[Debian-med-packaging] Bug#844140: mia: FTBFS: lxml.etree.XMLSyntaxError: None

[Lucas Nussbaum]

Source: mia
Version: 2.4.3-2
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20161111 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 '/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/python /<<PKGBUILDDIR>>/doc/miaxml2man.py /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/doc/mia-3drigidreg.xml >/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mia-3drigidreg.1
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && MIA_PLUGIN_TESTPATH=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/plugintest//usr/lib/x86_64-linux-gnu/mia-2.4/plugins ./mia-3dmaskseeded --help-xml /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml
> [ 98%] Built target mia-3dgetsize-xml
> [ 98%] Generating ../doc/mia-3dmaskseeded.xml
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && MIA_PLUGIN_TESTPATH=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/plugintest//usr/lib/x86_64-linux-gnu/mia-2.4/plugins ./mia-3dmaskseeded --help-xml /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml
> [ 98%] Linking CXX executable test-splineparzenmi
> cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/python /<<PKGBUILDDIR>>/doc/miaxml2man.py /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/doc/mia-3dmaskseeded.xml >/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mia-3dmaskseeded.1
> /usr/bin/c++   -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core 
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Built target mia-3drigidreg-man
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/doc/miaxml2man.py", line 149, in <module>
>     X=parse_file(sys.argv[1])
>   File "/<<PKGBUILDDIR>>/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.