me see what else I found:

jessie-> sid upgrades:

ucto.maintscript is missing, doing rm_conffile on the conffiles shipped
in jessie (use 0.9.6-2~ as prior version, if this gets fixed in -2).
If there was a post-jessie version shipping more conffiles in /etc,
clean them up as well.

  ucto: obsolete-conffile /etc/ucto/exotic-eos.eos
  ucto: obsolete-conffile /etc/ucto/nl_afk.abr
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl
  ucto: obsolete-conffile /etc/ucto/smiley.rule
  ucto: obsolete-conffile /etc/ucto/tokconfig-it
  ucto: obsolete-conffile /etc/ucto/standard-eos.eos
  ucto: obsolete-conffile /etc/ucto/tokconfig-sv
  ucto: obsolete-conffile /etc/ucto/tokconfig-fr
  ucto: obsolete-conffile /etc/ucto/exotic-quotes.quote
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl-twitter
  ucto: obsolete-conffile /etc/ucto/tokconfig-es
  ucto: obsolete-conffile /etc/ucto/url.rule
  ucto: obsolete-conffile /etc/ucto/e-mail.rule
  ucto: obsolete-conffile /etc/ucto/tokconfig-nl-sonarchat
  ucto: obsolete-conffile /etc/ucto/es.abr
  ucto: obsolete-conffile /etc/ucto/tokconfig-fy
  ucto: obsolete-conffile /etc/ucto/tokconfig-de
  ucto: obsolete-conffile /etc/ucto/tokconfig-en
  ucto: obsolete-conffile /etc/ucto/ligatures.filter
  ucto: obsolete-conffile /etc/ucto/standard-quotes.quote

frog looks fine

stretch -> sid upgrades:

  libucto2:amd64: obsolete-conffile /etc/ucto/textcat.cfg

  uctodata: obsolete-conffile /etc/ucto/spa.abr
  uctodata: obsolete-conffile /etc/ucto/por.abr
  uctodata: obsolete-conffile /etc/ucto/nld_afk.abr

frog looks fine, too


That's not RC, the upgrades went smooth, but it would still be great to
get this cleaned up properly.

But lets take a detailed look what happened here:

  Unpacking uctodata (0.4-1) over (0.3.1-1) ...
  dpkg: warning: unable to delete old directory '/etc/ucto': Directory
not empty
  Setting up uctodata (0.4-1) ...
  Obsolete conffile /etc/ucto/es.abr has been modified by you.
  Saving as /etc/ucto/es.abr.dpkg-bak ...
  Removing obsolete conffile /etc/ucto/exotic-eos.eos ...
  Removing obsolete conffile /etc/ucto/exotic-quotes.quote ...
  Removing obsolete conffile /etc/ucto/ligatures.filter ...
  Obsolete conffile /etc/ucto/nl_afk.abr has been modified by you.
  Saving as /etc/ucto/nl_afk.abr.dpkg-bak ...
  Obsolete conffile /etc/ucto/pt.abr has been modified by you.
  Saving as /etc/ucto/pt.abr.dpkg-bak ...
  Removing obsolete conffile /etc/ucto/tokconfig-deu ...
  Removing obsolete conffile /etc/ucto/tokconfig-eng ...
  Removing obsolete conffile /etc/ucto/tokconfig-spa ...
  Removing obsolete conffile /etc/ucto/tokconfig-fra ...
  Removing obsolete conffile /etc/ucto/tokconfig-fry ...
  Removing obsolete conffile /etc/ucto/tokconfig-ita ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-sonarchat ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-twitter ...
  Removing obsolete conffile /etc/ucto/tokconfig-nld-withplaceholder ...
  Removing obsolete conffile /etc/ucto/tokconfig-por ...
  Removing obsolete conffile /etc/ucto/tokconfig-rus ...
  Removing obsolete conffile /etc/ucto/tokconfig-swe ...
  Removing obsolete conffile /etc/ucto/tokconfig-tur ...
  Processing triggers for libc-bin (2.24-9) ...

You probably shouldn't call rm_conffile on the symlinks owned by
uctodata - these are no conffiles, but you seem to confuse dpkg by doing
this. Removing the conffiles from jessie is better left to
ucto.maintscript.

I think you found a bug in dpkg here :-)


  Preparing to unpack .../libucto2_0.9.6-1_amd64.deb ...
  Unpacking libucto2:amd64 (0.9.6-1) over (0.9.5-1) ...
  dpkg: warning: unable to delete old directory '/etc/ucto': Directory
not empty
  Setting up libgomp1:amd64 (6.3.0-4) ...
  Setting up libxml2:amd64 (2.9.4+dfsg1-2.2) ...
  Processing triggers for libc-bin (2.24-9) ...
  Setting up libucto2:amd64 (0.9.6-1) ...
  Removing obsolete conffile /etc/ucto/e-mail.rule ...
  Removing obsolete conffile /etc/ucto/smiley.rule ...
  Removing obsolete conffile /etc/ucto/url.rule ...
  Removing obsolete conffile /etc/ucto/standard-eos.eos ...
  Removing obsolete conffile /etc/ucto/standard-quotes.quote ...
  Removing obsolete conffile /etc/ucto/tokconfig-generic ...
  Processing triggers for libc-bin (2.24-9) ...


libucto2.maintscript is missing this line:

rm_conffile /etc/ucto/t

Bug#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

Hi,

just browsed the git commits in the web interface

spotted a typo (trailing "a") in frogdata.maintscript

echo "rm_conffile /etc/frog/${subdir}Frog.mbt.1.0.known.dddwfWaw.wgt 0.13.7~"a

BTW, you could also add the slash here:

for subdir in "" "nld/" "nl/"

besides that, everything looks ok on a quick glance

will report after I got piuparts results tomorrow ...


Andreas

-- 
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#838112: uctodata: fails to upgrade from jessie - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-23 19:17, Maarten van Gompel wrote:
> Hi Andreas, Mattia, et. al.
> 
>> uploads should happen early enough to allow automatic migration after 10
>> days on Feb 05 (so probably at most 2 days left)
> 
> Right. We have prepared new upstream releases for uctodata, ucto, frogdata and
> frog today that rely on the data being in share/ instead of etc/, and should
> therefore resolve this persistent bug. I updated all the debian packages
> accordingly. The fact I did frog and frogdata as well is because the same 
> issue
> might likely arise there and it depends on ucto anyhow. Putting the stuff in
> etc/ was unnecessary overengineering on our part.

piuparts probably didn't test frog* if their dependencies failed,
otherwise it would have found the same error there

> 
> I followed the documentation and created postint/preinst/postrm scripts for
> libucto2 (ucto), uctodata and frogdata that takes care of removing the old
> files, as you suggested. I tested it on migration from the previous releases
> and it works. Still, a second look from someone with more knowledge about 
> these
> things is highly appreciated.  I haven't been able to test the upgrade from 
> the
> jessie versions yet but I'll try to look into piuparts to do that. I think
> everything should be solved with the releases I prepared today (but again;
> double checks appreciated!)

I'll take a look

> @Mattia: Do you happen to be available on such short notice to sponsor/upload
> these four packages again?  Considering also the very tight deadline before 
> the
> freeze. Sorry for the inconvenience!

If needed, I can sponsor that as well

> For completion's sake, the packages are:
> 
> * https://anonscm.debian.org/cgit/debian-science/packages/uctodata.git
> * https://anonscm.debian.org/cgit/debian-science/packages/ucto.git
> * https://anonscm.debian.org/cgit/debian-science/packages/frogdata.git
> * https://anonscm.debian.org/cgit/debian-science/packages/frog.git
>  
> Regards,
> 
> PS: the postinst/preinst/postrm scripts are currently three copies of the same
> thing. I realize this is probably ugly (unnecessary duplication) and not the
> best way, but I didn't know what would be the best solution and since I was in
> a rush I left it like this.

use debian/$package.maintscript instead of doing it directly in maintscripts

put in there lines like

rm_conffile /etc/ucto/tokconfig-es 0.4-1~

no dpkg-maintscript-helper prefix, no default arguments, no trailing
comments!
use $VERSION_TO_BE_UPLOADED + "~" as prior-version argument

this will generate appropriate pre/post/inst/rm scripts with the same
content


Andreas (in a hurry)

-- 
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#838112: uctodata: fails to upgrade from 'jessie' - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-23 12:06, Maarten van Gompel wrote:
> Hi Andreas et al,
> 
> Short follow up: we discussed it internally and think it's indeed best to just
> move the 'configuration' files to /usr/share, as you pointed out; simplifying 
> the package and
> resolving the conflicts. 

so you'll need to add a log of rm_conffile to
{ucto,uctodata,libucto2}.maintscript

and you probably don't have add libucto-common either, if the library
packages no longer have conffiles

> We're currently working on new upstream releases for
> ucto, uctodata, frogdata, and frog  (the latter two have the same division and
> make the same mistake, and depends on ucto/uctodata too) that implement this. 
> I
> hope releasing four new packages so close to the freeze is not going to be a
> problem. At least it should fix this bug for good.

uploads should happen early enough to allow automatic migration after 10
days on Feb 05 (so probably at most 2 days left)


Andreas

-- 
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#838112: uctodata: fails to upgrade from 'jessie' - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

On 2017-01-22 09:48, Adrian Bunk wrote:
> es.abr was a conffile in the jessie ucto, that needs additional treatment.
> 
> The solution might be using mv_conffile from dpkg-maintscript-helper(1) 
> in a .maintscript to move the conffile to the new name spa.abr and the 
> new package (es.abr is now a symlink), but Andreas should comment on 
> that since he knows this better.

TL;DR: You have an ambitious task before you.

Let me see if I understand what's going on.

Renaming conffiles and changing the owning package at the same time is a
PITA.
You add an extra point by making the old name a symlink to the new one,
owned by the new package

In jessie, everything in /etc/ucto was owned by ucto.
In sid, a lot more stuff is in /etc/ucto, and either owned by uctodata
or libucto2, a m-a:same library package. These come from 2 different
source packages.

Yuck. While putting conffiles in m-a:same packages is allowed, I highly
discourage this. Even if I haven't seen this fail once, yet. I'm just
afraid, someone has to clean up a mess caused by this at some point in
the future. and I'm afraid, I won't keep my fingers out of then :-(

Before we start: Are these really conffiles? Supposed to be modified by
the local admin? Or are these rather data files that are not supposed to
be updated locally? And would better live in /usr/share in that case?

And nearly everything from jessie's /etc/ucto content is now renamed and
a symlink.

Can't you just fork the project? I'd suggest 'hpgb' and then use
/etc/hpgb for the conffiles. Oh, I forgot: we are in freeze, so no new
source packages ...

Oh yeah, it well be a mess. But we will do it right. Including making
dpkg forget about the old conffiles.

Right now, all upgrade attempts from jessie to stretch should always
have failed, so there is no further messed up state inbetween that
should be supported for clean upgrades.

can we move the conffiles from libucto2 to a new package, e.g.
ucto-common (which would be either m-a:foreign or m-a:allowed, but I
always mess up these two, I need to look up what's right?

* Which version introduced the new layout?
* can you give me a list of
  + removed conffiles
  + renamed conffiles (old name, new name, new owning package, whether
they have a compat symlink, did the content change between jessie and sid)

Do you *really* need the compat symlinks?

OK, packaging is in git. Need to check whether I have write permissions
there ...

rough plan:

ucto uses d-m-h move-conffile (but provides no new version, so the old
conffile should "disappear" and dpkg should forget about it.
Maybe it's better to rm_conffile it instead.

uctodata will probably need a Conflicts against ucto (<< current+fixed~)


Andreas

-- 
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#838112: uctodata: fails to upgrade from 'jessie' - trying to overwrite /etc/ucto/es.abr

[Andreas Beckmann]

Followup-For: Bug #838112
Control: found -1 0.3.1-1
Control: affects -1 + ucto

Hi,

that bug has just reappered:

  Preparing to unpack .../ucto_0.9.5-1_amd64.deb ...
  Unpacking ucto (0.9.5-1) over (0.5.3-3.1+b1) ...
  dpkg: warning: unable to delete old directory '/etc/ucto': Directory not empty
  Selecting previously unselected package uctodata.
  Preparing to unpack .../uctodata_0.3.1-1_all.deb ...
  Unpacking uctodata (0.3.1-1) ...
  dpkg: error processing archive 
/var/cache/apt/archives/uctodata_0.3.1-1_all.deb (--unpack):
   trying to overwrite '/etc/ucto/es.abr', which is also in package ucto 0.9.5-1


Andreas


ucto_0.9.5-1.log.gz
Description: application/gzip
-- 
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#851578: python-numba: fails to install: SyntaxError: invalid syntax

[Andreas Beckmann]

Package: python-numba
Version: 0.30.0-2
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package failed to install. As
per definition of the release team this makes the package too buggy for
a release, thus the severity.

>From the attached log (scroll to the bottom...):

  Selecting previously unselected package python-numba.
  (Reading database ... 
(Reading database ... 5949 files and directories currently installed.)
  Preparing to unpack .../python-numba_0.30.0-2_amd64.deb ...
  Unpacking python-numba (0.30.0-2) ...
  Setting up python-numba (0.30.0-2) ...
File "/usr/lib/python2.7/dist-packages/numba/tests/annotation_usecases.py", 
line 12
  def __init__(self, v: int):
  ^
  SyntaxError: invalid syntax
  
  dpkg: error processing package python-numba (--configure):
   subprocess installed post-installation script returned error exit status 101
  Errors were encountered while processing:
   python-numba


cheers,

Andreas


python-numba_0.30.0-2.log.gz
Description: application/gzip
-- 
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#851142: caffe-contrib: FTBFS in sid: libboost_python.so: undefined reference to several Py* symbols

[Andreas Beckmann]

Source: caffe-contrib
Version: 1.0.0~rc3+20161127-g24d2f67-4
Severity: serious
Justification: fails to build from source

Hi,

caffe-contrib suddenly started to FTBFS in sid:

[...]
[100%] Linking CXX executable ../../../test/test.testbin
cd 
"/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67/caffe_cuda_build/src/caffe/test"
 && /usr/bin/cmake -E cmake_link_script CMakeFiles/test.testbin.dir/link.txt 
--verbose=1
/usr/bin/clang++-3.8   -g -O2 
-fdebug-prefix-map=/build/caffe-contrib-1.0.0~rc3+20161127-g24d2f67=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wall  -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -Wall -Wno-
sign-compare -Wno-uninitialized -O3 -DNDEBUG  -Wl,-z,relro -Wl,-z,now 
-Wl,--as-needed CMakeFiles/test.testbin.dir/test_accuracy_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_argmax_layer.cpp.o CMakeFiles/test.testbi
n.dir/test_batch_norm_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_batch_reindex_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_benchmark.cpp.o 
CMakeFiles/test.testbin.dir/test_bias_layer.cpp.o CMakeFiles/test.testbi
n.dir/test_blob.cpp.o CMakeFiles/test.testbin.dir/test_caffe_main.cpp.o 
CMakeFiles/test.testbin.dir/test_common.cpp.o 
CMakeFiles/test.testbin.dir/test_concat_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_contrastive
_loss_layer.cpp.o CMakeFiles/test.testbin.dir/test_convolution_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_crop_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_data_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_data_t
ransformer.cpp.o CMakeFiles/test.testbin.dir/test_db.cpp.o 
CMakeFiles/test.testbin.dir/test_deconvolution_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_dummy_data_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_eltwise
_layer.cpp.o CMakeFiles/test.testbin.dir/test_embed_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_euclidean_loss_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_filler.cpp.o 
CMakeFiles/test.testbin.dir/test_filter_laye
r.cpp.o CMakeFiles/test.testbin.dir/test_flatten_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_gradient_based_solver.cpp.o 
CMakeFiles/test.testbin.dir/test_hdf5_output_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_hd
f5data_layer.cpp.o CMakeFiles/test.testbin.dir/test_hinge_loss_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_im2col_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_image_data_layer.cpp.o 
CMakeFiles/test.testbin.dir/tes
t_infogain_loss_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_inner_product_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_internal_thread.cpp.o 
CMakeFiles/test.testbin.dir/test_io.cpp.o CMakeFiles/test.testbin.dir/te
st_layer_factory.cpp.o CMakeFiles/test.testbin.dir/test_lrn_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_lstm_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_math_functions.cpp.o 
CMakeFiles/test.testbin.dir/test_maxpo
ol_dropout_layers.cpp.o 
CMakeFiles/test.testbin.dir/test_memory_data_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_multinomial_logistic_loss_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_mvn_layer.cpp.o CMakeFiles/te
st.testbin.dir/test_net.cpp.o 
CMakeFiles/test.testbin.dir/test_neuron_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_platform.cpp.o 
CMakeFiles/test.testbin.dir/test_pooling_layer.cpp.o 
CMakeFiles/test.testbin.dir/tes
t_power_layer.cpp.o CMakeFiles/test.testbin.dir/test_protobuf.cpp.o 
CMakeFiles/test.testbin.dir/test_random_number_generator.cpp.o 
CMakeFiles/test.testbin.dir/test_reduction_layer.cpp.o 
CMakeFiles/test.testbin.dir/
test_reshape_layer.cpp.o CMakeFiles/test.testbin.dir/test_rnn_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_scale_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_sigmoid_cross_entropy_loss_layer.cpp.o 
CMakeFiles/test.t
estbin.dir/test_slice_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_softmax_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_softmax_with_loss_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_solver.cpp.o CMakeFiles/test.te
stbin.dir/test_solver_factory.cpp.o 
CMakeFiles/test.testbin.dir/test_split_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_spp_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_stochastic_pooling.cpp.o CMakeFiles/test.test
bin.dir/test_syncedmem.cpp.o CMakeFiles/test.testbin.dir/test_tanh_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_threshold_layer.cpp.o 
CMakeFiles/test.testbin.dir/test_tile_layer.cpp.o CMakeFiles/test.testbin.dir/te
st_upgrade_proto.cpp.o CMakeFiles/test.testbin.dir/test_util_blas.cpp.o 
CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_test_im2col_kernel.cu.o  
-o ../../../test/test.testbin -rdynamic ../../../lib/libgtest.
a ../../../lib/libcaffe.so.1.0.0-rc3 ../../../lib/libproto.a -lboost_system 
-lboost_thread -lboost_filesystem -lboost_chrono -lboost_date_time 
-lboost_atomic -lpthread -lpthread -lglog -lgflags -lprotobuf -lhdf5_cp
p /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lpthread -lglog 
-lgflags -lprotobuf -lhdf5_cpp /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so 
-lsz -lz -ldl -lm -lhdf5_hl_cpp /usr/lib/x86_64-linux-gn

Bug#848137: Fwd: Re: Bug#848137: problem with the upgrade of tango-db

[Andreas Beckmann]

 Forwarded Message 
Subject: Re: Bug#848137: problem with the upgrade of tango-db
Date: Mon, 9 Jan 2017 10:00:59 +0100
From: Andreas Beckmann <a...@debian.org>
To: Paul Gevers <elb...@debian.org>

On 2017-01-08 22:29, Paul Gevers wrote:
> It would still be nice to confirm that this issue exists (in
> experimental) since 30 Mar 2015 (or dbconfig-common release 1.8.50).

Hi Paul,

here are my piuparts test results for tango-db in experimental and sid
I haven't looked at the old logs (and I would have only the most recent
log for any given version anyway, unless they got pruned as well).

Note that failures for database-needing packages may be false positives:
* in case another database-needing test is running in parallel, but in
that case the tests get retried quickly
* piuparts may need some manual tuning and hinting w.r.t. database
related tests for new db versions etc.

What's most interesting for you is probably a pass->fail transition
without a tango-db version change.

#unix-timestamp result package version
1365584782 fail tango-db 8.0.5+dfsg-1
1365972246 fail tango-db 8.0.5+dfsg-1
1366404361 fail tango-db 8.0.5+dfsg-1
1366837036 fail tango-db 8.0.5+dfsg-1
1367268394 fail tango-db 8.0.5+dfsg-1
1367700038 fail tango-db 8.0.5+dfsg-1
1458192160 pass tango-db 9.2.1+dfsg-1~exp1
1458326959 fail tango-db 9.2.2+dfsg-1~exp1
1458335108 fail tango-db 9.2.2+dfsg-1~exp1
1458343434 pass tango-db 9.2.2+dfsg-1~exp1
1461966656 fail tango-db 9.2.2+dfsg-1~exp1
1461971652 pass tango-db 9.2.2+dfsg-1~exp1
1462467635 pass tango-db 9.2.2+dfsg-1~exp3
1464182034 pass tango-db 9.2.2+dfsg-1~exp4
1466511633 pass tango-db 9.2.2+dfsg-1~exp4
1469243630 pass tango-db 9.2.2+dfsg-1~exp4
1471711054 fail tango-db 9.2.2+dfsg-1~exp4
1471712607 fail tango-db 9.2.2+dfsg-1~exp4
1471722930 fail tango-db 9.2.2+dfsg-1~exp4
1471731762 fail tango-db 9.2.2+dfsg-1~exp4
1471734746 fail tango-db 9.2.2+dfsg-1~exp4
1471744830 fail tango-db 9.2.2+dfsg-1~exp4
1471752732 fail tango-db 9.2.2+dfsg-1~exp4
1471756011 fail tango-db 9.2.2+dfsg-1~exp4
1471766128 fail tango-db 9.2.2+dfsg-1~exp4
1471778445 fail tango-db 9.2.2+dfsg-1~exp4
1471787659 fail tango-db 9.2.2+dfsg-1~exp4
1471796270 fail tango-db 9.2.2+dfsg-1~exp4
1471798510 fail tango-db 9.2.2+dfsg-1~exp4
1471809200 fail tango-db 9.2.2+dfsg-1~exp4
1471818401 fail tango-db 9.2.2+dfsg-1~exp4
1471820132 fail tango-db 9.2.2+dfsg-1~exp4
1471830853 fail tango-db 9.2.2+dfsg-1~exp4
1471848371 fail tango-db 9.2.2+dfsg-1~exp4
1471852816 fail tango-db 9.2.2+dfsg-1~exp4
1471860490 fail tango-db 9.2.2+dfsg-1~exp4
1471864122 fail tango-db 9.2.2+dfsg-1~exp4
1471875376 fail tango-db 9.2.2+dfsg-1~exp4
1471885775 fail tango-db 9.2.2+dfsg-1~exp4
1471895838 fail tango-db 9.2.2+dfsg-1~exp4
1471904684 fail tango-db 9.2.2+dfsg-1~exp4
1471906715 fail tango-db 9.2.2+dfsg-1~exp4
1471917794 fail tango-db 9.2.2+dfsg-1~exp4
1471933628 fail tango-db 9.2.2+dfsg-1~exp4
1471938701 fail tango-db 9.2.2+dfsg-1~exp4
1471946968 fail tango-db 9.2.2+dfsg-1~exp4
1471950442 fail tango-db 9.2.2+dfsg-1~exp4
1471960451 fail tango-db 9.2.2+dfsg-1~exp4
1471973073 fail tango-db 9.2.2+dfsg-1~exp4
1471985087 fail tango-db 9.2.2+dfsg-1~exp4
1471991323 fail tango-db 9.2.2+dfsg-1~exp4
1471994452 fail tango-db 9.2.2+dfsg-1~exp4
1472003277 fail tango-db 9.2.2+dfsg-1~exp4
1472021245 fail tango-db 9.2.2+dfsg-1~exp4
1472025925 fail tango-db 9.2.2+dfsg-1~exp4
1472033680 fail tango-db 9.2.2+dfsg-1~exp4
1472036410 fail tango-db 9.2.2+dfsg-1~exp4
1472047321 fail tango-db 9.2.2+dfsg-1~exp4
1472057904 fail tango-db 9.2.2+dfsg-1~exp4
1472068624 fail tango-db 9.2.2+dfsg-1~exp4
1472077391 fail tango-db 9.2.2+dfsg-1~exp4
1472079604 fail tango-db 9.2.2+dfsg-1~exp4
1472090371 fail tango-db 9.2.2+dfsg-1~exp4
1472105325 fail tango-db 9.2.2+dfsg-1~exp4
1472112064 fail tango-db 9.2.2+dfsg-1~exp4
1472120114 fail tango-db 9.2.2+dfsg-1~exp4
1472123114 fail tango-db 9.2.2+dfsg-1~exp4
1472133445 fail tango-db 9.2.2+dfsg-1~exp4
1472145070 fail tango-db 9.2.2+dfsg-1~exp4
1472155177 fail tango-db 9.2.2+dfsg-1~exp4
1472163647 fail tango-db 9.2.2+dfsg-1~exp4
1472166891 fail tango-db 9.2.2+dfsg-1~exp4
1472177617 fail tango-db 9.2.2+dfsg-1~exp4
1472187922 fail tango-db 9.2.2+dfsg-1~exp4
1472198226 fail tango-db 9.2.2+dfsg-1~exp4
1472207582 fail tango-db 9.2.2+dfsg-1~exp4
1472209921 fail tango-db 9.2.2+dfsg-1~exp4
1472221050 fail tango-db 9.2.2+dfsg-1~exp4
1472230232 fail tango-db 9.2.2+dfsg-1~exp4
1472241988 fail tango-db 9.2.2+dfsg-1~exp4
1472252592 fail tango-db 9.2.2+dfsg-1~exp4
1472263460 fail tango-db 9.2.2+dfsg-1~exp4
1472278410 fail tango-db 9.2.2+dfsg-1~exp4
1472284927 fail tango-db 9.2.2+dfsg-1~exp4
1472292821 fail tango-db 9.2.2+dfsg-1~exp4
1472295713 fail tango-db 9.2.2+dfsg-1~exp4
1472306964 fail tango-db 9.2.2+dfsg-1~exp4
1472317336 fail tango-db 9.2.2+dfsg-1~exp4
1472328077 fail tango-db 9.2.2+dfsg-1~exp4
1472335687 fail tango-db 9.2.2+dfsg-1~exp4
1472339378 fail tango-db 9.2.2+dfsg-1~exp4
1472350020 fail tango-db 9.2.2+dfsg-1~exp4
147

Bug#848137: problem with the upgrade of tango-db

[Andreas Beckmann]

On 2017-01-04 21:55, Paul Gevers wrote:
> Hi Frederic-Emmanuel, Andreas,
> 
> @Andreas, am I correct in the assumption that jessie to stretch with
> tango-db was fine until MariaDB became the default? Or was this
> migration with tango-db just never tested before? Have you seen other
> dbconfig-common dependent packages fail since MariaDB became default (or
> maybe since dbconfig-common 2.0.5 (26-08-2016)?

I can't remember the details right now, but it is possible that this
started to fail after the mariadb switch (which is a non-trivial thing
to test with piuparts). I could try to find some older logs ...
And I don't remember any other package having a similar issue.

I needed, I could do further checks (or log lookup) next week.


Andreas

-- 
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#850026: vmtk: transitive B-D on both libssl-dev and libssl1.0-dev

[Andreas Beckmann]

Source: vmtk
Version: 1.3+dfsg-2
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Hi,

vmtk cannot be built any longer, since it transitively Build-Depends on
both libssl-dev and libssl1.0-dev which conflict with each other.


Andreas

-- 
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#848344: cgns-convert: /usr/bin/unitconv is already used by xcrysden

[Andreas Beckmann]

Package: cgns-convert
Version: 3.3.0-1
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts
Control: affects -1 + xcrysden

Hi,

during a test with piuparts I noticed your package ships a binary that
is already used by the unrelated package xcrysden:

  /usr/bin/unitconv

Since xcrysden uses that binary name for a long time already, it's
probably your package that will have to rename it.


Andreas


xcrysden=1.5.60-1+b1_cgns-convert=3.3.0-1.log.gz
Description: application/gzip
-- 
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#848137: tango-db: fails to upgrade from 'jessie': mysqldump: tango has insufficent privileges to SHOW CREATE PROCEDURE `class_att_prop`!

[Andreas Beckmann]

Package: tango-db
Version: 9.2.5~rc1+dfsg1-2
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'jessie'.
It installed fine in 'jessie', then the upgrade to 'stretch' fails.

>From the attached log (scroll to the bottom...):

  Setting up tango-db (9.2.5~rc1+dfsg1-2) ...
  Installing new version of config file /etc/init.d/tango-db ...
  Determining localhost credentials from /etc/mysql/debian.cnf: succeeded.
  dbconfig-common: writing config to /etc/dbconfig-common/tango-db.conf
  Replacing config file /etc/dbconfig-common/tango-db.conf with new version
  creating database backup in 
/var/cache/dbconfig-common/backups/tango-db_8.1.2c+dfsg-5.2016-12-14-10.08.39.
  error encountered backing up the old database:
  mysqldump: tango has insufficent privileges to SHOW CREATE PROCEDURE 
`class_att_prop`!
  dbconfig-common: tango-db configure: aborted.
  dbconfig-common: flushing administrative password
  dpkg: error processing package tango-db (--configure):
   subprocess installed post-installation script returned error exit status 1

In jessie, tango-db used mysql-server-5.5 (via mysql-server).
The upgrade of tango-db was performed after mysql-server had been upgraded
to mariadb-server-10.0 (via default-mysql-server) and was started again.


cheers,

Andreas


tango-db_9.2.5~rc1+dfsg1-2.log.gz
Description: application/gzip
-- 
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#847142: libdune-common-dev: fails to upgrade from 'sid' - trying to overwrite /usr/include/dune/common/concept.hh

[Andreas Beckmann]

Package: libdune-common-dev
Version: 2.5.0~rc1-3
Severity: serious
User: debian...@lists.debian.org
Usertags: piuparts

Hi,

during a test with piuparts I noticed your package fails to upgrade from
'sid' to 'experimental'.
It installed fine in 'sid', then the upgrade to 'experimental' fails
because it tries to overwrite other packages files without declaring a
Breaks+Replaces relation.

See policy 7.6 at
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-replaces

>From the attached log (scroll to the bottom...):

  Preparing to unpack .../3-libdune-common-dev_2.5.0~rc1-3_amd64.deb ...
  Unpacking libdune-common-dev:amd64 (2.5.0~rc1-3) over (2.4.1-1) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-6NB7R6/3-libdune-common-dev_2.5.0~rc1-3_amd64.deb 
(--unpack):
   trying to overwrite '/usr/include/dune/common/concept.hh', which is also in 
package libdune-functions-dev 2.4~20160825g0fd5975-1
  dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
  Errors were encountered while processing:
   /tmp/apt-dpkg-install-6NB7R6/3-libdune-common-dev_2.5.0~rc1-3_amd64.deb


cheers,

Andreas


libdune-functions-dev=2.4~20160825g0fd5975-1_libdune-common-dev=2.5.0~rc1-3.log.gz
Description: application/gzip
-- 
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#843931: libgtkdatabox-0.9.3-0-{, lib}glade: fails to upgrade from 'testing' - trying to overwrite /usr/lib/glade/modules/libgladedatabox.a, ...

[Andreas Beckmann]

Followup-For: Bug #843931
Control: found -1 1:0.9.3.0+dfsg-2

Hi,

on overwrite conflict is still present:

  Selecting previously unselected package libgtkdatabox-0.9.3-0-libglade.
  Preparing to unpack 
.../1-libgtkdatabox-0.9.3-0-libglade_1%3a0.9.3.0+dfsg-2_amd64.deb ...
  Unpacking libgtkdatabox-0.9.3-0-libglade (1:0.9.3.0+dfsg-2) ...
  dpkg: error processing archive 
/tmp/apt-dpkg-install-uBOSpu/1-libgtkdatabox-0.9.3-0-libglade_1%3a0.9.3.0+dfsg-2_amd64.deb
 (--unpack):
   trying to overwrite '/usr/lib/x86_64-linux-gnu/libglade/2.0/libdatabox.a', 
which is also in package libgtkdatabox-0.9.2-0-libglade 1:0.9.2.0+dfsg-1
  Errors were encountered while processing:
   
/tmp/apt-dpkg-install-uBOSpu/1-libgtkdatabox-0.9.3-0-libglade_1%3a0.9.3.0+dfsg-2_amd64.deb


Andreas

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