=> Building biology/clustalw build started at Tue Oct 4 01:53:48 PDT 2016 port directory: /usr/ports/biology/clustalw building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: ports@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../03//usr/ports/biology/clustalw/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=clustalw-2.1_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/clustalw XDG_CONFIG_HOME=/wrkdirs/biology/clustalw HOME=/wrkdirs/biology/clustalw TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/clustalw XDG_CONFIG_HOME=/wrkdirs/biology/clustalw HOME=/wrkdirs/biology/clustalw TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/clustalw" EXAMPLESDIR="share/examples/clustalw" DATADIR="share/clustalw" WWWDIR="www/clustalw" ETCDIR="etc/clustalw" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clustalw DOCSDIR=/usr/local/share/doc/clustalw EXAMPLESDIR=/usr/local/share/examples/clustalw WWWDIR=/usr/local/www/clustalw ETCDIR=/usr/local/etc/clustalw --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> NOTICE: The clustalw port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port =========================================================================== =================================================== ===> clustalw-2.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> clustalw-2.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustalw-2.1_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The clustalw port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by clustalw-2.1_1 for building =========================================================================== =================================================== ===> NOTICE: The clustalw port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by clustalw-2.1_1 for building => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The clustalw port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by clustalw-2.1_1 for building ===> Extracting for clustalw-2.1_1 => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for clustalw-2.1_1 ===> Applying ports patches for clustalw-2.1_1 =========================================================================== =================================================== =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for clustalw-2.1_1 configure: loading site script /usr/ports/Templates/config.site checking build system type... x86_64-portbld-dragonfly4.7 checking host system type... x86_64-portbld-dragonfly4.7 checking target system type... x86_64-portbld-dragonfly4.7 configure: WARNING: "Couldn't determine target operating system. Using Unix" building for dragonfly4.7 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) 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 =========================================================================== =================================================== ===> Building for clustalw-2.1_1 --- all-recursive --- Making all in m4 Making all in src --- all --- /usr/bin/make all-recursive --- all-recursive --- --- FullPairwiseAlign.o --- --- FastPairwiseAlign.o --- --- MSFFileParser.o --- --- FileReader.o --- --- PIRFileParser.o --- --- FullPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp --- FastPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp --- MSFFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp --- PIRFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT PIRFileParser.o -MD -MP -MF .deps/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp --- FileReader.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp --- FastPairwiseAlign.o --- In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FastPairwiseAlign.h:9, from ./pairwise/FastPairwiseAlign.cpp:10: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- FullPairwiseAlign.o --- In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FullPairwiseAlign.h:9, from ./pairwise/FullPairwiseAlign.cpp:9: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- FileReader.o --- In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./fileInput/FileReader.cpp:29: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- FastPairwiseAlign.o --- mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po --- RSFFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RSFFileParser.o -MD -MP -MF .deps/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp --- MSFFileParser.o --- mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po --- GDEFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT GDEFileParser.o -MD -MP -MF .deps/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp --- FullPairwiseAlign.o --- mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po --- InFileStream.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InFileStream.o -MD -MP -MF .deps/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp --- PIRFileParser.o --- mv -f .deps/PIRFileParser.Tpo .deps/PIRFileParser.Po --- ClustalFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClustalFileParser.o -MD -MP -MF .deps/ClustalFileParser.Tpo -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp --- InFileStream.o --- mv -f .deps/InFileStream.Tpo .deps/InFileStream.Po --- PearsonFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT PearsonFileParser.o -MD -MP -MF .deps/PearsonFileParser.Tpo -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp --- FileReader.o --- mv -f .deps/FileReader.Tpo .deps/FileReader.Po --- FileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT FileParser.o -MD -MP -MF .deps/FileParser.Tpo -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp --- RSFFileParser.o --- mv -f .deps/RSFFileParser.Tpo .deps/RSFFileParser.Po --- EMBLFileParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT EMBLFileParser.o -MD -MP -MF .deps/EMBLFileParser.Tpo -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp --- FileParser.o --- mv -f .deps/FileParser.Tpo .deps/FileParser.Po --- RootedClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RootedClusterTree.o -MD -MP -MF .deps/RootedClusterTree.Tpo -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/../ClusterTree.h:20, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- GDEFileParser.o --- mv -f .deps/GDEFileParser.Tpo .deps/GDEFileParser.Po --- UPGMAAlgorithm.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UPGMAAlgorithm.o -MD -MP -MF .deps/UPGMAAlgorithm.Tpo -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/UPGMAAlgorithm.h:8, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ClustalFileParser.o --- mv -f .deps/ClustalFileParser.Tpo .deps/ClustalFileParser.Po --- Node.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp --- PearsonFileParser.o --- mv -f .deps/PearsonFileParser.Tpo .deps/PearsonFileParser.Po --- RootedGuideTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -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/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedGuideTree.cpp:10: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- EMBLFileParser.o --- mv -f .deps/EMBLFileParser.Tpo .deps/EMBLFileParser.Po --- RootedTreeOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT RootedTreeOutput.o -MD -MP -MF .deps/RootedTreeOutput.Tpo -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp --- RootedGuideTree.o --- mv -f .deps/RootedGuideTree.Tpo .deps/RootedGuideTree.Po --- Tree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Tree.o -MD -MP -MF .deps/Tree.Tpo -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp --- RootedClusterTree.o --- mv -f .deps/RootedClusterTree.Tpo .deps/RootedClusterTree.Po --- ClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClusterTree.o -MD -MP -MF .deps/ClusterTree.Tpo -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/ClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Tree.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Node.o --- mv -f .deps/Node.Tpo .deps/Node.Po --- TreeInterface.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT TreeInterface.o -MD -MP -MF .deps/TreeInterface.Tpo -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp --- RootedTreeOutput.o --- In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedTreeOutput.h:15, from ./tree/UPGMA/RootedTreeOutput.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ --- UPGMAAlgorithm.o --- mv -f .deps/UPGMAAlgorithm.Tpo .deps/UPGMAAlgorithm.Po --- RootedTreeOutput.o --- ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- UnRootedClusterTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UnRootedClusterTree.o -MD -MP -MF .deps/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp --- TreeInterface.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, from ./tree/TreeInterface.cpp:15: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- RootedTreeOutput.o --- mv -f .deps/RootedTreeOutput.Tpo .deps/RootedTreeOutput.Po --- ClusterTreeOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClusterTreeOutput.o -MD -MP -MF .deps/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp --- UnRootedClusterTree.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ClusterTreeOutput.o --- In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTreeOutput.h:11, from ./tree/ClusterTreeOutput.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Tree.o --- mv -f .deps/Tree.Tpo .deps/Tree.Po --- RandomGenerator.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -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 --- NJTree.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT NJTree.o -MD -MP -MF .deps/NJTree.Tpo -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp --- ClusterTreeOutput.o --- mv -f .deps/ClusterTreeOutput.Tpo .deps/ClusterTreeOutput.Po --- AlignmentSteps.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT AlignmentSteps.o -MD -MP -MF .deps/AlignmentSteps.Tpo -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp --- UnRootedClusterTree.o --- mv -f .deps/UnRootedClusterTree.Tpo .deps/UnRootedClusterTree.Po --- InteractiveMenu.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InteractiveMenu.o -MD -MP -MF .deps/InteractiveMenu.Tpo -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp --- TreeInterface.o --- mv -f .deps/TreeInterface.Tpo .deps/TreeInterface.Po --- CommandLineParser.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT CommandLineParser.o -MD -MP -MF .deps/CommandLineParser.Tpo -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp --- InteractiveMenu.o --- In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- AlignmentSteps.o --- mv -f .deps/AlignmentSteps.Tpo .deps/AlignmentSteps.Po --- SubMatrix.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT SubMatrix.o -MD -MP -MF .deps/SubMatrix.Tpo -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp --- ClusterTree.o --- mv -f .deps/ClusterTree.Tpo .deps/ClusterTree.Po --- Iteration.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Iteration.o -MD -MP -MF .deps/Iteration.Tpo -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp --- CommandLineParser.o --- In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Iteration.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- SubMatrix.o --- In file included from ./substitutionMatrix/SubMatrix.cpp:15:0: ./substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- NJTree.o --- mv -f .deps/NJTree.Tpo .deps/NJTree.Po --- MSA.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -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 ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/MSA.h:10, from ./multipleAlign/MSA.cpp:16: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- InteractiveMenu.o --- mv -f .deps/InteractiveMenu.Tpo .deps/InteractiveMenu.Po --- MyersMillerProfileAlign.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT MyersMillerProfileAlign.o -MD -MP -MF .deps/MyersMillerProfileAlign.Tpo -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileAlignAlgorithm.h:10, from ./multipleAlign/MyersMillerProfileAlign.h:10, from ./multipleAlign/MyersMillerProfileAlign.cpp:10: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Iteration.o --- mv -f .deps/Iteration.Tpo .deps/Iteration.Po --- ProfileStandard.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ProfileStandard.o -MD -MP -MF .deps/ProfileStandard.Tpo -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, from ./multipleAlign/ProfileStandard.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- SubMatrix.o --- mv -f .deps/SubMatrix.Tpo .deps/SubMatrix.Po --- ProfileWithSub.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ProfileWithSub.o -MD -MP -MF .deps/ProfileWithSub.Tpo -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp --- ProfileStandard.o --- mv -f .deps/ProfileStandard.Tpo .deps/ProfileStandard.Po --- ProfileBase.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -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/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/ProfileBase.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- MSA.o --- mv -f .deps/MSA.Tpo .deps/MSA.Po --- LowScoreSegProfile.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT LowScoreSegProfile.o -MD -MP -MF .deps/LowScoreSegProfile.Tpo -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/LowScoreSegProfile.h:13, from ./multipleAlign/LowScoreSegProfile.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ProfileWithSub.o --- In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, from ./multipleAlign/ProfileWithSub.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- MyersMillerProfileAlign.o --- mv -f .deps/MyersMillerProfileAlign.Tpo .deps/MyersMillerProfileAlign.Po --- OutputFile.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT OutputFile.o -MD -MP -MF .deps/OutputFile.Tpo -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp --- ProfileWithSub.o --- mv -f .deps/ProfileWithSub.Tpo .deps/ProfileWithSub.Po --- UserParameters.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT UserParameters.o -MD -MP -MF .deps/UserParameters.Tpo -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp --- LowScoreSegProfile.o --- mv -f .deps/LowScoreSegProfile.Tpo .deps/LowScoreSegProfile.Po --- Utility.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Utility.o -MD -MP -MF .deps/Utility.Tpo -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp --- CommandLineParser.o --- mv -f .deps/CommandLineParser.Tpo .deps/CommandLineParser.Po --- InvalidCombination.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT InvalidCombination.o -MD -MP -MF .deps/InvalidCombination.Tpo -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp --- ProfileBase.o --- mv -f .deps/ProfileBase.Tpo .deps/ProfileBase.Po --- DebugLog.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT DebugLog.o -MD -MP -MF .deps/DebugLog.Tpo -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp --- InvalidCombination.o --- mv -f .deps/InvalidCombination.Tpo .deps/InvalidCombination.Po --- ClustalWResources.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ClustalWResources.o -MD -MP -MF .deps/ClustalWResources.Tpo -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp --- OutputFile.o --- mv -f .deps/OutputFile.Tpo .deps/OutputFile.Po --- VectorOutOfRange.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT VectorOutOfRange.o -MD -MP -MF .deps/VectorOutOfRange.Tpo -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp --- DebugLog.o --- mv -f .deps/DebugLog.Tpo .deps/DebugLog.Po --- SymMatrix.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT SymMatrix.o -MD -MP -MF .deps/SymMatrix.Tpo -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp --- VectorOutOfRange.o --- mv -f .deps/VectorOutOfRange.Tpo .deps/VectorOutOfRange.Po --- Stats.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp --- SymMatrix.o --- mv -f .deps/SymMatrix.Tpo .deps/SymMatrix.Po --- Help.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Help.o -MD -MP -MF .deps/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp --- Stats.o --- In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: ./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ClustalWResources.o --- mv -f .deps/ClustalWResources.Tpo .deps/ClustalWResources.Po --- Alignment.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Alignment.o -MD -MP -MF .deps/Alignment.Tpo -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./alignment/Alignment.h:42, from ./alignment/Alignment.cpp:25: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Utility.o --- mv -f .deps/Utility.Tpo .deps/Utility.Po --- AlignmentOutput.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT AlignmentOutput.o -MD -MP -MF .deps/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp --- Stats.o --- mv -f .deps/Stats.Tpo .deps/Stats.Po --- ObjectiveScore.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT ObjectiveScore.o -MD -MP -MF .deps/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp --- UserParameters.o --- mv -f .deps/UserParameters.Tpo .deps/UserParameters.Po --- Sequence.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Sequence.o -MD -MP -MF .deps/Sequence.Tpo -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp --- AlignmentOutput.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./alignment/Alignment.h:42, from ./alignment/AlignmentOutput.h:24, from ./alignment/AlignmentOutput.cpp:27: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ObjectiveScore.o --- In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./alignment/ObjectiveScore.h:15, from ./alignment/ObjectiveScore.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Help.o --- mv -f .deps/Help.Tpo .deps/Help.Po --- Clustal.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT Clustal.o -MD -MP -MF .deps/Clustal.Tpo -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp --- ObjectiveScore.o --- mv -f .deps/ObjectiveScore.Tpo .deps/ObjectiveScore.Po --- main.o --- c++ -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -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/../substitutionMatrix/globalmatrix.h:8:0, from ./alignment/Alignment.h:42, from ./main.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Clustal.o --- In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Sequence.o --- mv -f .deps/Sequence.Tpo .deps/Sequence.Po --- main.o --- mv -f .deps/main.Tpo .deps/main.Po --- Alignment.o --- mv -f .deps/Alignment.Tpo .deps/Alignment.Po --- AlignmentOutput.o --- mv -f .deps/AlignmentOutput.Tpo .deps/AlignmentOutput.Po --- Clustal.o --- mv -f .deps/Clustal.Tpo .deps/Clustal.Po --- clustalw2 --- c++ -pipe -O2 -fno-strict-aliasing -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 Iteration.o:Iteration.cpp:function clustalw::Iteration::removeFirstIterate(clustalw::Alignment*): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for clustalw-2.1_1 ===> Generating temporary packing list Making install in m4 test -z "/usr/local/share/aclocal" || /bin/mkdir -p "/wrkdirs/biology/clustalw/stage/usr/local/share/aclocal" Making install in src test -z "/usr/local/bin" || /bin/mkdir -p "/wrkdirs/biology/clustalw/stage/usr/local/bin" install -s -m 555 clustalw2 '/wrkdirs/biology/clustalw/stage/usr/local/bin' ln -sf clustalw2 /wrkdirs/biology/clustalw/stage/usr/local/bin/clustalw ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for clustalw-2.1_1 file sizes/checksums [2]: . done packing files [2]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for clustalw-2.1_1 build of biology/clustalw ended at Tue Oct 4 01:54:50 PDT 2016 build time: 00:01:02