[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_i386_12 #17731
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Oct 1 14:06:00 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_i386_12/17731/------------------------------------------
[...truncated 16079 lines...]
@@ -3762,7 +3773,7 @@
In file included from clustalW/Clustal.h:20:0,
from mainwindow.h:45,
from moc_mainwindow.cpp:9:
-clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
+clustalW/alignment/AlignmentOutput.h:81:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<ofstream> fastaOutFile;
^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
@@ -3776,11 +3787,11 @@
template<typename> class auto_ptr;
^~~~~~~~
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PairwiseParams.h -o moc_PairwiseParams.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PairwiseParams.o moc_PairwiseParams.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PairwiseParams.o moc_PairwiseParams.cpp
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. ProteinGapParameters.h -o moc_ProteinGapParameters.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. PSPrinter.h -o moc_PSPrinter.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PSPrinter.o moc_PSPrinter.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_PSPrinter.o moc_PSPrinter.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
@@ -3788,58 +3799,58 @@
from ColorParameters.h:11,
from PSPrinter.h:11,
from moc_PSPrinter.cpp:9:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SaveSeqFile.h -o moc_SaveSeqFile.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from SaveSeqFile.h:9,
from moc_SaveSeqFile.cpp:9:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SearchForString.h -o moc_SearchForString.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SearchForString.o moc_SearchForString.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SearchForString.o moc_SearchForString.cpp
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SecStructOptions.h -o moc_SecStructOptions.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SecStructOptions.o moc_SecStructOptions.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SecStructOptions.o moc_SecStructOptions.cpp
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. SeqNameWidget.h -o moc_SeqNameWidget.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0,
from clustalW/alignment/Alignment.h:42,
from SeqNameWidget.h:41,
from moc_SeqNameWidget.cpp:9:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeFormatOptions.h -o moc_TreeFormatOptions.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from TreeOutputFileNames.h:10,
from moc_TreeOutputFileNames.cpp:9:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
In file included from moc_TreeOutputFileNames.cpp:9:0:
-TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
+TreeOutputFileNames.h:73:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<clustalw::TreeNames> treeFileNames;
^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
@@ -3849,20 +3860,20 @@
template<typename> class auto_ptr;
^~~~~~~~
/usr/lib/i386-linux-gnu/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. WritePostscriptFile.h -o moc_WritePostscriptFile.cpp
-g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-1st/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
+g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -g -O2 -fdebug-prefix-map=/build-2nd/clustalx-2.1+lgpl=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0,
from clustalW/alignment/Alignment.h:42,
from ClustalQtParams.h:13,
from WritePostscriptFile.h:10,
from moc_WritePostscriptFile.cpp:9:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printInFormat(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
^~~~~~~~~~~~~~
In file included from moc_WritePostscriptFile.cpp:9:0:
-WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
+WritePostscriptFile.h:88:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
auto_ptr<PostscriptFileParams> params;
^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
@@ -3874,7 +3885,7 @@
g++ -Wl,-O1 -fPIE -pie -Wl,-z,relro -Wl,-z,now -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o -L/usr/lib/i386-linux-gnu -lQtXml -lQtGui -lQtCore -lpthread
Iteration.o: In function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
./clustalW/multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
-make[1]: Leaving directory '/build-1st/clustalx-2.1+lgpl'
+make[1]: Verzeichnis „/build-2nd/clustalx-2.1+lgpl“ wird verlassen
dh_auto_test
fakeroot debian/rules binary
dh binary
@@ -3884,9 +3895,9 @@
dh_install
dh_installdocs
debian/rules override_dh_installchangelogs
-make[1]: Entering directory '/build-1st/clustalx-2.1+lgpl'
+make[1]: Verzeichnis „/build-2nd/clustalx-2.1+lgpl“ wird betreten
dh_installchangelogs debian/CHANGELOG.upstream
-make[1]: Leaving directory '/build-1st/clustalx-2.1+lgpl'
+make[1]: Verzeichnis „/build-2nd/clustalx-2.1+lgpl“ wird verlassen
dh_installman
dh_installmime
dh_perl
@@ -3903,8 +3914,8 @@
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'clustalx-dbgsym' in '../clustalx-dbgsym_2.1+lgpl-5_i386.deb'.
-dpkg-deb: building package 'clustalx' in '../clustalx_2.1+lgpl-5_i386.deb'.
+dpkg-deb: Paket »clustalx-dbgsym« wird in »../clustalx-dbgsym_2.1+lgpl-5_i386.deb« gebaut.
+dpkg-deb: Paket »clustalx« wird in »../clustalx_2.1+lgpl-5_i386.deb« gebaut.
dpkg-genbuildinfo --build=any,all --buildinfo-id=i386
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any,all >../clustalx_2.1+lgpl-5_i386.changes
@@ -3912,12 +3923,14 @@
dpkg-source --after-build clustalx-2.1+lgpl
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/2016/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/2016/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/35644 and its subdirectories
-I: Current time: Fri Nov 3 08:11:51 GMT+12 2017
-I: pbuilder-time-stamp: 1509739911
+I: removing directory /srv/workspace/pbuilder/2016 and its subdirectories
+I: Current time: Son Okt 2 04:02:11 GMT-14 2016
+I: pbuilder-time-stamp: 1475330531
Compressing the 2nd log...
/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/clustalx_2.1+lgpl-5.diff: 93.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/clustalx_2.1+lgpl-5.diff.gz
b2/build.log: 93.9%
+ echo 'Compressing the 1st log...'
Compressing the 1st log...
+ gzip -9cvn b1/build.log
b1/build.log: 94.0%
+ chmod 644 /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/clustalx_2.1+lgpl-5.build1.log.gz
+ update_rbuildlog
+ chmod 644 /srv/reproducible-results/rbuild-debian-NAN485MS/tmp.Y7k0Q6gh7G
+ mv /srv/reproducible-results/rbuild-debian-NAN485MS/tmp.Y7k0Q6gh7G /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/i386/clustalx_2.1+lgpl-5.rbuild.log
+ RBUILDLOG=/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/i386/clustalx_2.1+lgpl-5.rbuild.log
+ '[' 0 -eq 1 ']'
+ '[' 0 -eq 0 ']'
+ call_diffoscope_on_buildinfo_files
++ mktemp --tmpdir=/srv/reproducible-results/rbuild-debian-NAN485MS
+ local TMPLOG=/srv/reproducible-results/rbuild-debian-NAN485MS/tmp.Tw1DS2P0YK
+ local TIMEOUT=120m
+ DBDSUITE=unstable
+ '[' unstable = experimental ']'
+ set -x
++ mktemp --tmpdir=/srv/reproducible-results/rbuild-debian-NAN485MS -d dbd-tmp-XXXXXXX
+ local TEMP=/srv/reproducible-results/rbuild-debian-NAN485MS/dbd-tmp-SngwDSv
++ schroot --directory /srv/reproducible-results/rbuild-debian-NAN485MS -c source:jenkins-reproducible-unstable-diffoscope diffoscope -- --version
+ DIFFOSCOPE='diffoscope 61'
++ echo diffoscope 61
++ grep '^E: 15binfmt: update-binfmts: unable to open'
++ true
+ LOG_RESULT=
+ '[' '!' -z '' ']'
+ log_info 'diffoscope 61 will be used to compare the two builds:'
+ _log I: 'diffoscope 61 will be used to compare the two builds:'
+ local prefix=I:
+ shift 1
++ date -u
+ tee -a /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/i386/clustalx_2.1+lgpl-5.rbuild.log
+ echo -e 'Sat Oct 1 14:02:15 UTC 2016 I: diffoscope 61 will be used to compare the two builds:'
Sat Oct 1 14:02:15 UTC 2016 I: diffoscope 61 will be used to compare the two builds:
+ set +e
+ set -x
+ timeout 120m nice schroot --directory /srv/reproducible-results/rbuild-debian-NAN485MS -c source:jenkins-reproducible-unstable-diffoscope -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian-NAN485MS/dbd-tmp-SngwDSv ; diffoscope --html /srv/reproducible-results/rbuild-debian-NAN485MS/clustalx_2.1+lgpl-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian-NAN485MS/clustalx_2.1+lgpl-5.diffoscope.txt /srv/reproducible-results/rbuild-debian-NAN485MS/b1/clustalx_2.1+lgpl-5_i386.buildinfo /srv/reproducible-results/rbuild-debian-NAN485MS/b2/clustalx_2.1+lgpl-5_i386.buildinfo'
+ RESULT=0
++ grep '^E: 15binfmt: update-binfmts: unable to open' /srv/reproducible-results/rbuild-debian-NAN485MS/tmp.Tw1DS2P0YK
++ true
+ LOG_RESULT=
+ '[' '!' -z '' ']'
+ false
+ set +x
_ _ _
___| |_ _ ___| |_ __ _| |_ __
/ __| | | | / __| __/ _` | \ \/ /
| (__| | |_| \__ \ || (_| | |> <
\___|_|\__,_|___/\__\__,_|_/_/\_\
Sat Oct 1 14:02:17 UTC 2016 I: diffoscope 61 found no differences in the changes files, and a .buildinfo file also exists.
Sat Oct 1 14:02:17 UTC 2016 I: clustalx from unstable built successfully and reproducibly on i386.
Error: database is locked
Error: database is locked
/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/i386/clustalx_2.1+lgpl-5.rbuild.log: 93.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/i386/clustalx_2.1+lgpl-5.rbuild.log.gz
INFO: Starting at 2016-10-01 14:05:00.044725
CRITICAL: SQLite database locked, could not execute query:
CRITICAL: "SELECT r.status, r.version, r.build_date FROM results AS r JOIN sources AS s ON r.package_id=s.id WHERE s.name="clustalx" AND s.architecture="amd64" AND s.suite="testing""
CRITICAL: Exiting script.
INFO: Finished at 2016-10-01 14:06:00.157200, took: 0:01:00.112504
Warning: cannot update html pages for clustalx
Sat 1 Oct 14:06:00 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-e8aWFAo1, which will now be removed.
Build step 'Execute shell' marked build as failure
More information about the Qa-jenkins-scm
mailing list