printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild clustalw2 2>&1 The package 'clustalw2' will be built without being installed. Reading build dependency for clustalw2-2.1-1... Reading dependency for clustalw2-2.1-1... Reading build conflict for clustalw2-2.1-1... The following package will be rebuilt: clustalw2 curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/clustalw-2.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 17 342k 17 60573 0 0 43946 0 0:00:07 0:00:01 0:00:06 43957 100 342k 100 342k 0 0 184k 0 0:00:01 0:00:01 --:--:-- 184k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-clustalw2-2.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-clustalw2-2.1-1' in `/sw/build.build/fink-buildlock-clustalw2-2.1-1_2014.08.04-21.46.56_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-clustalw2-2.1-1_2014.08.04-21.46.56_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-clustalw2-2.1-1. (Reading database ... 4740 files and directories currently installed.) Unpacking fink-buildlock-clustalw2-2.1-1 (from .../fink-buildlock-clustalw2-2.1-1_2014.08.04-21.46.56_darwin-x86_64.deb) ... Setting up fink-buildlock-clustalw2-2.1-1 (2014.08.04-21.46.56) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.fkE7m env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/clustalw-2.1.tar.gz clustalw-2.1/ clustalw-2.1/src/ clustalw-2.1/src/Help.cpp clustalw-2.1/src/general/ clustalw-2.1/src/general/UserParameters.cpp clustalw-2.1/src/general/statsObject.h clustalw-2.1/src/general/RandomAccessLList.h clustalw-2.1/src/general/general.h clustalw-2.1/src/general/SequenceNotFoundException.h clustalw-2.1/src/general/param.h clustalw-2.1/src/general/OutputFile.h clustalw-2.1/src/general/Utility.h clustalw-2.1/src/general/ClustalWResources.h clustalw-2.1/src/general/InvalidCombination.cpp clustalw-2.1/src/general/SymMatrix.cpp clustalw-2.1/src/general/VectorUtility.h clustalw-2.1/src/general/SquareMat.h clustalw-2.1/src/general/Utility.cpp clustalw-2.1/src/general/DebugLog.cpp clustalw-2.1/src/general/Stats.h clustalw-2.1/src/general/userparams.h clustalw-2.1/src/general/UserParameters.h clustalw-2.1/src/general/ClustalWResources.cpp clustalw-2.1/src/general/Stats.cpp clustalw-2.1/src/general/utils.h clustalw-2.1/src/general/DebugLog.h clustalw-2.1/src/general/VectorOutOfRange.cpp clustalw-2.1/src/general/VectorOutOfRange.h clustalw-2.1/src/general/clustalw.h clustalw-2.1/src/general/Array2D.h clustalw-2.1/src/general/SymMatrix.h clustalw-2.1/src/general/OutputFile.cpp clustalw-2.1/src/general/debuglogObject.h clustalw-2.1/src/Clustal.cpp clustalw-2.1/src/clustalw_version.h.in clustalw-2.1/src/multipleAlign/ clustalw-2.1/src/multipleAlign/LowScoreSegProfile.h clustalw-2.1/src/multipleAlign/ProfileAlignAlgorithm.h clustalw-2.1/src/multipleAlign/ProfileWithSub.cpp clustalw-2.1/src/multipleAlign/Iteration.h clustalw-2.1/src/multipleAlign/ProfileBase.h clustalw-2.1/src/multipleAlign/ProfileStandard.h clustalw-2.1/src/multipleAlign/LowScoreSegProfile.cpp clustalw-2.1/src/multipleAlign/ProfileBase.cpp clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.h clustalw-2.1/src/multipleAlign/ProfileWithSub.h clustalw-2.1/src/multipleAlign/Iteration.cpp clustalw-2.1/src/multipleAlign/MSA.h clustalw-2.1/src/multipleAlign/MyersMillerProfileAlign.cpp clustalw-2.1/src/multipleAlign/ProfileStandard.cpp clustalw-2.1/src/multipleAlign/MSA.cpp clustalw-2.1/src/Makefile.am clustalw-2.1/src/clustalw_version.h clustalw-2.1/src/Makefile.in clustalw-2.1/src/Help.h clustalw-2.1/src/Clustal.h clustalw-2.1/src/fileInput/ clustalw-2.1/src/fileInput/ClustalFileParser.h clustalw-2.1/src/fileInput/PearsonFileParser.h clustalw-2.1/src/fileInput/MSFFileParser.h clustalw-2.1/src/fileInput/PIRFileParser.h clustalw-2.1/src/fileInput/RSFFileParser.cpp clustalw-2.1/src/fileInput/MSFFileParser.cpp clustalw-2.1/src/fileInput/PIRFileParser.cpp clustalw-2.1/src/fileInput/RSFFileParser.h clustalw-2.1/src/fileInput/GDEFileParser.cpp clustalw-2.1/src/fileInput/ClustalFileParser.cpp clustalw-2.1/src/fileInput/InFileStream.h clustalw-2.1/src/fileInput/FileReader.cpp clustalw-2.1/src/fileInput/EMBLFileParser.h clustalw-2.1/src/fileInput/InFileStream.cpp clustalw-2.1/src/fileInput/PearsonFileParser.cpp clustalw-2.1/src/fileInput/GDEFileParser.h clustalw-2.1/src/fileInput/FileReader.h clustalw-2.1/src/fileInput/FileParser.h clustalw-2.1/src/fileInput/FileParser.cpp clustalw-2.1/src/fileInput/EMBLFileParser.cpp clustalw-2.1/src/main.cpp clustalw-2.1/src/substitutionMatrix/ clustalw-2.1/src/substitutionMatrix/SubMatrix.cpp clustalw-2.1/src/substitutionMatrix/globalmatrix.h clustalw-2.1/src/substitutionMatrix/matrices.h clustalw-2.1/src/substitutionMatrix/SubMatrix.h clustalw-2.1/src/alignment/ clustalw-2.1/src/alignment/AlignmentOutput.cpp clustalw-2.1/src/alignment/ObjectiveScore.cpp clustalw-2.1/src/alignment/Sequence.h clustalw-2.1/src/alignment/ObjectiveScore.h clustalw-2.1/src/alignment/Alignment.cpp clustalw-2.1/src/alignment/AlignmentOutput.h clustalw-2.1/src/alignment/Alignment.h clustalw-2.1/src/alignment/Sequence.cpp clustalw-2.1/src/pairwise/ clustalw-2.1/src/pairwise/FullPairwiseAlign.cpp clustalw-2.1/src/pairwise/PairwiseAlignBase.h clustalw-2.1/src/pairwise/FastPairwiseAlign.h clustalw-2.1/src/pairwise/FastPairwiseAlign.cpp clustalw-2.1/src/pairwise/FullPairwiseAlign.h clustalw-2.1/src/interface/ clustalw-2.1/src/interface/InteractiveMenu.cpp clustalw-2.1/src/interface/CommandLineParser.cpp clustalw-2.1/src/interface/CommandLineParser.h clustalw-2.1/src/interface/InteractiveMenu.h clustalw-2.1/src/config.h.in clustalw-2.1/src/tree/ clustalw-2.1/src/tree/UPGMA/ clustalw-2.1/src/tree/UPGMA/Node.cpp clustalw-2.1/src/tree/UPGMA/upgmadata.h clustalw-2.1/src/tree/UPGMA/RootedClusterTree.h clustalw-2.1/src/tree/UPGMA/Node.h clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.cpp clustalw-2.1/src/tree/UPGMA/RootedGuideTree.cpp clustalw-2.1/src/tree/UPGMA/RootedGuideTree.h clustalw-2.1/src/tree/UPGMA/RootedClusterTree.cpp clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.cpp clustalw-2.1/src/tree/UPGMA/RootedTreeOutput.h clustalw-2.1/src/tree/UPGMA/UPGMAAlgorithm.h clustalw-2.1/src/tree/RandomGenerator.h clustalw-2.1/src/tree/ClusterTreeOutput.h clustalw-2.1/src/tree/ClusterTree.h clustalw-2.1/src/tree/UnRootedClusterTree.h clustalw-2.1/src/tree/ClusterTreeAlgorithm.h clustalw-2.1/src/tree/RandomGenerator.cpp clustalw-2.1/src/tree/UnRootedClusterTree.cpp clustalw-2.1/src/tree/Tree.h clustalw-2.1/src/tree/NJTree.h clustalw-2.1/src/tree/ClusterTreeOutput.cpp clustalw-2.1/src/tree/NJTree.cpp clustalw-2.1/src/tree/TreeInterface.h clustalw-2.1/src/tree/TreeInterface.cpp clustalw-2.1/src/tree/AlignmentSteps.h clustalw-2.1/src/tree/Tree.cpp clustalw-2.1/src/tree/dayhoff.h clustalw-2.1/src/tree/AlignmentSteps.cpp clustalw-2.1/src/tree/ClusterTree.cpp clustalw-2.1/configure clustalw-2.1/configure.ac clustalw-2.1/config.sub clustalw-2.1/install-sh clustalw-2.1/Makefile.am clustalw-2.1/aclocal.m4 clustalw-2.1/Makefile.in clustalw-2.1/clustalw_help clustalw-2.1/README clustalw-2.1/missing clustalw-2.1/m4/ clustalw-2.1/m4/Makefile.am clustalw-2.1/m4/Makefile.in clustalw-2.1/config.guess clustalw-2.1/depcomp clustalw-2.1/COPYING.LESSER clustalw-2.1/COPYING sudo -u fink-bld [ENV] sh -c /tmp/fink.57BBs [ -r /sw/fink/dists/stable/main/finkinfo/sci/clustalw2.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.aeMPV patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/clustalw2.patch patching file src/general/VectorOutOfRange.cpp sudo -u fink-bld [ENV] sh -c /tmp/fink.NS4h4 ./configure --prefix=/sw checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking target system type... i386-apple-darwin13.3.0 building for darwin13.3.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands make Making all in m4 make[1]: Nothing to be done for `all'. Making all in src /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT PIRFileParser.o -MD -MP -MF .deps/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT RSFFileParser.o -MD -MP -MF .deps/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT GDEFileParser.o -MD -MP -MF .deps/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT InFileStream.o -MD -MP -MF .deps/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp In file included from ./pairwise/FastPairwiseAlign.cpp:10: In file included from ./pairwise/FastPairwiseAlign.h:9: In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:In file included from ./fileInput/FileReader.cpp:29: In file included from ./fileInput/FileReader.hIn file included from ./pairwise/FullPairwiseAlign.cpp:9: :12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96In file included from ./pairwise/FullPairwiseAlign.h:9: : In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ :62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/InFileStream.Tpo .deps/InFileStream.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ClustalFileParser.o -MD -MP -MF .deps/ClustalFileParser.Tpo -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp mv -f .deps/PIRFileParser.Tpo .deps/PIRFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT PearsonFileParser.o -MD -MP -MF .deps/PearsonFileParser.Tpo -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT FileParser.o -MD -MP -MF .deps/FileParser.Tpo -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp mv -f .deps/RSFFileParser.Tpo .deps/RSFFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT EMBLFileParser.o -MD -MP -MF .deps/EMBLFileParser.Tpo -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp mv -f .deps/GDEFileParser.Tpo .deps/GDEFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT RootedClusterTree.o -MD -MP -MF .deps/RootedClusterTree.Tpo -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp 2 warnings generated. mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT UPGMAAlgorithm.o -MD -MP -MF .deps/UPGMAAlgorithm.Tpo -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp 2 warnings generated. mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp 2 warnings generated. mv -f .deps/FileReader.Tpo .deps/FileReader.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT RootedGuideTree.o -MD -MP -MF .deps/RootedGuideTree.Tpo -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: In file included from ./tree/UPGMA/RootedClusterTree.h:8: In file included from ./tree/UPGMA/../ClusterTree.h:20: In file included from ./tree/UPGMA/../../alignment/Alignment.h:42: In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from ./tree/UPGMA/UPGMAAlgorithm.h:8: In file included from ./tree/UPGMA/RootedGuideTree.h:17: In file included from ./tree/UPGMA/../../alignment/Alignment.h:42: In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/FileParser.Tpo .deps/FileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT RootedTreeOutput.o -MD -MP -MF .deps/RootedTreeOutput.Tpo -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp mv -f .deps/ClustalFileParser.Tpo .deps/ClustalFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Tree.o -MD -MP -MF .deps/Tree.Tpo -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp In file included from ./tree/UPGMA/RootedGuideTree.cpp:10: In file included from ./tree/UPGMA/RootedGuideTree.h:17: In file included from ./tree/UPGMA/../../alignment/Alignment.h:42: In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/EMBLFileParser.Tpo .deps/EMBLFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ClusterTree.o -MD -MP -MF .deps/ClusterTree.Tpo -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp 2 warnings generated. mv -f .deps/UPGMAAlgorithm.Tpo .deps/UPGMAAlgorithm.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT TreeInterface.o -MD -MP -MF .deps/TreeInterface.Tpo -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp mv -f .deps/Node.Tpo .deps/Node.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT UnRootedClusterTree.o -MD -MP -MF .deps/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp 2 warnings generated. mv -f .deps/PearsonFileParser.Tpo .deps/PearsonFileParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ClusterTreeOutput.o -MD -MP -MF .deps/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp mv -f .deps/RootedClusterTree.Tpo .deps/RootedClusterTree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT RandomGenerator.o -MD -MP -MF .deps/RandomGenerator.Tpo -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp mv -f .deps/RandomGenerator.Tpo .deps/RandomGenerator.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT NJTree.o -MD -MP -MF .deps/NJTree.Tpo -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp 2 warnings generated. mv -f .deps/RootedGuideTree.Tpo .deps/RootedGuideTree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT AlignmentSteps.o -MD -MP -MF .deps/AlignmentSteps.Tpo -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp In file included from ./tree/UPGMA/RootedTreeOutput.cpp:9: In file included from ./tree/UPGMA/RootedTreeOutput.h:15: In file included from ./tree/UPGMA/RootedGuideTree.h:17: In file included from ./tree/UPGMA/../../alignment/Alignment.h:42: In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./tree/Tree.cpp:10: In file included from ./tree/Tree.h:13: In file included from ./tree/../alignment/Alignment.h:42: In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. mv -f .deps/RootedTreeOutput.Tpo .deps/RootedTreeOutput.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT InteractiveMenu.o -MD -MP -MF .deps/InteractiveMenu.Tpo -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp In file included from ./tree/ClusterTree.cpp:9: In file included from ./tree/ClusterTree.h:20: In file included from ./tree/../alignment/Alignment.h:42: In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./tree/TreeInterface.cpp:15: In file included from ./tree/TreeInterface.h:19: In file included from ./tree/../alignment/Alignment.h:42: In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./tree/UnRootedClusterTree.cpp:9: In file included from ./tree/UnRootedClusterTree.h:8: In file included from ./tree/ClusterTree.h:20: In file included from ./tree/../alignment/Alignment.h:42: In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./tree/ClusterTreeOutput.cpp:9: In file included from ./tree/ClusterTreeOutput.h:11: In file included from ./tree/../alignment/Alignment.h:42: In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/AlignmentSteps.Tpo .deps/AlignmentSteps.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT CommandLineParser.o -MD -MP -MF .deps/CommandLineParser.Tpo -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp 2 warnings generated. mv -f .deps/ClusterTreeOutput.Tpo .deps/ClusterTreeOutput.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT SubMatrix.o -MD -MP -MF .deps/SubMatrix.Tpo -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp mv -f .deps/NJTree.Tpo .deps/NJTree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Iteration.o -MD -MP -MF .deps/Iteration.Tpo -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp 2 warnings generated. mv -f .deps/TreeInterface.Tpo .deps/TreeInterface.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT MSA.o -MD -MP -MF .deps/MSA.Tpo -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:18: In file included from ./fileInput/FileReader.h:12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. mv -f .deps/Tree.Tpo .deps/Tree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT MyersMillerProfileAlign.o -MD -MP -MF .deps/MyersMillerProfileAlign.Tpo -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp 2 warnings generated. 2 warnings generated. mv -f .deps/ClusterTree.Tpo .deps/ClusterTree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ProfileStandard.o -MD -MP -MF .deps/ProfileStandard.Tpo -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp mv -f .deps/UnRootedClusterTree.Tpo .deps/UnRootedClusterTree.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ProfileWithSub.o -MD -MP -MF .deps/ProfileWithSub.Tpo -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:18: In file included from ./fileInput/FileReader.h:12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./substitutionMatrix/SubMatrix.cpp:15: ./substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./multipleAlign/Iteration.cpp:13: In file included from ./multipleAlign/Iteration.h:8: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./multipleAlign/MSA.cpp:16: In file included from ./multipleAlign/MSA.h:10: In file included from ./multipleAlign/ProfileBase.h:14: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. In file included from ./multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from ./multipleAlign/MyersMillerProfileAlign.h:10: In file included from ./multipleAlign/ProfileAlignAlgorithm.h:10: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/InteractiveMenu.Tpo .deps/InteractiveMenu.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ProfileBase.o -MD -MP -MF .deps/ProfileBase.Tpo -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp In file included from ./multipleAlign/ProfileStandard.cpp:9: In file included from ./multipleAlign/ProfileStandard.h:9: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./multipleAlign/ProfileWithSub.cpp:9: In file included from ./multipleAlign/ProfileWithSub.h:9: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. mv -f .deps/ProfileStandard.Tpo .deps/ProfileStandard.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT LowScoreSegProfile.o -MD -MP -MF .deps/LowScoreSegProfile.Tpo -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp 2 warnings generated. mv -f .deps/MSA.Tpo .deps/MSA.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT OutputFile.o -MD -MP -MF .deps/OutputFile.Tpo -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp 2 warnings generated. mv -f .deps/ProfileWithSub.Tpo .deps/ProfileWithSub.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT UserParameters.o -MD -MP -MF .deps/UserParameters.Tpo -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp ./multipleAlign/Iteration.cpp:231:17: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] tmpnam (buffer); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ 2 warnings generated. mv -f .deps/CommandLineParser.Tpo .deps/CommandLineParser.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Utility.o -MD -MP -MF .deps/Utility.Tpo -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp In file included from ./multipleAlign/ProfileBase.cpp:9: In file included from ./multipleAlign/ProfileBase.h:14: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. In file included from ./multipleAlign/LowScoreSegProfile.cpp:9: In file included from ./multipleAlign/LowScoreSegProfile.h:13: In file included from ./multipleAlign/../alignment/Alignment.h:42: In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/MyersMillerProfileAlign.Tpo .deps/MyersMillerProfileAlign.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT InvalidCombination.o -MD -MP -MF .deps/InvalidCombination.Tpo -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp 2 warnings generated. mv -f .deps/SubMatrix.Tpo .deps/SubMatrix.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT DebugLog.o -MD -MP -MF .deps/DebugLog.Tpo -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp 3 warnings generated. mv -f .deps/Iteration.Tpo .deps/Iteration.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ClustalWResources.o -MD -MP -MF .deps/ClustalWResources.Tpo -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp 2 warnings generated. mv -f .deps/LowScoreSegProfile.Tpo .deps/LowScoreSegProfile.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT VectorOutOfRange.o -MD -MP -MF .deps/VectorOutOfRange.Tpo -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp mv -f .deps/OutputFile.Tpo .deps/OutputFile.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT SymMatrix.o -MD -MP -MF .deps/SymMatrix.Tpo -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp mv -f .deps/UserParameters.Tpo .deps/UserParameters.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp 2 warnings generated. mv -f .deps/ProfileBase.Tpo .deps/ProfileBase.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Help.o -MD -MP -MF .deps/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp mv -f .deps/InvalidCombination.Tpo .deps/InvalidCombination.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Alignment.o -MD -MP -MF .deps/Alignment.Tpo -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp mv -f .deps/Utility.Tpo .deps/Utility.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT AlignmentOutput.o -MD -MP -MF .deps/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp mv -f .deps/SymMatrix.Tpo .deps/SymMatrix.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT ObjectiveScore.o -MD -MP -MF .deps/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp ./general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds] delim[1] = 0; ^ ~ ./general/ClustalWResources.cpp:104:5: note: array 'delim' declared here char delim[1]; ^ mv -f .deps/VectorOutOfRange.Tpo .deps/VectorOutOfRange.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Sequence.o -MD -MP -MF .deps/Sequence.Tpo -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp mv -f .deps/DebugLog.Tpo .deps/DebugLog.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT Clustal.o -MD -MP -MF .deps/Clustal.Tpo -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp In file included from ./general/Stats.cpp:15: In file included from ./general/../alignment/Alignment.h:42: In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8: ./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 1 warning generated. mv -f .deps/ClustalWResources.Tpo .deps/ClustalWResources.Po g++ -DHAVE_CONFIG_H -I. -I/sw/include -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp In file included from ./alignment/Alignment.cpp:25: In file included from ./alignment/Alignment.h:42: In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./alignment/AlignmentOutput.cpp:27: In file included from ./alignment/AlignmentOutput.h:24: In file included from ./alignment/Alignment.h:42: In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ mv -f .deps/Help.Tpo .deps/Help.Po 2 warnings generated. mv -f .deps/Stats.Tpo .deps/Stats.Po In file included from ./alignment/ObjectiveScore.cpp:10: In file included from ./alignment/ObjectiveScore.h:15: In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:18: In file included from ./fileInput/FileReader.h:12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ In file included from ./main.cpp:10: In file included from ./alignment/Alignment.h:42: In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 2 warnings generated. mv -f .deps/ObjectiveScore.Tpo .deps/ObjectiveScore.Po 2 warnings generated. mv -f .deps/Sequence.Tpo .deps/Sequence.Po mv -f .deps/main.Tpo .deps/main.Po 2 warnings generated. mv -f .deps/Alignment.Tpo .deps/Alignment.Po 2 warnings generated. mv -f .deps/Clustal.Tpo .deps/Clustal.Po 2 warnings generated. mv -f .deps/AlignmentOutput.Tpo .deps/AlignmentOutput.Po g++ -g -O2 -L/sw/lib -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o make[1]: Nothing to be done for `all-am'. /bin/rm -rf /sw/build.build/root-clustalw2-2.1-1 /bin/mkdir -p /sw/build.build/root-clustalw2-2.1-1/sw /bin/mkdir -p /sw/build.build/root-clustalw2-2.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-clustalw2-2.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.VGp8E /usr/bin/strip src/clustalw2 /usr/bin/make -w install DESTDIR=/sw/build.build/root-clustalw2-2.1-1 make: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' Making install in m4 make[1]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/m4' make[2]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/m4' make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/share/aclocal" || .././install-sh -c -d "/sw/build.build/root-clustalw2-2.1-1/sw/share/aclocal" make[2]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/m4' make[1]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/m4' Making install in src make[1]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' make[2]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' make[3]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' test -z "/sw/bin" || .././install-sh -c -d "/sw/build.build/root-clustalw2-2.1-1/sw/bin" /usr/bin/install -c clustalw2 '/sw/build.build/root-clustalw2-2.1-1/sw/bin' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' make[2]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' make[1]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1/src' make[1]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' make[2]: Entering directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' make[1]: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' make: Leaving directory `/sw/build.build/clustalw2-2.1-1/clustalw-2.1' /usr/bin/install -d -m 755 /sw/build.build/root-clustalw2-2.1-1/sw/lib/clustalw2 /usr/bin/install -m 644 clustalw_help /sw/build.build/root-clustalw2-2.1-1/sw/lib/clustalw2 sudo -u fink-bld [ENV] sh -c /tmp/fink.72DRl /usr/bin/install -d -m 700 /sw/build.build/root-clustalw2-2.1-1/sw/share/doc/clustalw2 /bin/cp -r COPYING /sw/build.build/root-clustalw2-2.1-1/sw/share/doc/clustalw2/ /bin/cp -r README /sw/build.build/root-clustalw2-2.1-1/sw/share/doc/clustalw2/ /bin/chmod -R go=u-w /sw/build.build/root-clustalw2-2.1-1/sw/share/doc/clustalw2 /bin/rm -f /sw/build.build/root-clustalw2-2.1-1/sw/info/dir /sw/build.build/root-clustalw2-2.1-1/sw/info/dir.old /sw/build.build/root-clustalw2-2.1-1/sw/share/info/dir /sw/build.build/root-clustalw2-2.1-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-clustalw2-2.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `clustalw2' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/clustalw2_2.1-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-clustalw2-2.1-1 (Reading database ... 4741 files and directories currently installed.) Removing fink-buildlock-clustalw2-2.1-1 ...