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mention of a truncated file in a build log



Greeting Fellow Debianists,

I have recently uploaded a large software package which got handled by
autobuilds.

In this build log,

https://buildd.debian.org/status/fetch.php?pkg=openms&arch=s390x&ver=1.9.0-2&stamp=1362609406&file=log

an error was related to a corrupted file (--->>> below):

Linking CXX shared library lib/libOpenMS.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/OpenMS.dir/link.txt --verbose=1
/usr/bin/c++  -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4
-Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -fopenmp -O3
-DNDEBUG  -Wl,-z,relro -fopenmp -shared -Wl,-soname,libOpenMS.so.1 -o
lib/libOpenMS.so.1.9.0
CMakeFiles/OpenMS.dir/source/CONCEPT/ClassTest.C.o
CMakeFiles/OpenMS.dir/source/CONCEPT/Constants.C.o
[ ... tens of object files removed ... ]
CMakeFiles/OpenMS.dir/source/SIMULATION/LABELING/ICPLLabeler.C.o CMakeFiles/OpenMS.dir/include/OpenMS/SYSTEM/moc_FileWatcher.cxx.o CMakeFiles/OpenMS.dir/include/OpenMS/FORMAT/moc_MascotRemoteQuery.cxx.o -lQtOpenGL -lQtSvg -lQtWebKit -lQtXmlPatterns -lQtGui -lQtTest -lQtXml -lQtSql -lQtNetwork -lQtCore -lgsl -lgslcblas -lsvm -lsvm -lm -lxerces-c -lboost_iostreams-mt -lboost_date_time-mt -lboost_math_c99-mt -lbz2 -lz -lglpk 
/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/APPLICATIONS/TOPPBase.h: In member function 'void OpenMS::TOPPBase::registerParamEntry_(const OpenMS::Param::ParamEntry&, const OpenMS::String&, const OpenMS::String&)':
/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/APPLICATIONS/TOPPBase.h:163:52: warning: 'type' may be used uninitialized in this function [-Wuninitialized]
/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C:761:45: note: 'type' was declared here

--->>> 

CMakeFiles/OpenMS.dir/source/APPLICATIONS/TOPPBase.C.o: file not recognized: File truncated
collect2: ld returned 1 exit status
make[4]: *** [lib/libOpenMS.so.1.9.0] Error 1
make[4]: Leaving directory `/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build'
make[3]: *** [CMakeFiles/OpenMS.dir/all] Error 2
make[3]: Leaving directory `/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build'
make[2]: *** [CMakeFiles/TOPP.dir/rule] Error 2
make[2]: Leaving directory `/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build'
make[1]: *** [TOPP] Error 2
make[1]: *** Waiting for unfinished jobs....

When perusing up the build log, the TOPPBase.C.o could be built fine,
although with warnings:

8<

 Building CXX object CMakeFiles/OpenMS.dir/source/APPLICATIONS/TOPPBase.C.o
/usr/bin/c++   -DOpenMS_EXPORTS -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WEBKIT_LIB -DQT_TEST_LIB -DQT_XML_LIB -DQT_SQL_LIB -DQT_NETWORK_LIB -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WEBKIT_LIB -DQT_TEST_LIB -DQT_XML_LIB -DQT_SQL_LIB -DQT_NETWORK_LIB -DQT_NO_DEBUG -DQT_NO_DEBUG -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2   -fopenmp -O3 -DNDEBUG -fPIC -I/usr/include/libsvm -I/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include -I/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build/include -I/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/contrib/include -I/opt/local/include -I/usr/local/include -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtSvg -I/usr/include/qt4/QtWebKit -I/usr/include/qt4/QtTest -I/usr/include/qt4/QtXml -I/usr/include/qt4/QtSql -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtDesigner -I/usr/include/qt4/QtDeclarative -I/usr/include/qt4/QtScriptTools -I/usr/include/qt4/QtDBus -I/usr/include/qt4/QtXmlPatterns -I/usr/include/qt4/QtHelp -I/usr/include/qt4/QtUiTools -I/usr/include/qt4/QtScript -I/usr/include/qt4/Qt3Support -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/usr/share/qt4/mkspecs/default    -Wall -Wextra -Wno-non-virtual-dtor -Wno-long-long -Wno-variadic-macros --pedantic -fPIC -o CMakeFiles/OpenMS.dir/source/APPLICATIONS/TOPPBase.C.o -c /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C
In file included from /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/DATASTRUCTURES/Param.h:32:0,
                 from /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/DATASTRUCTURES/ToolDescription.h:33,
                 from /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/APPLICATIONS/ToolHandler.h:31,
                 from /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/include/OpenMS/APPLICATIONS/TOPPBase.h:31,
                 from /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C:28:
/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C: In member function 'void OpenMS::TOPPBase::readConsoleSize_()':
/build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C:538:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
/usr/bin/cmake -E cmake_progress_report /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build/CMakeFiles 

>8

My question is: is there a way to trigger rebuilding of the whole
software so as to establish if the failure is reproducible ? If the
failure is reproduced, given that the software builds fine on amd64,
would that possibly mean that there are problems with
zandonai.debian.org at the hardware level?

Any idea on that matter?

Cheers,
Filippo

-- 
Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu
Researcher at CNRS and Debian Developer <lopippo@debian.org>
Author of ``massXpert''     at http://www.massxpert.org


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