=> Building biology/clustalx Started : Friday, 15 MAR 2019 at 13:04:45 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- QT_SELECT=qt4 QMAKEMODULES="/construction/biology/clustalx/clustalx-2.1/mkspecs/modules:/usr/local/share/qt4/mkspecs/modules" QTDIR="/usr/local/lib/qt4" QMAKE="/usr/local/lib/qt4/bin/qmake" MOC="/usr/local/lib/qt4/bin/moc" RCC="/usr/local/lib/qt4/bin/rcc" UIC="/usr/local/lib/qt4/bin/uic" QMAKESPEC="/usr/local/share/qt4/mkspecs/freebsd-g++" XDG_DATA_HOME=/construction/biology/clustalx XDG_CONFIG_HOME=/construction/biology/clustalx HOME=/construction/biology/clustalx TMPDIR="/tmp" PATH=/construction/biology/clustalx/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --with-qt-includes=/usr/local/include/qt4 --with-qt-libraries=/usr/local/lib/qt4 --with-extra-includes=/usr/local/include --with-extra-libs=/usr/local/lib -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- QT_SELECT=qt4 QMAKEMODULES="/construction/biology/clustalx/clustalx-2.1/mkspecs/modules:/usr/local/share/qt4/mkspecs/modules" XDG_DATA_HOME=/construction/biology/clustalx XDG_CONFIG_HOME=/construction/biology/clustalx HOME=/construction/biology/clustalx TMPDIR="/tmp" PATH=/construction/biology/clustalx/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- INSTALL_ROOT=/construction/biology/clustalx/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- QT_BINDIR="lib/qt4/bin" QT_INCDIR="include/qt4" QT_LIBDIR="lib/qt4" QT_ARCHDIR="lib/qt4" QT_PLUGINDIR="lib/qt4/plugins" QT_LIBEXECDIR="libexec/qt4" QT_IMPORTDIR="lib/qt4/imports" QT_QMLDIR="lib/qt4/qml" QT_DATADIR="share/qt4" QT_DOCDIR="share/doc/qt4" QT_L10NDIR="share/qt4/translations" QT_EXAMPLEDIR="share/examples/qt4" QT_TESTDIR="share/qt4/tests" QT_MKSPECDIR="share/qt4/mkspecs" QT_QTCHOOSERDIR="etc/xdg/qtchooser" DEBUG="@comment " OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/clustalx" EXAMPLESDIR="share/examples/clustalx" DATADIR="share/clustalx" WWWDIR="www/clustalx" ETCDIR="etc/clustalx" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clustalx DOCSDIR=/usr/local/share/doc/clustalx EXAMPLESDIR=/usr/local/share/examples/clustalx WWWDIR=/usr/local/www/clustalx ETCDIR=/usr/local/etc/clustalx -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> License LGPL3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> clustalx-2.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> clustalx-2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalx-2.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalx-2.1 for building => SHA256 Checksum OK for clustalx-2.1.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalx-2.1 for building ===> Extracting for clustalx-2.1 => SHA256 Checksum OK for clustalx-2.1.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for clustalx-2.1 ===> Applying ports patches for clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> clustalx-2.1 depends on file: /usr/local/lib/qt4/bin/moc - not found ===> Installing existing package /packages/All/qt4-moc-4.8.7_2.txz Installing qt4-moc-4.8.7_2... `-- Installing qtchooser-66... `-- Extracting qtchooser-66: .......... done Extracting qt4-moc-4.8.7_2: .... done Message from qtchooser-66: qtchooser is a wrapper that allows selecting whether Qt4 or Qt5 binaries for qmake, moc and other tools will be run when invoking the binaries in $PATH. By default, the Qt5 versions are run. It is possible to change the behavior by setting the QT_SELECT environment variable to "qt4". See qtchooser(1) for more information. Message from qt4-moc-4.8.7_2: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> clustalx-2.1 depends on file: /usr/local/lib/qt4/bin/moc - found ===> Returning to build of clustalx-2.1 ===> clustalx-2.1 depends on file: /usr/local/lib/qt4/bin/qmake - not found ===> Installing existing package /packages/All/qt4-qmake-4.8.7_2.txz Installing qt4-qmake-4.8.7_2... Extracting qt4-qmake-4.8.7_2: .......... done Message from qt4-qmake-4.8.7_2: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> clustalx-2.1 depends on file: /usr/local/lib/qt4/bin/qmake - found ===> Returning to build of clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> clustalx-2.1 depends on shared library: libQtCore.so - not found ===> Installing existing package /packages/All/qt4-corelib-4.8.7_14.txz Installing qt4-corelib-4.8.7_14... `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done `-- Installing glib-2.56.3_3,1... | `-- Installing libffi-3.2.1_3... | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libiconv-1.14_11... | `-- Extracting libiconv-1.14_11: .......... done | `-- Installing libxml2-2.9.8... | `-- Extracting libxml2-2.9.8: .......... done | `-- Installing pcre-8.42_1... | `-- Extracting pcre-8.42_1: .......... done | `-- Installing python27-2.7.15... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing libressl-2.8.3... | | `-- Extracting libressl-2.8.3: .......... done | | `-- Installing ncurses-6.1.20190112... | | `-- Extracting ncurses-6.1.20190112: .......... done | | `-- Installing readline-7.0.5... | | `-- Extracting readline-7.0.5: .......... done | `-- Extracting python27-2.7.15: .......... done `-- Extracting glib-2.56.3_3,1: .......... done No schema files found: doing nothing. `-- Installing icu-63.1_1,1... `-- Extracting icu-63.1_1,1: .......... done Extracting qt4-corelib-4.8.7_14: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from qt4-corelib-4.8.7_14: ====================================================================== Qt 4 can be built with optional support for: - Common UNIX Printing System (CUPS) (enabled by default) - Network Audio System (NAS) - Qt style that renders using GTK (QGTKSTYLE) In order to enable them, you have to add QT4_OPTIONS= CUPS NAS QGTKSTYLE to your /etc/make.conf and compile devel/qt4-corelib and x11-toolkits/qt4-gui ports. Attention! Whenever you change the QT4_OPTIONS both devel/qt4-corelib and x11-toolkits/qt4-gui ports must be rebuilt! ====================================================================== ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> clustalx-2.1 depends on shared library: libQtCore.so - found (/usr/local/lib/qt4/libQtCore.so) ===> Returning to build of clustalx-2.1 ===> clustalx-2.1 depends on shared library: libQtGui.so - not found ===> Installing existing package /packages/All/qt4-gui-4.8.7_6.txz Installing qt4-gui-4.8.7_6... `-- Installing cups-2.2.10... | `-- Installing avahi-app-0.7_2... | | `-- Installing dbus-1.12.12... | | `-- Installing libICE-1.0.9_3,1... | | `-- Extracting libICE-1.0.9_3,1: .......... done | | `-- Installing libSM-1.2.3,1... | | `-- Extracting libSM-1.2.3,1: .......... done | | `-- Installing libX11-1.6.7,1... | | | `-- Installing libXau-1.0.8_5... | | | `-- Extracting libXau-1.0.8_5: .......... done | | | `-- Installing libXdmcp-1.1.2_2... | | | `-- Installing xorgproto-2018.4... | | | `-- Extracting xorgproto-2018.4: .......... done | | | `-- Extracting libXdmcp-1.1.2_2: ......... done | | | `-- Installing libxcb-1.13.1... | | | `-- Installing libpthread-stubs-0.4... | | | `-- Extracting libpthread-stubs-0.4: .... done | | | `-- Extracting libxcb-1.13.1: .......... done | | `-- Extracting libX11-1.6.7,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | `-- Extracting dbus-1.12.12: ......... done | | `-- Installing dbus-glib-0.110... | | `-- Extracting dbus-glib-0.110: .......... done | | `-- Installing gdbm-1.18.1... | | `-- Extracting gdbm-1.18.1: .......... done | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: .... done | | `-- Installing gobject-introspection-1.56.1,1... | | `-- Installing python36-3.6.8... | | `-- Extracting python36-3.6.8: .......... done | | `-- Extracting gobject-introspection-1.56.1,1: .......... done | | `-- Installing libdaemon-0.14_1... | | `-- Extracting libdaemon-0.14_1: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. | `-- Extracting avahi-app-0.7_2: .......... done | `-- Installing gnutls-3.6.6_2... | | `-- Installing ca_root_nss-3.42.1... | | `-- Extracting ca_root_nss-3.42.1: ........ done | | `-- Installing gmp-6.1.2_1... | | `-- Extracting gmp-6.1.2_1: .......... done | | `-- Installing libidn2-2.1.1... | | `-- Installing libunistring-0.9.10_1... | | `-- Extracting libunistring-0.9.10_1: .......... done | | `-- Extracting libidn2-2.1.1: .......... done | | `-- Installing libtasn1-4.13_1... | | `-- Extracting libtasn1-4.13_1: .......... done | | `-- Installing nettle-3.4.1_1... | | `-- Extracting nettle-3.4.1_1: .......... done | | `-- Installing p11-kit-0.23.15... | | `-- Extracting p11-kit-0.23.15: .......... done | | `-- Installing trousers-0.3.14_2... | | `-- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting tpm-emulator-0.7.4_2: ......... done ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. | | `-- Extracting trousers-0.3.14_2: .......... done | `-- Extracting gnutls-3.6.6_2: .......... done | `-- Installing libpaper-1.1.24.4... | `-- Extracting libpaper-1.1.24.4: .......... done ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. `-- Extracting cups-2.2.10: .......... done `-- Installing encodings-1.0.4_4,1... | `-- Installing font-util-1.3.1... | `-- Extracting font-util-1.3.1: .......... done `-- Extracting encodings-1.0.4_4,1: .......... done `-- Installing fontconfig-2.12.6,1... | `-- Installing freetype2-2.9.1... | `-- Extracting freetype2-2.9.1: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: caching, new cache contents: 0 fonts, 2 dirs /usr/local/share/fonts/encodings: caching, new cache contents: 0 fonts, 1 dirs /usr/local/share/fonts/encodings/large: caching, new cache contents: 0 fonts, 0 dirs /usr/local/share/fonts/util: caching, new cache contents: 0 fonts, 0 dirs /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded `-- Installing libXcursor-1.1.15_2... | `-- Installing libXfixes-5.0.3_2... | `-- Extracting libXfixes-5.0.3_2: .......... done | `-- Installing libXrender-0.9.10_2... | `-- Extracting libXrender-0.9.10_2: .......... done `-- Extracting libXcursor-1.1.15_2: .......... done `-- Installing libXext-1.3.3_3,1... `-- Extracting libXext-1.3.3_3,1: .......... done `-- Installing libXi-1.7.9_2,1... `-- Extracting libXi-1.7.9_2,1: .......... done `-- Installing libXinerama-1.1.4_2,1... `-- Extracting libXinerama-1.1.4_2,1: .......... done `-- Installing libXrandr-1.5.1_2... `-- Extracting libXrandr-1.5.1_2: .......... done `-- Installing libXt-1.1.5_2,1... `-- Extracting libXt-1.1.5_2,1: .......... done `-- Installing png-1.6.36... `-- Extracting png-1.6.36: .......... done `-- Installing xdg-utils-1.1.3... | `-- Installing hicolor-icon-theme-0.17... | `-- Extracting hicolor-icon-theme-0.17: . done | `-- Installing xprop-1.2.3... | | `-- Installing libXmu-1.1.2_5,1... | | `-- Extracting libXmu-1.1.2_5,1: .......... done | `-- Extracting xprop-1.2.3: .. done | `-- Installing xset-1.2.4_2... | | `-- Installing libXfontcache-1.0.5_5... | | `-- Extracting libXfontcache-1.0.5_5: .......... done | `-- Extracting xset-1.2.4_2: .. done `-- Extracting xdg-utils-1.1.3: .......... done `-- Installing xorg-fonts-truetype-7.7_1... | `-- Installing dejavu-2.37... | | `-- Installing mkfontdir-1.0.7... | | `-- Installing mkfontscale-1.1.3_2... | | | `-- Installing libfontenc-1.1.4... | | | `-- Extracting libfontenc-1.1.4: ......... done | | `-- Extracting mkfontscale-1.1.3_2: ..... done | | `-- Extracting mkfontdir-1.0.7: ..... done | `-- Extracting dejavu-2.37: .......... done | `-- Installing font-bh-ttf-1.0.3_3... | `-- Extracting font-bh-ttf-1.0.3_3: .......... done | `-- Installing font-misc-ethiopic-1.0.3_3... | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done | `-- Installing font-misc-meltho-1.0.3_3... | `-- Extracting font-misc-meltho-1.0.3_3: .......... done Extracting qt4-gui-4.8.7_6: .......... done Message from python36-3.6.8: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from ca_root_nss-3.42.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from trousers-0.3.14_2: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. Message from qt4-gui-4.8.7_6: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> clustalx-2.1 depends on shared library: libQtGui.so - found (/usr/local/lib/qt4/libQtGui.so) ===> Returning to build of clustalx-2.1 ===> clustalx-2.1 depends on shared library: libQtXml.so - not found ===> Installing existing package /packages/All/qt4-xml-4.8.7_2.txz Installing qt4-xml-4.8.7_2... Extracting qt4-xml-4.8.7_2: .......... done Message from qt4-xml-4.8.7_2: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Qt4 has been EOL since december 2015. It is scheduled to be removed on or after 2019-03-15. ===> clustalx-2.1 depends on shared library: libQtXml.so - found (/usr/local/lib/qt4/libQtXml.so) ===> Returning to build of clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for clustalx-2.1 --- moc_AlignmentFormatOptions.cpp --- --- moc_AlignmentParameters.cpp --- --- moc_AlignmentViewerWidget.cpp --- --- moc_AlignmentWidget.cpp --- --- moc_AlignOutputFileNames.cpp --- --- moc_AlignmentViewerWidget.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp --- moc_AlignmentFormatOptions.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp --- moc_AlignmentWidget.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include AlignmentWidget.h -o moc_AlignmentWidget.cpp --- moc_AlignOutputFileNames.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp --- moc_AlignmentParameters.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include AlignmentParameters.h -o moc_AlignmentParameters.cpp --- moc_BootstrapTreeDialog.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp --- moc_ColorFileXmlParser.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp --- moc_ColumnScoreParams.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp --- moc_FileDialog.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include FileDialog.h -o moc_FileDialog.cpp --- moc_HelpDisplayWidget.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp --- moc_HistogramWidget.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include HistogramWidget.h -o moc_HistogramWidget.cpp --- moc_LowScoringSegParams.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include LowScoringSegParams.h -o moc_LowScoringSegParams.cpp --- moc_mainwindow.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include mainwindow.h -o moc_mainwindow.cpp --- moc_PairwiseParams.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include PairwiseParams.h -o moc_PairwiseParams.cpp --- moc_ProteinGapParameters.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp --- moc_PSPrinter.cpp --- --- moc_SaveSeqFile.cpp --- --- moc_PSPrinter.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include PSPrinter.h -o moc_PSPrinter.cpp --- moc_SaveSeqFile.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include SaveSeqFile.h -o moc_SaveSeqFile.cpp --- moc_SearchForString.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include SearchForString.h -o moc_SearchForString.cpp --- moc_SecStructOptions.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include SecStructOptions.h -o moc_SecStructOptions.cpp --- moc_SeqNameWidget.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include SeqNameWidget.h -o moc_SeqNameWidget.cpp --- moc_TreeFormatOptions.cpp --- --- moc_TreeOutputFileNames.cpp --- --- moc_TreeFormatOptions.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include TreeFormatOptions.h -o moc_TreeFormatOptions.cpp --- moc_TreeOutputFileNames.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include TreeOutputFileNames.h -o moc_TreeOutputFileNames.cpp --- moc_WritePostscriptFile.cpp --- /usr/local/lib/qt4/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include WritePostscriptFile.h -o moc_WritePostscriptFile.cpp --- AlignmentFormatOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp --- AlignmentParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentParameters.o AlignmentParameters.cpp --- AlignmentViewerWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentViewerWidget.o AlignmentViewerWidget.cpp --- AlignmentWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentWidget.o AlignmentWidget.cpp --- AlignOutputFileNames.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignOutputFileNames.o AlignOutputFileNames.cpp --- AlignmentViewerWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- AlignmentParameters.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)': AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] void AlignmentParameters::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ --- AlignmentViewerWidget.o --- In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from AlignmentViewerWidget.cpp:68: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': AlignmentViewerWidget.cpp:588:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = 0; i < len && i < gapMask->size(); i++) ~~^~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeSecStructData()': AlignmentViewerWidget.cpp:645:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (i = 0; i < len && i < _secStructMask->size();i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp:652:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = 0; i < len && i < ssMask.size(); i++) ~~^~~~~~~~~~~~~~~ AlignmentViewerWidget.cpp: In member function 'virtual void AlignmentViewerWidget::resizeEvent(QResizeEvent*)': AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) ~~~~~~~~~~~~~~~^~~~~ --- AlignmentWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from AlignmentWidget.cpp:49: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from AlignmentWidget.cpp:49: AlignmentWidget.h: In constructor 'AlignmentWidget::AlignmentWidget(int, int, QFont*, QWidget*)': AlignmentWidget.h:170:10: warning: 'AlignmentWidget::blackAndWhite' will be initialized after [-Wreorder] bool blackAndWhite; ^~~~~~~~~~~~~ AlignmentWidget.h:161:27: warning: 'std::vector >* AlignmentWidget::selectedColoredRes' [-Wreorder] std::vector* selectedColoredRes; ^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:65:1: warning: when initialized here [-Wreorder] AlignmentWidget::AlignmentWidget(int boxwidth, int boxsize, QFont* font, QWidget *parent) ^~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] for(unsigned int j = 0; j < lengthLongestSeq; j++) ~~^~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:235:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(code >= 0 && code < conservationPixmaps->size()) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:268:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:280:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:291:86: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] if(colMask.getRowSize() > (i - extraRow) && colMask.getColSize() > j) ~~~~~~~~~~~~~~~~~~~~~^~~ AlignmentWidget.cpp:215:9: warning: unused variable 'codeForSpace' [-Wunused-variable] int codeForSpace = clustalw::userParameters->resIndex( ^~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generateSecStructurePixmaps()': AlignmentWidget.cpp:333:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(i < secStructPixmaps->size() && i < secStructInfo.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::drawContents(QPainter*, int, int, int, int)': AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(selectedRes >= selectedColoredRes->size()) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int j = 1; j <= strongGroup.size(); j++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:693:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int j = 1; j <= weakGroup.size(); j++) ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:700:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if((i + _fRes - 1 < (*alignment)[j].size()) && ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:701:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] (i + _fRes - 1 < (*alignment)[_fSeq].size())) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:725:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp:771:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ~~^~~~~~~~~~~~~~~~~~~ --- AlignOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from AlignOutputFileNames.h:10, from AlignOutputFileNames.cpp:26: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from AlignOutputFileNames.cpp:26: AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from AlignOutputFileNames.h:9, from AlignOutputFileNames.cpp:26: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- AlignmentWidget.o --- AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': AlignmentWidget.cpp:878:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int j = 0; j < aminoAcid.size(); j++) ~~^~~~~~~~~~~~~~~~~~ --- BootstrapTreeDialog.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp --- ColorFileXmlParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ColorFileXmlParser.o ColorFileXmlParser.cpp ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] // tr("colorrules not found in the parameter file, using\ ^ --- ColorParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ColorParameters.o ColorParameters.cpp --- ColumnScoreParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ColumnScoreParams.o ColumnScoreParams.cpp --- FileDialog.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o FileDialog.o FileDialog.cpp --- ColorParameters.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorParameters.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)': ColorParameters.cpp:160:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = 0; i < colorPar.size(); i++) ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:174:26: warning: unused variable 'temp' [-Wunused-variable] char temp = colorPar[i].consensusConditionList[j].toAscii(); ^~~~ ColorParameters.cpp:157:10: warning: unused variable 'showRes' [-Wunused-variable] char showRes = res.toAscii(); ^~~~~~~ ColorParameters.cpp:158:10: warning: unused variable 'showCon' [-Wunused-variable] char showCon = consensus.toAscii(); ^~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getResidueColorNum(QChar, QChar)': ColorParameters.cpp:197:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = 0; i < colorPar.size(); i++) ~~^~~~~~~~~~~~~~~~~ ColorParameters.cpp:211:26: warning: unused variable 'temp' [-Wunused-variable] char temp = colorPar[i].consensusConditionList[j].toAscii(); ^~~~ ColorParameters.cpp:194:10: warning: unused variable 'showRes' [-Wunused-variable] char showRes = res.toAscii(); ^~~~~~~ ColorParameters.cpp:195:10: warning: unused variable 'showCon' [-Wunused-variable] char showCon = consensus.toAscii(); ^~~~~~~ ColorParameters.cpp: In member function 'void ColorParameters::printColorInfo()': ColorParameters.cpp:229:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 0; i < colors.size(); i++) ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'int ColorParameters::getIndexOfColor(QColor)': ColorParameters.cpp:238:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 0; i < colors.size(); i++) ~~^~~~~~~~~~~~~~~ ColorParameters.cpp: In member function 'QColor ColorParameters::getColorFromNum(int)': ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(colorNum > 0 && colorNum - 1 < colorPar.size()) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ --- BootstrapTreeDialog.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from BootstrapTreeDialog.cpp:18: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from BootstrapTreeDialog.cpp:18: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from BootstrapTreeDialog.h:10, from BootstrapTreeDialog.cpp:18: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- ColorFileXmlParser.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from ColorFileXmlParser.cpp:3: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] QTreeWidgetItem *parentItem) ~~~~~~~~~~~~~~~~~^~~~~~~~~~ ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) ~~~~~~~~~~~~~~~~~^~~~~~~~~~ ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)': ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) ~~~~~~~~~~~~~~~~~^~~~~~~~~~ --- HardCodedColorScheme.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o HardCodedColorScheme.o HardCodedColorScheme.cpp --- HelpDisplayWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o HelpDisplayWidget.o HelpDisplayWidget.cpp --- HistogramWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o HistogramWidget.o HistogramWidget.cpp --- KeyController.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o KeyController.o KeyController.cpp --- HardCodedColorScheme.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from HardCodedColorScheme.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- LowScoringSegParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o LowScoringSegParams.o LowScoringSegParams.cpp --- main.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o main.o main.cpp --- ColumnScoreParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from ColumnScoreParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)': ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] void ColumnScoreParams::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ --- main.o --- In file included from main.cpp:21: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- HelpDisplayWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HelpDisplayWidget.h:18, from HelpDisplayWidget.cpp:15: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- mainwindow.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o mainwindow.o mainwindow.cpp --- HistogramWidget.o --- HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/qt4/QtGui/qpolygon.h:45, from /usr/local/include/qt4/QtGui/qmatrix.h:45, from /usr/local/include/qt4/QtGui/qtransform.h:44, from /usr/local/include/qt4/QtGui/qimage.h:45, from /usr/local/include/qt4/QtGui/qpixmap.h:50, from /usr/local/include/qt4/QtGui/QPixmap:1, from HistogramWidget.h:23, from HistogramWidget.cpp:23: /usr/local/include/qt4/QtCore/qvector.h: In instantiation of 'void QVector::realloc(int, int) [with T = QPixmap]': /usr/local/include/qt4/QtCore/qvector.h:343:3: required from 'void QVector::resize(int) [with T = QPixmap]' HistogramWidget.cpp:268:29: required from here /usr/local/include/qt4/QtCore/qvector.h:503:25: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'QVector::Data' {aka 'struct QVectorTypedData'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] ::memcpy(x.p, p, sizeOfTypedData() + (qMin(aalloc, d->alloc) - 1) * sizeof(T)); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/qt4/QtGui/qpolygon.h:45, from /usr/local/include/qt4/QtGui/qmatrix.h:45, from /usr/local/include/qt4/QtGui/qtransform.h:44, from /usr/local/include/qt4/QtGui/qimage.h:45, from /usr/local/include/qt4/QtGui/qpixmap.h:50, from /usr/local/include/qt4/QtGui/QPixmap:1, from HistogramWidget.h:23, from HistogramWidget.cpp:23: /usr/local/include/qt4/QtCore/qvector.h:94:8: note: 'QVector::Data' {aka 'struct QVectorTypedData'} declared here struct QVectorTypedData : private QVectorData ^~~~~~~~~~~~~~~~ --- PairwiseParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o PairwiseParams.o PairwiseParams.cpp --- main.o --- In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from main.cpp:24: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from main.cpp:24: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/substitutionMatrix/../general/SquareMat.h:9, from clustalW/substitutionMatrix/../general/clustalw.h:43, from clustalW/substitutionMatrix/SubMatrix.h:28, from main.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- PostscriptFileParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o PostscriptFileParams.o PostscriptFileParams.cpp --- LowScoringSegParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)': LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] void LowScoringSegParams::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ --- HelpDisplayWidget.o --- HelpDisplayWidget.cpp: In member function 'std::__cxx11::string* HelpDisplayWidget::loadHelpInformation(char)': HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] catch(ifstream::failure e) ^ HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] int i, number, nlines; ^~~~~~ --- mainwindow.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- PostscriptFileParams.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from PostscriptFileParams.h:4, from PostscriptFileParams.cpp:1: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProteinGapParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ProteinGapParameters.o ProteinGapParameters.cpp --- mainwindow.o --- In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from mainwindow.cpp:98: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- PSPrinter.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o PSPrinter.o PSPrinter.cpp --- mainwindow.o --- In file included from mainwindow.cpp:99: WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:100: AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:101: TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from mainwindow.cpp:102: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from mainwindow.cpp:98: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ mainwindow.cpp: In member function 'virtual void MainWindow::showEvent(QShowEvent*)': mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter] void MainWindow::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)': mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] void MainWindow::writeViewer1AsPostscript(int type) ~~~~^~~~ --- QTUtility.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o QTUtility.o QTUtility.cpp --- Resources.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Resources.o Resources.cpp --- PairwiseParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8, from PairwiseParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ PairwiseParams.cpp: In member function 'virtual void PairwiseParams::showEvent(QShowEvent*)': PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] void PairwiseParams::showEvent(QShowEvent* event) ~~~~~~~~~~~~^~~~~ --- SaveSeqFile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SaveSeqFile.o SaveSeqFile.cpp --- SearchForString.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SearchForString.o SearchForString.cpp --- PSPrinter.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from PSPrinter.h:11, from PSPrinter.cpp:20: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(res.isLetter() && resNumber.size() > i - data->firstSeq) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(res.isLetter() && resNumber.size() > seq) ~~~~~~~~~~~~~~~~~^~~~~ PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(res.isLetter() && resNumber.size() > i) ~~~~~~~~~~~~~~~~~^~~ PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable] int err; ^~~ PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable] int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local ^~~~~~~ PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable] int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local ^~~~~~~ PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)': PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(data->nameHeader.size() > ix) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = fr; i <= lr && i < ruler.length(); i++) ~~^~~~~~~~~~~~~~~~ PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)': PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(i = fr + 1; i <= lr && i < data->histogram->size(); i++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~ PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable] int psX, psY, curveBottom; ^~~ --- SecStructOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SecStructOptions.o SecStructOptions.cpp --- SeqNameWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SeqNameWidget.o SeqNameWidget.cpp --- TreeFormatOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o TreeFormatOptions.o TreeFormatOptions.cpp --- TreeOutputFileNames.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o TreeOutputFileNames.o TreeOutputFileNames.cpp --- SaveSeqFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from SaveSeqFile.cpp:26: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- SeqNameWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from SeqNameWidget.cpp:59: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)': SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable] QRect redrawRect = event->rect(); ^~~~~~~~~~ --- WritePostscriptFile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o WritePostscriptFile.o WritePostscriptFile.cpp --- Clustal.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Clustal.o clustalW/Clustal.cpp --- Help.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Help.o clustalW/Help.cpp --- Alignment.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Alignment.o clustalW/alignment/Alignment.cpp --- Clustal.o --- In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/fileInput/../alignment/Alignment.h:42, from clustalW/fileInput/FileReader.h:12, from clustalW/Clustal.h:18, from clustalW/Clustal.cpp:27: clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/Clustal.h:18, from clustalW/Clustal.cpp:27: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from clustalW/Clustal.cpp:27: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.cpp:33: clustalW/tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::align(std::__cxx11::string*, bool)': clustalW/Clustal.cpp:162:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/Clustal.cpp: In member function 'void clustalw::Clustal::doAlignUseOldTree(std::__cxx11::string*)': clustalW/Clustal.cpp:837:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/general/SquareMat.h:9, from clustalW/general/clustalw.h:43, from clustalW/Clustal.h:15, from clustalW/Clustal.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- AlignmentOutput.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp --- Alignment.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/Alignment.cpp:25: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)': clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^~~~~~~~~~ --- AlignmentOutput.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/AlignmentOutput.h:24, from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/alignment/AlignmentOutput.cpp:27: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/alignment/AlignmentOutput.cpp:535:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/alignment/AlignmentOutput.h:20, from clustalW/alignment/AlignmentOutput.cpp:27: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)': clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch(exception e) ^ clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)': clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=] catch(VectorOutOfRange e) ^ --- WritePostscriptFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from WritePostscriptFile.cpp:24: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from WritePostscriptFile.cpp:24: WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from WritePostscriptFile.cpp:27: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from WritePostscriptFile.cpp:24: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- TreeOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from TreeOutputFileNames.cpp:17: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from TreeOutputFileNames.cpp:17: TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from TreeOutputFileNames.h:9, from TreeOutputFileNames.cpp:17: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- ObjectiveScore.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp --- Sequence.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Sequence.o clustalW/alignment/Sequence.cpp --- ObjectiveScore.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ClustalFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp --- EMBLFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp --- FileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o FileParser.o clustalW/fileInput/FileParser.cpp --- FileReader.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o FileReader.o clustalW/fileInput/FileReader.cpp --- GDEFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp --- InFileStream.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o InFileStream.o clustalW/fileInput/InFileStream.cpp --- FileReader.o --- In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/fileInput/../alignment/Alignment.h:42, from clustalW/fileInput/FileReader.h:12, from clustalW/fileInput/FileReader.cpp:29: clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/fileInput/FileReader.cpp:29: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::__cxx11::string*)': clustalW/fileInput/FileReader.cpp:155:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fileParser; // Means we dont need to delete it! ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/fileInput/FileReader.cpp: At global scope: clustalW/fileInput/FileReader.cpp:426:42: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/fileInput/FileReader.h:11, from clustalW/fileInput/FileReader.cpp:29: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr&)': clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch(exception ex) ^~ --- MSFFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp --- PearsonFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp --- PIRFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp --- PearsonFileParser.o --- clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::__cxx11::string*)': clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) ~~~~~~~~^~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] void PearsonFileParser::getSecStructure(vector& gapPenaltyMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter] vector& secStructMask, string& secStructName, ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter] vector& secStructMask, string& secStructName, ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter] int &structPenalties, int length) ~~~~^~~~~~ --- RSFFileParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp --- PIRFileParser.o --- clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:292:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] void PIRFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:45: warning: unused parameter 'secStructName' [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ~~~~^~~~~~ --- MSFFileParser.o --- clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector clustalw::MSFFileParser::getSeqRange(int, int, std::__cxx11::string*)': clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter] vector MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) ~~~~~~~~^~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual void clustalw::MSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': clustalW/fileInput/MSFFileParser.cpp:246:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:246:81: warning: unused parameter 'secStructMask' [-Wunused-parameter] void MSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:45: warning: unused parameter 'secStructName' [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ~~~~~~~~^~~~~~~~~~~~~ clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter] string& secStructName, int &structPenalties, int length) ~~~~^~~~~~ --- RSFFileParser.o --- clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector&, std::vector&, std::__cxx11::string&, int&, int)': clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter] void RSFFileParser::getSecStructure(vector& gapPenaltyMask, vector& secStructMask, ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ --- ClustalWResources.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ClustalWResources.o clustalW/general/ClustalWResources.cpp --- DebugLog.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o DebugLog.o clustalW/general/DebugLog.cpp --- OutputFile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o OutputFile.o clustalW/general/OutputFile.cpp --- Stats.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Stats.o clustalW/general/Stats.cpp --- SymMatrix.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SymMatrix.o clustalW/general/SymMatrix.cpp --- UserParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o UserParameters.o clustalW/general/UserParameters.cpp --- OutputFile.o --- In file included from clustalW/general/OutputFile.cpp:9: clustalW/general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/general/OutputFile.h:8, from clustalW/general/OutputFile.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- Utility.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Utility.o clustalW/general/Utility.cpp --- Stats.o --- In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- VectorOutOfRange.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp --- CommandLineParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp --- ClustalWResources.o --- clustalW/general/ClustalWResources.cpp: In member function 'std::__cxx11::string clustalw::ClustalWResources::findFile(std::__cxx11::string, clustalw::ClustalWResourcePathType) const': clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds] delim[1] = 0; ~~~~~~~^ --- Utility.o --- clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)': clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] int n; ^ --- UserParameters.o --- clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)': clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] UserParameters::UserParameters(bool log) ~~~~~^~~ --- Utility.o --- clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)': clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) ~~~~~~~~^~~~~~~~~~~~~ --- InteractiveMenu.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp --- Iteration.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Iteration.o clustalW/multipleAlign/Iteration.cpp --- CommandLineParser.o --- In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/../general/SquareMat.h:9, from clustalW/interface/../general/clustalw.h:43, from clustalW/interface/../Clustal.h:15, from clustalW/interface/CommandLineParser.h:18, from clustalW/interface/CommandLineParser.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- InteractiveMenu.o --- In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/interface/../fileInput/../alignment/Alignment.h:42, from clustalW/interface/../fileInput/FileReader.h:12, from clustalW/interface/../Clustal.h:18, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/interface/../Clustal.h:18, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/interface/../Clustal.h:20, from clustalW/interface/InteractiveMenu.h:15, from clustalW/interface/InteractiveMenu.cpp:23: clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/interface/InteractiveMenu.cpp:21: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()': clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=] catch(bad_alloc) ^~~~~~~~~ --- Iteration.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- InteractiveMenu.o --- clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()': clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=] clustalObj->getHelp('C'); ~~~~~~~~~~~~~~~~~~~^~~~~ clustalW/interface/InteractiveMenu.cpp:521:13: note: here case 'Q': ^~~~ --- Iteration.o --- In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/multipleAlign/Iteration.cpp:17: clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/multipleAlign/../alignment/Alignment.h:38, from clustalW/multipleAlign/Iteration.h:8, from clustalW/multipleAlign/Iteration.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count; ^~~~~ --- LowScoreSegProfile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/LowScoreSegProfile.h:13, from clustalW/multipleAlign/LowScoreSegProfile.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- MSA.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o MSA.o clustalW/multipleAlign/MSA.cpp --- MyersMillerProfileAlign.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp --- ProfileBase.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp --- MyersMillerProfileAlign.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10, from clustalW/multipleAlign/MyersMillerProfileAlign.h:10, from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- MSA.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, from clustalW/multipleAlign/MSA.h:10, from clustalW/multipleAlign/MSA.cpp:16: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, clustalw::AlignmentSteps*, int)': clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^~~~~~~~~~~~~~ clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::seqsAlignToProfile(clustalw::Alignment*, clustalw::DistMatrix*, std::vector*, int, std::__cxx11::string)': clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] string phylipName) ~~~~~~~^~~~~~~~~~ --- ProfileBase.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileBase.h:14, from clustalW/multipleAlign/ProfileBase.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProfileStandard.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp --- ProfileWithSub.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileWithSub.h:9, from clustalW/multipleAlign/ProfileWithSub.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ProfileStandard.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/multipleAlign/../alignment/Alignment.h:42, from clustalW/multipleAlign/ProfileStandard.h:9, from clustalW/multipleAlign/ProfileStandard.cpp:9: clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- FastPairwiseAlign.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp --- FullPairwiseAlign.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp --- SubMatrix.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp --- AlignmentSteps.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp --- FastPairwiseAlign.o --- In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FastPairwiseAlign.h:9, from clustalW/pairwise/FastPairwiseAlign.cpp:10: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- FullPairwiseAlign.o --- In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/pairwise/../alignment/Alignment.h:42, from clustalW/pairwise/PairwiseAlignBase.h:10, from clustalW/pairwise/FullPairwiseAlign.h:9, from clustalW/pairwise/FullPairwiseAlign.cpp:9: clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- ClusterTree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ClusterTree.o clustalW/tree/ClusterTree.cpp --- ClusterTreeOutput.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp --- NJTree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o NJTree.o clustalW/tree/NJTree.cpp --- SubMatrix.o --- In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)': clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter] void SubMatrix::tempInterface(int alignResidueType, int alignType) ~~~~^~~~~~~~~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp:1613:57: warning: unused parameter 'alignType' [-Wunused-parameter] void SubMatrix::tempInterface(int alignResidueType, int alignType) ~~~~^~~~~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1657:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^~~~~~ clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])': clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^~~~~~ --- ClusterTree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/ClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/ClusterTree.cpp:9: clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/ClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)': clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^~ clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^~ --- RandomGenerator.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp --- Tree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Tree.o clustalW/tree/Tree.cpp --- ClusterTreeOutput.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTreeOutput.h:11, from clustalW/tree/ClusterTreeOutput.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- TreeInterface.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o TreeInterface.o clustalW/tree/TreeInterface.cpp --- Tree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/Tree.cpp:10: clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/Tree.cpp:278:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr Tree::createSets(int firstSeq, int lastSeq) ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/Tree.cpp: In member function 'std::auto_ptr clustalw::Tree::createSets(int, int)': clustalW/tree/Tree.cpp:280:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progAlignSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/../alignment/Alignment.h:38, from clustalW/tree/Tree.h:13, from clustalW/tree/Tree.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- SubMatrix.o --- clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)': clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized in this function [-Wmaybe-uninitialized] return (maxRes); ^ --- UnRootedClusterTree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp --- Node.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o Node.o clustalW/tree/UPGMA/Node.cpp --- RootedClusterTree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp --- RootedGuideTree.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp --- TreeInterface.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/TreeInterface.h:19, from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:38:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:57:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:102:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:108:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:133:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:138:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:15: clustalW/tree/TreeInterface.h:142:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/TreeInterface.cpp:17: clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/TreeInterface.cpp:18: clustalW/tree/Tree.h:26:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr createSets(int firstSeq, int lastSeq); ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UnRootedClusterTree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/../alignment/Alignment.h:42, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/ClusterTree.h:23, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/ClusterTree.h:16, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- TreeInterface.o --- In file included from clustalW/tree/TreeInterface.cpp:23: clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp:31:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp:103:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp:195:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': clustalW/tree/TreeInterface.cpp:200:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/tree/TreeInterface.cpp:208:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::__cxx11::string*, std::vector*, int, int, bool*)': clustalW/tree/TreeInterface.cpp:214:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/tree/TreeInterface.cpp:439:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::__cxx11::string*, std::vector*, int, int, bool*)': clustalW/tree/TreeInterface.cpp:445:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/tree/TreeInterface.cpp:485:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': clustalW/tree/TreeInterface.cpp:490:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: At global scope: clustalW/tree/TreeInterface.cpp:503:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/TreeInterface.cpp: In member function 'std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string*, bool*)': clustalW/tree/TreeInterface.cpp:506:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/TreeInterface.h:17, from clustalW/tree/TreeInterface.cpp:15: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- RootedTreeOutput.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp --- RootedGuideTree.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/RootedGuideTree.cpp:10: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- RootedClusterTree.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/../ClusterTree.h:20, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from clustalW/tree/UPGMA/../ClusterTree.h:23, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/../../general/OutputFile.h:26:14: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr file; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/../ClusterTree.h:70:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr quickDistMat; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: clustalW/tree/UPGMA/RootedClusterTree.h:22:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11: clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/UPGMA/RootedClusterTree.cpp:17:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/UPGMA/RootedClusterTree.cpp: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)': clustalW/tree/UPGMA/RootedClusterTree.cpp:21:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from clustalW/tree/UPGMA/../ClusterTree.h:16, from clustalW/tree/UPGMA/RootedClusterTree.h:8, from clustalW/tree/UPGMA/RootedClusterTree.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UPGMAAlgorithm.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp --- RootedTreeOutput.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/RootedTreeOutput.h:15, from clustalW/tree/UPGMA/RootedTreeOutput.cpp:9: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_AlignOutputFileNames.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_AlignOutputFileNames.o moc_AlignOutputFileNames.cpp --- moc_AlignmentViewerWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_AlignmentViewerWidget.o moc_AlignmentViewerWidget.cpp --- moc_AlignmentWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_AlignmentWidget.o moc_AlignmentWidget.cpp --- moc_AlignmentParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_AlignmentParameters.o moc_AlignmentParameters.cpp --- UPGMAAlgorithm.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/tree/UPGMA/../../alignment/Alignment.h:42, from clustalW/tree/UPGMA/RootedGuideTree.h:17, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:8, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_AlignmentViewerWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from moc_AlignmentViewerWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_AlignmentWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from moc_AlignmentWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_AlignOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from AlignOutputFileNames.h:10, from moc_AlignOutputFileNames.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_AlignOutputFileNames.cpp:9: AlignOutputFileNames.h:106:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr outFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from AlignOutputFileNames.h:9, from moc_AlignOutputFileNames.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- UPGMAAlgorithm.o --- In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: clustalW/tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr progSteps; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/tree/UPGMA/../../general/SquareMat.h:9, from clustalW/tree/UPGMA/../../general/clustalw.h:43, from clustalW/tree/UPGMA/UPGMAAlgorithm.h:6, from clustalW/tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- moc_AlignmentFormatOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp --- moc_BootstrapTreeDialog.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp --- moc_ColumnScoreParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp --- moc_FileDialog.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_FileDialog.o moc_FileDialog.cpp --- moc_HelpDisplayWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp --- moc_HistogramWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_HistogramWidget.o moc_HistogramWidget.cpp --- moc_BootstrapTreeDialog.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from BootstrapTreeDialog.h:11, from moc_BootstrapTreeDialog.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_BootstrapTreeDialog.cpp:9: BootstrapTreeDialog.h:70:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from BootstrapTreeDialog.h:10, from moc_BootstrapTreeDialog.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- moc_ProteinGapParameters.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp --- moc_mainwindow.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_mainwindow.o moc_mainwindow.cpp --- moc_PairwiseParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_PairwiseParams.o moc_PairwiseParams.cpp --- moc_HelpDisplayWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HelpDisplayWidget.h:18, from moc_HelpDisplayWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_LowScoringSegParams.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp --- moc_ColorFileXmlParser.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp --- moc_SearchForString.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_SearchForString.o moc_SearchForString.cpp --- moc_PSPrinter.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_PSPrinter.o moc_PSPrinter.cpp --- moc_mainwindow.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_SaveSeqFile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp --- moc_mainwindow.o --- In file included from clustalW/Clustal.h:18, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/fileInput/FileReader.h:42:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] void checkInfile(int* nseqs, auto_ptr& fileParser); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] bool openExplicitFile(auto_ptr& outFile, string fileName); ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:69:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] string openOutputFile(auto_ptr& outFile, string prompt, string path, ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:75:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr clustalOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:76:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gcgOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:77:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nbrfOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:78:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr phylipOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:79:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr gdeOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:80:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr nexusOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from clustalW/Clustal.h:20, from mainwindow.h:45, from moc_mainwindow.cpp:9: clustalW/alignment/AlignmentOutput.h:81:9: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fastaOutFile; ^~~~~~~~ In file included from /usr/include/c++/8.0/bits/locale_conv.h:41, from /usr/include/c++/8.0/locale:43, from /usr/include/c++/8.0/iomanip:43, from clustalW/alignment/Alignment.h:38, from AlignmentViewerWidget.h:36, from mainwindow.h:37, from moc_mainwindow.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- moc_ColorFileXmlParser.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from ColorFileXmlParser.h:9, from moc_ColorFileXmlParser.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_SecStructOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_SecStructOptions.o moc_SecStructOptions.cpp --- moc_PSPrinter.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from HardCodedColorScheme.h:8, from ColorParameters.h:11, from PSPrinter.h:11, from moc_PSPrinter.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_SeqNameWidget.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp --- moc_TreeFormatOptions.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp --- moc_SaveSeqFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from moc_SaveSeqFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_WritePostscriptFile.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp --- moc_TreeOutputFileNames.o --- c++ -c -pipe -O2 -fno-strict-aliasing -Wall -W -pthread -D_THREAD_SAFE -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-g++ -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I. -I/usr/local/include/qt4 -I/usr/local/include -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp --- moc_SeqNameWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from moc_SeqNameWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ --- moc_WritePostscriptFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from moc_WritePostscriptFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_WritePostscriptFile.cpp:9: WritePostscriptFile.h:88:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr params; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from WritePostscriptFile.h:9, from moc_WritePostscriptFile.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- moc_TreeOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from moc_TreeOutputFileNames.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^~~~~~~~~~~~~~ In file included from moc_TreeOutputFileNames.cpp:9: TreeOutputFileNames.h:73:5: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr treeFileNames; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from TreeOutputFileNames.h:9, from moc_TreeOutputFileNames.cpp:9: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ --- clustalx --- c++ -Wl,-O1 -pthread -Wl,-rpath,/usr/local/lib/qt4 -o clustalx AlignmentFormatOptions.o AlignmentParameters.o AlignmentViewerWidget.o AlignmentWidget.o AlignOutputFileNames.o BootstrapTreeDialog.o ColorFileXmlParser.o ColorParameters.o ColumnScoreParams.o FileDialog.o HardCodedColorScheme.o HelpDisplayWidget.o HistogramWidget.o KeyController.o LowScoringSegParams.o main.o mainwindow.o PairwiseParams.o PostscriptFileParams.o ProteinGapParameters.o PSPrinter.o QTUtility.o Resources.o SaveSeqFile.o SearchForString.o SecStructOptions.o SeqNameWidget.o TreeFormatOptions.o TreeOutputFileNames.o WritePostscriptFile.o Clustal.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o ClustalFileParser.o EMBLFileParser.o FileParser.o FileReader.o GDEFileParser.o InFileStream.o MSFFileParser.o PearsonFileParser.o PIRFileParser.o RSFFileParser.o ClustalWResources.o DebugLog.o OutputFile.o Stats.o SymMatrix.o UserParameters.o Utility.o VectorOutOfRange.o CommandLineParser.o InteractiveMenu.o Iteration.o LowScoreSegProfile.o MSA.o MyersMillerProfileAlign.o ProfileBase.o ProfileStandard.o ProfileWithSub.o FastPairwiseAlign.o FullPairwiseAlign.o SubMatrix.o AlignmentSteps.o ClusterTree.o ClusterTreeOutput.o NJTree.o RandomGenerator.o Tree.o TreeInterface.o UnRootedClusterTree.o Node.o RootedClusterTree.o RootedGuideTree.o RootedTreeOutput.o UPGMAAlgorithm.o moc_AlignmentFormatOptions.o moc_AlignmentParameters.o moc_AlignmentViewerWidget.o moc_AlignmentWidget.o moc_AlignOutputFileNames.o moc_BootstrapTreeDialog.o moc_ColorFileXmlParser.o moc_ColumnScoreParams.o moc_FileDialog.o moc_HelpDisplayWidget.o moc_HistogramWidget.o moc_LowScoringSegParams.o moc_mainwindow.o moc_PairwiseParams.o moc_ProteinGapParameters.o moc_PSPrinter.o moc_SaveSeqFile.o moc_SearchForString.o moc_SecStructOptions.o moc_SeqNameWidget.o moc_TreeFormatOptions.o moc_TreeOutputFileNames.o moc_WritePostscriptFile.o -L/usr/local/lib/qt4 -L/usr/local/lib -lQtXml -L/usr/local/lib/qt4 -L/usr/local/lib -lQtGui -lQtCore Iteration.o:Iteration.cpp:function clustalw::Iteration::removeFirstIterate(clustalw::Alignment*): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> clustalx-2.1 depends on file: /usr/local/lib/qt4/bin/moc - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for clustalx-2.1 ===> Generating temporary packing list install -s -m 555 /construction/biology/clustalx/clustalx-2.1/clustalx /construction/biology/clustalx/stage/usr/local/bin install -m 0644 /construction/biology/clustalx/clustalx-2.1/col*.xml /construction/biology/clustalx/clustalx-2.1/clustalx.hlp /construction/biology/clustalx/stage/usr/local/share/clustalx ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for clustalx-2.1 file sizes/checksums [8]: . done packing files [8]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 15 MAR 2019 at 13:07:36 UTC Duration: 00:02:50