=>> Building biology/clustalw build started at Mon Jul 6 04:54:07 JST 2026 port directory: /usr/ports/biology/clustalw package name: clustalw-2.1_3 building for: FreeBSD s15amd64-setuptools2-job-08 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 537 Apr 13 23:05 /usr/ports/biology/clustalw/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 1c3394560c4f3b7e3e79480f17b767e3a58bd951 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 08 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-setuptools2 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustalw/work/.cache HOME=/wrkdirs/usr/ports/biology/clustalw/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustalw/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/clustalw/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustalw/work/.cache HOME=/wrkdirs/usr/ports/biology/clustalw/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustalw/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/clustalw/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=15.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib 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 PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License LGPL3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> clustalw-2.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-08] Installing pkg-2.7.5... [s15amd64-setuptools2-job-08] Extracting pkg-2.7.5: .......... done ===> clustalw-2.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustalw-2.1_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License LGPL3 accepted by the user => clustalw-2.1.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/clustalw-2.1.tar.gz clustalw-2.1.tar.gz 342 kB 274 kBps 01s ===> Fetching all distfiles required by clustalw-2.1_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalw-2.1_3 for building => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalw-2.1_3 for building ===> Extracting for clustalw-2.1_3 => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for clustalw-2.1_3 ===> Applying FreeBSD patches for clustalw-2.1_3 from /usr/ports/biology/clustalw/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for clustalw-2.1_3 configure: loading site script /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd15.1 checking host system type... amd64-portbld-freebsd15.1 checking target system type... amd64-portbld-freebsd15.1 building for freebsd15.1 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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for clustalw-2.1_3 Making all in m4 Making all in src /usr/bin/make all-recursive c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp In file included from ./pairwise/FullPairwiseAlign.cpp:9: In 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.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:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp In file included from ./fileInput/FileReader.cpp:29: 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./fileInput/FileReader.cpp:29: ./fileInput/FileReader.h:42:38: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./fileInput/FileReader.cpp:155:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 155 | auto_ptr fileParser; // Means we dont need to delete it! | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./fileInput/FileReader.cpp:426:42: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 5 warnings generated. mv -f .deps/FileReader.Tpo .deps/FileReader.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT PIRFileParser.o -MD -MP -MF .deps/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp mv -f .deps/PIRFileParser.Tpo .deps/PIRFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT RSFFileParser.o -MD -MP -MF .deps/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp mv -f .deps/RSFFileParser.Tpo .deps/RSFFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT GDEFileParser.o -MD -MP -MF .deps/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp mv -f .deps/GDEFileParser.Tpo .deps/GDEFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT InFileStream.o -MD -MP -MF .deps/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp mv -f .deps/InFileStream.Tpo .deps/InFileStream.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/ClustalFileParser.Tpo .deps/ClustalFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/PearsonFileParser.Tpo .deps/PearsonFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT FileParser.o -MD -MP -MF .deps/FileParser.Tpo -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp ./fileInput/FileParser.cpp:37:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 37 | register int i; | ^~~~~~~~ ./fileInput/FileParser.cpp:38:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 38 | register char c; | ^~~~~~~~ 2 warnings generated. mv -f .deps/FileParser.Tpo .deps/FileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/EMBLFileParser.Tpo .deps/EMBLFileParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 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:23: ./tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: In file included from ./tree/UPGMA/RootedClusterTree.h:8: ./tree/UPGMA/../ClusterTree.h:70:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 21 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 9 warnings generated. mv -f .deps/RootedClusterTree.Tpo .deps/RootedClusterTree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 5 warnings generated. mv -f .deps/UPGMAAlgorithm.Tpo .deps/UPGMAAlgorithm.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp mv -f .deps/Node.Tpo .deps/Node.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/RootedGuideTree.Tpo .deps/RootedGuideTree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT RootedTreeOutput.o -MD -MP -MF .deps/RootedTreeOutput.Tpo -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/RootedTreeOutput.Tpo .deps/RootedTreeOutput.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./tree/Tree.cpp:10: ./tree/Tree.h:26:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/Tree.cpp:278:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/Tree.cpp:280:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 280 | auto_ptr progAlignSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 5 warnings generated. mv -f .deps/Tree.Tpo .deps/Tree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./tree/ClusterTree.cpp:9: In file included from ./tree/ClusterTree.h:23: ./tree/../general/OutputFile.h:26:14: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/ClusterTree.cpp:9: ./tree/ClusterTree.h:70:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 4 warnings generated. mv -f .deps/ClusterTree.Tpo .deps/ClusterTree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT TreeInterface.o -MD -MP -MF .deps/TreeInterface.Tpo -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:38:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:57:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:102:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:108:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:133:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:138:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:142:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:17: In file included from ./tree/UnRootedClusterTree.h:8: In file included from ./tree/ClusterTree.h:23: ./tree/../general/OutputFile.h:26:14: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:17: In file included from ./tree/UnRootedClusterTree.h:8: ./tree/ClusterTree.h:70:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:18: ./tree/Tree.h:26:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/TreeInterface.cpp:23: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:31:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 31 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:103:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 103 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:195:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 195 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:200:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 200 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:208:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 208 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:214:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 214 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:439:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 439 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:445:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 445 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:485:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 485 | auto_ptr | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:490:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 490 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:503:1: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 503 | auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./tree/TreeInterface.cpp:506:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 506 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 25 warnings generated. mv -f .deps/TreeInterface.Tpo .deps/TreeInterface.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT UnRootedClusterTree.o -MD -MP -MF .deps/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | 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:23: ./tree/../general/OutputFile.h:26:14: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./tree/UnRootedClusterTree.cpp:9: In file included from ./tree/UnRootedClusterTree.h:8: ./tree/ClusterTree.h:70:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 4 warnings generated. mv -f .deps/UnRootedClusterTree.Tpo .deps/UnRootedClusterTree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT ClusterTreeOutput.o -MD -MP -MF .deps/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/ClusterTreeOutput.Tpo .deps/ClusterTreeOutput.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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 c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT NJTree.o -MD -MP -MF .deps/NJTree.Tpo -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp ./tree/NJTree.cpp:164:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 164 | register int i; | ^~~~~~~~ 1 warning generated. mv -f .deps/NJTree.Tpo .deps/NJTree.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT AlignmentSteps.o -MD -MP -MF .deps/AlignmentSteps.Tpo -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp mv -f .deps/AlignmentSteps.Tpo .deps/AlignmentSteps.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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 ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:18: In file included from ./interface/../fileInput/FileReader.h:12: In file included from ./interface/../fileInput/../alignment/Alignment.h:42: In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:18: ./interface/../fileInput/FileReader.h:42:38: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/InteractiveMenu.cpp:23: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 12 warnings generated. mv -f .deps/InteractiveMenu.Tpo .deps/InteractiveMenu.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT CommandLineParser.o -MD -MP -MF .deps/CommandLineParser.Tpo -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.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 ./interface/../fileInput/FileReader.h:12: In file included from ./interface/../fileInput/../alignment/Alignment.h:42: In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:18: ./interface/../fileInput/FileReader.h:42:38: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./interface/CommandLineParser.cpp:13: In file included from ./interface/CommandLineParser.h:18: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 12 warnings generated. mv -f .deps/CommandLineParser.Tpo .deps/CommandLineParser.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT SubMatrix.o -MD -MP -MF .deps/SubMatrix.Tpo -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp In file included from ./substitutionMatrix/SubMatrix.cpp:15: ./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/SubMatrix.Tpo .deps/SubMatrix.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Iteration.o -MD -MP -MF .deps/Iteration.Tpo -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:38:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:57:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:102:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:108:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:133:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:138:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:142:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 9 warnings generated. mv -f .deps/Iteration.Tpo .deps/Iteration.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/MSA.Tpo .deps/MSA.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/MyersMillerProfileAlign.Tpo .deps/MyersMillerProfileAlign.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/ProfileStandard.Tpo .deps/ProfileStandard.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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 ./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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/ProfileWithSub.Tpo .deps/ProfileWithSub.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/ProfileBase.Tpo .deps/ProfileBase.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/LowScoreSegProfile.Tpo .deps/LowScoreSegProfile.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT OutputFile.o -MD -MP -MF .deps/OutputFile.Tpo -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp In file included from ./general/OutputFile.cpp:9: ./general/OutputFile.h:26:14: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. mv -f .deps/OutputFile.Tpo .deps/OutputFile.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT UserParameters.o -MD -MP -MF .deps/UserParameters.Tpo -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp ./general/UserParameters.cpp:475:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 475 | register int i; | ^~~~~~~~ 1 warning generated. mv -f .deps/UserParameters.Tpo .deps/UserParameters.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Utility.o -MD -MP -MF .deps/Utility.Tpo -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp ./general/Utility.cpp:53:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 53 | register int p; | ^~~~~~~~ 1 warning generated. mv -f .deps/Utility.Tpo .deps/Utility.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT InvalidCombination.o -MD -MP -MF .deps/InvalidCombination.Tpo -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp mv -f .deps/InvalidCombination.Tpo .deps/InvalidCombination.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT DebugLog.o -MD -MP -MF .deps/DebugLog.Tpo -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp mv -f .deps/DebugLog.Tpo .deps/DebugLog.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT ClustalWResources.o -MD -MP -MF .deps/ClustalWResources.Tpo -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp ./general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (that has type 'char[1]') [-Warray-bounds] 106 | delim[1] = 0; | ^ ~ ./general/ClustalWResources.cpp:104:5: note: array 'delim' declared here 104 | char delim[1]; | ^ 1 warning generated. mv -f .deps/ClustalWResources.Tpo .deps/ClustalWResources.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT VectorOutOfRange.o -MD -MP -MF .deps/VectorOutOfRange.Tpo -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp ./general/VectorOutOfRange.cpp:28:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] 28 | return outputMessage.c_str(); | ^~~~~~~~~~~~~ ./general/VectorOutOfRange.cpp:37:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] 37 | return outputMessage.c_str(); | ^~~~~~~~~~~~~ 2 warnings generated. mv -f .deps/VectorOutOfRange.Tpo .deps/VectorOutOfRange.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/SymMatrix.Tpo .deps/SymMatrix.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/Stats.Tpo .deps/Stats.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Help.o -MD -MP -MF .deps/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp mv -f .deps/Help.Tpo .deps/Help.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ ./alignment/Alignment.cpp:47:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 47 | register int sl; /* which have code = gap_pos2 */ | ^~~~~~~~ ./alignment/Alignment.cpp:122:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 122 | register int sl; /* which have code = gap_pos2 */ | ^~~~~~~~ ./alignment/Alignment.cpp:617:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] 617 | register int sl; | ^~~~~~~~ 5 warnings generated. mv -f .deps/Alignment.Tpo .deps/Alignment.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT AlignmentOutput.o -MD -MP -MF .deps/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:69:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:75:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:76:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:77:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:78:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:79:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:80:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:81:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./alignment/AlignmentOutput.cpp:512:40: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 512 | bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./alignment/AlignmentOutput.cpp:535:40: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 535 | string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 13 warnings generated. mv -f .deps/AlignmentOutput.Tpo .deps/AlignmentOutput.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT ObjectiveScore.o -MD -MP -MF .deps/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ 2 warnings generated. mv -f .deps/ObjectiveScore.Tpo .deps/ObjectiveScore.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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/Sequence.Tpo .deps/Sequence.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT Clustal.o -MD -MP -MF .deps/Clustal.Tpo -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:18: ./fileInput/FileReader.h:42:38: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:69:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:75:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:76:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:77:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:78:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:79:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:80:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:27: In file included from ./Clustal.h:20: ./alignment/AlignmentOutput.h:81:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:38:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:57:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:102:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:108:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:133:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:138:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:142:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./Clustal.cpp:162:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 162 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ ./Clustal.cpp:837:5: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 837 | auto_ptr progSteps; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 21 warnings generated. mv -f .deps/Clustal.Tpo .deps/Clustal.Po c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp 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: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^ In file included from ./main.cpp:16: ./fileInput/FileReader.h:42:38: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:68:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:69:31: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:75:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:76:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:77:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:78:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:79:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:80:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from ./main.cpp:17: In file included from ./interface/InteractiveMenu.h:15: In file included from ./interface/../Clustal.h:20: ./interface/../alignment/AlignmentOutput.h:81:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^ /usr/include/c++/v1/__memory/auto_ptr.h:29:7: note: 'auto_ptr' has been explicitly marked deprecated here 29 | class _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr { | ^ /usr/include/c++/v1/__config:728:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 728 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 12 warnings generated. mv -f .deps/main.Tpo .deps/main.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++14 -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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for clustalw-2.1_3 ===> Generating temporary packing list Making install in m4 test -z "/usr/local/share/aclocal" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustalw/work/stage/usr/local/share/aclocal" Making install in src test -z "/usr/local/bin" || /bin/mkdir -p "/wrkdirs/usr/ports/biology/clustalw/work/stage/usr/local/bin" install -s -m 555 clustalw2 '/wrkdirs/usr/ports/biology/clustalw/work/stage/usr/local/bin' /bin/ln -sf clustalw2 /wrkdirs/usr/ports/biology/clustalw/work/stage/usr/local/bin/clustalw ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-07-05T19:54:07+0000' 'PKG_NOTE_ports_top_git_hash=18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1c3394560c4f3b7e3e79480f17b767e3a58bd951' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.8' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for clustalw-2.1_3 ===> Building clustalw-2.1_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for clustalw-2.1_3 build of biology/clustalw | clustalw-2.1_3 ended at Mon Jul 6 04:56:15 JST 2026 build time: 00:02:09