Bug#844140: mia: FTBFS: lxml.etree.XMLSyntaxError: None

2016-11-14 Thread Gert Wollny 


I don't think that the bug is related to threading/locking failures
within mia, i.e. compiling the package by using g++-5* and 
-fsanitize=thread doesn't show any locking problems (specifically no
double un-locking of a mutex). 

Specifically, the error hints at 

   ./mia-3dmaskseeded --help-xml  

not generating the required output that is later used by the python
program that actually fails. And this command is run without reported
errors, i.e. it doesn't crash like it seems to be what would be
expected from threading errors that are revealed when TSX is enabled. 

In addition, the only place in the code where mutex locking is applied
when running the command like given above is a piece of code that is
shared by all other command line tools in mia, and running these tools
with the the same command line option (--help-xml) don't fail.

It would be nice to know whether the failure was exactly at the same
point when the build was tried, or whether there were differences
there?

Are there any other options, apart from using the thread sanitizer,
that can help me to debug this problem?


Best, 
Gert 

* g++-5, because for g++-6 on Debian the thread sanitizer is currently
broken (#796246). 

Bug#844140: mia: FTBFS: lxml.etree.XMLSyntaxError: None

2016-11-12 Thread Lucas Nussbaum 
Source: mia
Version: 2.4.3-2
Severity: serious
Tags: stretch sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-2016 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[4]: Entering directory '/<>/obj-x86_64-linux-gnu'
> [ 97%] Generating mia-3drigidreg.1
> [ 97%] Built target mia-3dtrackpixelmovement-xml
> [ 98%] Generating ../doc/mia-3dmaskseeded.xml
> [ 98%] Built target mia-3disosurface-from-volume-xml
> [ 98%] Built target mia-3drigidreg-xml
> cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/python 
> /<>/doc/miaxml2man.py 
> /<>/obj-x86_64-linux-gnu/doc/mia-3drigidreg.xml 
> >/<>/obj-x86_64-linux-gnu/src/mia-3drigidreg.1
> cd /<>/obj-x86_64-linux-gnu/src && 
> MIA_PLUGIN_TESTPATH=/<>/obj-x86_64-linux-gnu/plugintest//usr/lib/x86_64-linux-gnu/mia-2.4/plugins
>  ./mia-3dmaskseeded --help-xml 
> /<>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml
> [ 98%] Built target mia-3dgetsize-xml
> [ 98%] Generating ../doc/mia-3dmaskseeded.xml
> cd /<>/obj-x86_64-linux-gnu/src && 
> MIA_PLUGIN_TESTPATH=/<>/obj-x86_64-linux-gnu/plugintest//usr/lib/x86_64-linux-gnu/mia-2.4/plugins
>  ./mia-3dmaskseeded --help-xml 
> /<>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml
> [ 98%] Linking CXX executable test-splineparzenmi
> cd /<>/obj-x86_64-linux-gnu/mia/core && /usr/bin/cmake -E 
> cmake_link_script CMakeFiles/test-splineparzenmi.dir/link.txt --verbose=1
> [ 98%] Generating mia-3dmaskseeded.1
> cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/python 
> /<>/doc/miaxml2man.py 
> /<>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml 
> >/<>/obj-x86_64-linux-gnu/src/mia-3dmaskseeded.1
> /usr/bin/c++   -g -O2 -fdebug-prefix-map=/<>=. 
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
> -D_FORTIFY_SOURCE=2   -std=c++11 -fvisibility=hidden   -Wl,-z,relro 
> -Wl,-z,now -Wl,--as-needed -fvisibility=hidden 
> CMakeFiles/test-splineparzenmi.dir/test_splineparzenmi.cc.o  -o 
> test-splineparzenmi -rdynamic libmiacore-2.4.so.2.0.1 
> -lboost_unit_test_framework -lgsl -lgslcblas -lm -lboost_filesystem 
> -lboost_system -lpthread -ldl -lfftw3f -lxml++-2.6 -lxml2 -lglibmm-2.4 
> -lgobject-2.0 -lglib-2.0 -lsigc-2.0 -litpp 
> -Wl,-rpath,/<>/obj-x86_64-linux-gnu/mia/core 
> make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu'
> [ 98%] Built target mia-3drigidreg-man
> make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu'
> Traceback (most recent call last):
>   File "/<>/doc/miaxml2man.py", line 149, in 
> X=parse_file(sys.argv[1])
>   File "/<>/doc/miareadxml.py", line 781, in parse_file
> root = etree.XML(stringstree)
>   File "src/lxml/lxml.etree.pyx", line 3192, in lxml.etree.XML 
> (src/lxml/lxml.etree.c:77490)
>   File "src/lxml/parser.pxi", line 1830, in lxml.etree._parseMemoryDocument 
> (src/lxml/lxml.etree.c:116674)
>   File "src/lxml/parser.pxi", line 1718, in lxml.etree._parseDoc 
> (src/lxml/lxml.etree.c:115324)
>   File "src/lxml/parser.pxi", line 1090, in lxml.etree._BaseParser._parseDoc 
> (src/lxml/lxml.etree.c:109723)
>   File "src/lxml/parser.pxi", line 584, in 
> lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:103584)
>   File "src/lxml/parser.pxi", line 694, in lxml.etree._handleParseResult 
> (src/lxml/lxml.etree.c:105238)
>   File "src/lxml/parser.pxi", line 635, in lxml.etree._raiseParseError 
> (src/lxml/lxml.etree.c:104381)
> lxml.etree.XMLSyntaxError: None
> [ 98%] Built target mia-2dsegment-local-cmeans-man
> src/CMakeFiles/mia-3dmaskseeded-man.dir/build.make:63: recipe for target 
> 'src/mia-3dmaskseeded.1' failed
> make[4]: *** [src/mia-3dmaskseeded.1] Error 1

The full build log is available from:
   http://aws-logs.debian.net/2016/11/11/mia_2.4.3-2_unstable.log

This failure happens on a CPU with TSX extensions available, but is not
reproducible on a machine without them. For context, I recommend reading the
thread starting at https://lists.debian.org/debian-devel/2016/11/msg00210.html

The node used is an Amazon EC2 VM with 64 cores. /proc/cpuinfo says:
   model: 79
   model name : Intel(R) Xeon(R) CPU E5-2686 v4 @ 2.30GHz
   stepping : 1

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.