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=openmsarch=s390xver=1.9.0-2stamp=1362609406file=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,
