=> Building biology/clustalx Started : Thursday, 30 AUG 2018 at 13:02:08 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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=gcc50 -------------------------------------------------- -- 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=gcc50 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 -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" 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=5.3 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=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> 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_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> clustalx-2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustalx-2.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalx-2.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> 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 -------------------------------------------------------------------------------- ===> 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-39... `-- Extracting qtchooser-39: .......... done Extracting qt4-moc-4.8.7_2: .... done Message from qtchooser-39: 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. ===> 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 ===> 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_13.txz Installing qt4-corelib-4.8.7_13... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done `-- Installing glib-2.50.3_4,1... | `-- Installing libffi-3.2.1_2... | `-- Extracting libffi-3.2.1_2: .......... done | `-- Installing libiconv-1.14_11... | `-- Extracting libiconv-1.14_11: .......... done | `-- Installing pcre-8.42... | `-- Extracting pcre-8.42: .......... done | `-- Installing perl5-5.26.2... | `-- Extracting perl5-5.26.2: .......... done | `-- Installing python27-2.7.15... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting python27-2.7.15: .......... done `-- Extracting glib-2.50.3_4,1: .......... done No schema files found: doing nothing. `-- Installing icu-62.1_1,1... `-- Extracting icu-62.1_1,1: .......... done Extracting qt4-corelib-4.8.7_13: .......... done Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. 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_13: ====================================================================== 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! ====================================================================== ===> 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_4.txz Installing qt4-gui-4.8.7_4... `-- Installing cups-2.2.8_1... | `-- Installing avahi-app-0.6.31_6... | | `-- Installing dbus-glib-0.108... | | `-- Installing dbus-1.10.16_1... | | | `-- Installing libICE-1.0.9_1,1... | | | `-- Installing xproto-7.0.31... | | | `-- Extracting xproto-7.0.31: .......... done | | | `-- Extracting libICE-1.0.9_1,1: .......... done | | | `-- Installing libSM-1.2.2_3,1... | | | `-- Extracting libSM-1.2.2_3,1: .......... done | | | `-- Installing libX11-1.6.5,1... | | | `-- Installing kbproto-1.0.7... | | | `-- Extracting kbproto-1.0.7: .......... done | | | `-- Installing libXau-1.0.8_3... | | | `-- Extracting libXau-1.0.8_3: .......... done | | | `-- Installing libXdmcp-1.1.2... | | | `-- Extracting libXdmcp-1.1.2: ......... done | | | `-- Installing libxcb-1.13... | | | | `-- Installing libpthread-stubs-0.4... | | | | `-- Extracting libpthread-stubs-0.4: .... done | | | | `-- Installing libxml2-2.9.7... | | | | `-- Extracting libxml2-2.9.7: .......... done | | | `-- Extracting libxcb-1.13: .......... done | | | `-- Extracting libX11-1.6.5,1: .......... done ===> Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. | | `-- Extracting dbus-1.10.16_1: ......... done | | `-- Extracting dbus-glib-0.108: .......... done | | `-- Installing gdbm-1.13_1... | | `-- Extracting gdbm-1.13_1: .......... done | | `-- Installing gnome_subr-1.0... | | `-- Extracting gnome_subr-1.0: .... done | | `-- Installing gobject-introspection-1.50.0_1,1... | | `-- Extracting gobject-introspection-1.50.0_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-0.6.31_6: .......... done | `-- Installing gnutls-3.5.18... | | `-- Installing ca_root_nss-3.38... | | `-- Extracting ca_root_nss-3.38: ........ done | | `-- Installing gmp-6.1.2... | | `-- Extracting gmp-6.1.2: .......... done | | `-- Installing libidn2-2.0.5... | | `-- Installing libunistring-0.9.10... | | `-- Extracting libunistring-0.9.10: .......... done | | `-- Extracting libidn2-2.0.5: .......... done | | `-- Installing libtasn1-4.13... | | `-- Extracting libtasn1-4.13: .......... done | | `-- Installing nettle-3.4... | | `-- Extracting nettle-3.4: .......... done | | `-- Installing p11-kit-0.23.12... | | `-- Extracting p11-kit-0.23.12: .......... 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-3.5.18: .......... 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-2.2.8_1: .......... 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... | `-- Installing libXfixes-5.0.3... | | `-- Installing fixesproto-5.0... | | `-- Extracting fixesproto-5.0: ....... done | `-- Extracting libXfixes-5.0.3: .......... done | `-- Installing libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: ....... done | `-- Extracting libXrender-0.9.10: .......... done `-- Extracting libXcursor-1.1.15: .......... done `-- Installing libXext-1.3.3_1,1... | `-- Installing xextproto-7.3.0... | `-- Extracting xextproto-7.3.0: .......... done `-- Extracting libXext-1.3.3_1,1: .......... done `-- Installing libXi-1.7.9,1... | `-- Installing inputproto-2.3.2... | `-- Extracting inputproto-2.3.2: ........ done `-- Extracting libXi-1.7.9,1: .......... done `-- Installing libXinerama-1.1.3_3,1... | `-- Installing xineramaproto-1.2.1... | `-- Extracting xineramaproto-1.2.1: ..... done `-- Extracting libXinerama-1.1.3_3,1: .......... done `-- Installing libXrandr-1.5.1... | `-- Installing randrproto-1.5.0... | `-- Extracting randrproto-1.5.0: ....... done `-- Extracting libXrandr-1.5.1: .......... done `-- Installing libXt-1.1.5,1... `-- Extracting libXt-1.1.5,1: .......... done `-- Installing png-1.6.34... `-- Extracting png-1.6.34: .......... done `-- Installing xdg-utils-1.1.1... | `-- Installing hicolor-icon-theme-0.15... | `-- Extracting hicolor-icon-theme-0.15: . done | `-- Installing xprop-1.2.3... | | `-- Installing libXmu-1.1.2_3,1... | | `-- Extracting libXmu-1.1.2_3,1: .......... done | `-- Extracting xprop-1.2.3: .. done | `-- Installing xset-1.2.4... | | `-- Installing libXfontcache-1.0.5_3... | | `-- Installing fontcacheproto-0.1.3... | | `-- Extracting fontcacheproto-0.1.3: ....... done | | `-- Extracting libXfontcache-1.0.5_3: .......... done | `-- Extracting xset-1.2.4: .. done `-- Extracting xdg-utils-1.1.1: .......... done `-- Installing xorg-fonts-truetype-7.7_1... | `-- Installing dejavu-2.37... | | `-- Installing mkfontdir-1.0.7... | | `-- Installing mkfontscale-1.1.3... | | | `-- Installing libfontenc-1.1.3_1... | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | `-- Extracting mkfontscale-1.1.3: ..... 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_4: .......... done Message from ca_root_nss-3.38: ********************************* 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. ===> 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 ===> 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_BootstrapTreeDialog.cpp --- --- moc_ColorFileXmlParser.cpp --- --- moc_ColumnScoreParams.cpp --- --- moc_FileDialog.cpp --- --- moc_HelpDisplayWidget.cpp --- --- moc_HistogramWidget.cpp --- --- moc_LowScoringSegParams.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_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_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_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_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_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_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 --- /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 --- --- moc_SecStructOptions.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 --- --- 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_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_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 --- --- AlignmentViewerWidget.o --- --- 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 --- 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 --- --- ColorParameters.o --- --- 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 --- 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 --- HardCodedColorScheme.o --- --- HelpDisplayWidget.o --- --- 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 --- ColorFileXmlParser.o --- ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment] // tr("colorrules not found in the parameter file, using\ ^ --- HardCodedColorScheme.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ColorParameters.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- ColorParameters.o --- ColorParameters.cpp: In member function 'QColor ColorParameters::getResidueColor(QChar, QChar)': ColorParameters.cpp:160:18: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare] if(colorNum > 0 && colorNum - 1 < colorPar.size()) ^ --- 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 --- HelpDisplayWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from 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 --- HelpDisplayWidget.o --- HelpDisplayWidget.cpp: In member function 'std::__cxx11::string* HelpDisplayWidget::loadHelpInformation(char)': HelpDisplayWidget.cpp:61:13: warning: variable 'number' set but not used [-Wunused-but-set-variable] int i, number, nlines; ^ --- AlignmentParameters.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from AlignmentParameters.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter] void AlignmentParameters::showEvent(QShowEvent* event) ^ --- AlignmentViewerWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from AlignmentViewerWidget.cpp:66: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- AlignmentWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from AlignmentWidget.cpp:49: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- AlignmentViewerWidget.o --- AlignmentViewerWidget.cpp: In member function 'int AlignmentViewerWidget::makeGapPenaltyData()': AlignmentViewerWidget.cpp:588:37: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < len && i < _secStructMask->size();i++) ^ AlignmentViewerWidget.cpp:652:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(i = 0; i < len && i < ssMask.size(); i++) ^ AlignmentViewerWidget.cpp: At global scope: AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter] void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event ) ^ --- AlignmentWidget.o --- In file included from AlignmentWidget.cpp:49:0: 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) ^ --- mainwindow.o --- --- AlignmentWidget.o --- AlignmentWidget.cpp: In member function 'void AlignmentWidget::calculatePixMaps()': AlignmentWidget.cpp:225:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(unsigned int j = 0; j < lengthLongestSeq; j++) ^ --- 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 --- AlignmentWidget.o --- AlignmentWidget.cpp:235:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(code >= 0 && code < conservationPixmaps->size()) ^ AlignmentWidget.cpp:268:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(codeForAA >=0 && codeForAA < lowScoreColoredRes->size()) ^ AlignmentWidget.cpp:280:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(codeForAA >=0 && codeForAA < exceptionalColoredRes->size()) ^ AlignmentWidget.cpp:291:86: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare] if(selectedRes >= selectedColoredRes->size()) ^ AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()': AlignmentWidget.cpp:689:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 1; j <= strongGroup.size(); j++) ^ AlignmentWidget.cpp:693:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 1; j <= weakGroup.size(); j++) ^ AlignmentWidget.cpp:700:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if((i + _fRes - 1 < (*alignment)[j].size()) && ^ AlignmentWidget.cpp:701:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] (i + _fRes - 1 < (*alignment)[_fSeq].size())) ^ AlignmentWidget.cpp:725:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ^ AlignmentWidget.cpp:737:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ^ AlignmentWidget.cpp:760:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= strongGroup.size(); k++) ^ AlignmentWidget.cpp:771:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int k = 1; k <= weakGroup.size(); k++) ^ AlignmentWidget.cpp: In member function 'void AlignmentWidget::makeColorMask(clustalw::Array2D*, ColorParameters*)': AlignmentWidget.cpp:878:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ^ AlignmentWidget.cpp: In member function 'QString AlignmentWidget::initConsensus()': AlignmentWidget.cpp:927:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res + 1 < (*alignment)[currentSeq].size() && (lastSeq >= currentSeq)) ^ AlignmentWidget.cpp: In member function 'void AlignmentWidget::generatePixMaps()': AlignmentWidget.cpp:1039:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int j = 0; j < aminoAcid.size(); j++) ^ --- 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 main.cpp:21:0: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ColorFileXmlParser.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter] QTreeWidgetItem *parentItem) ^ ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter] void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem) ^ ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter] int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem) ^ --- AlignOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- BootstrapTreeDialog.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ColumnScoreParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from ColumnScoreParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter] void ColumnScoreParams::showEvent(QShowEvent* event) ^ --- PostscriptFileParams.o --- --- ProteinGapParameters.o --- --- 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 --- 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 --- HistogramWidget.o --- HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)': HistogramWidget.cpp:180:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ^ HistogramWidget.cpp:198:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(column >= 0 && column < arrayOfHeights->size()) ^ --- 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 --- PostscriptFileParams.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- LowScoringSegParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from LowScoringSegParams.cpp:22: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter] void LowScoringSegParams::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 --- 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 --- PairwiseParams.o --- In file included from clustalW/substitutionMatrix/globalmatrix.h:8:0, from PairwiseParams.cpp:23: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter] void PairwiseParams::showEvent(QShowEvent* event) ^ --- 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 --- mainwindow.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Clustal.o --- 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 --- mainwindow.o --- mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter] void MainWindow::showEvent(QShowEvent* event) ^ --- 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 --- mainwindow.o --- mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter] void MainWindow::writeViewer1AsPostscript(int type) ^ --- Clustal.o --- In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- PSPrinter.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- PSPrinter.o --- PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)': PSPrinter.cpp:207:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res.isLetter() && resNumber.size() > i - data->firstSeq) ^ PSPrinter.cpp:307:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(res.isLetter() && resNumber.size() > seq) ^ PSPrinter.cpp:421:67: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare] if(data->nameHeader.size() > ix) ^ --- Alignment.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from clustalW/alignment/Alignment.cpp:25: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- PSPrinter.o --- PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)': PSPrinter.cpp:730:30: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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; ^ --- 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 --- SeqNameWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from SeqNameWidget.cpp:59: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from 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(); ^ --- SaveSeqFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from SaveSeqFile.cpp:23: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- AlignmentOutput.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ObjectiveScore.o --- 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 --- --- WritePostscriptFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from WritePostscriptFile.cpp:24: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Sequence.o --- 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:8:0, from clustalW/alignment/ObjectiveScore.h:15, from clustalW/alignment/ObjectiveScore.cpp:10: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ClustalFileParser.o --- 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 --- TreeOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from TreeOutputFileNames.cpp:17: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- GDEFileParser.o --- 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 --- 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 --- FileReader.o --- In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- 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 --- MSFFileParser.o --- 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: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) ^ --- PIRFileParser.o --- 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) ^ --- RSFFileParser.o --- 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 --- PearsonFileParser.o --- clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter] Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) ^ 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) ^ --- 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 --- 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 is above array bounds [-Warray-bounds] delim[1] = 0; ^ --- 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 --- 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 --- 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 --- Stats.o --- In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/general/../alignment/Alignment.h:42, from clustalW/general/Stats.cpp:15: clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- 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; ^ clustalW/general/Utility.cpp: At global scope: clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter] void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj) ^ --- UserParameters.o --- clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter] UserParameters::UserParameters(bool log) ^ --- CommandLineParser.o --- In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- Iteration.o --- 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 --- 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 --- 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 --- InteractiveMenu.o --- In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- Iteration.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 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; ^ --- MyersMillerProfileAlign.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- MSA.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- LowScoreSegProfile.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- MSA.o --- 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: At global scope: clustalW/multipleAlign/MSA.cpp:359:35: warning: unused parameter 'phylipName' [-Wunused-parameter] string phylipName) ^ --- ProfileStandard.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ProfileWithSub.o --- 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 --- 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 --- ProfileBase.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ProfileWithSub.o --- In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- FastPairwiseAlign.o --- In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- --- FullPairwiseAlign.o --- In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- SubMatrix.o --- In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15:0: clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 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 --- 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 --- ClusterTree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ 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; ^ --- 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 --- 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 --- 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 --- ClusterTreeOutput.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- Tree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- UnRootedClusterTree.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- ClusterTreeOutput.o --- In file included from clustalW/tree/../alignment/../general/clustalw.h:44:0, from clustalW/tree/../alignment/../general/Utility.h:15, from clustalW/tree/../alignment/../general/utils.h:8, from clustalW/tree/../alignment/../general/UserParameters.h:22, from clustalW/tree/../alignment/../general/userparams.h:8, from clustalW/tree/../alignment/Sequence.h:20, from clustalW/tree/../alignment/Alignment.h:41, from clustalW/tree/ClusterTreeOutput.h:11, from clustalW/tree/ClusterTreeOutput.cpp:9: clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printPhylipTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::ClusterTreeOutput::printNexusTree(clustalw::PhyloTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*, std::vector*)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ --- 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); ^ --- TreeInterface.o --- In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- 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 --- 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 --- RootedClusterTree.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- RootedGuideTree.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- RootedTreeOutput.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- moc_AlignmentParameters.o --- --- moc_ColumnScoreParams.o --- --- 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 --- 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_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 --- UPGMAAlgorithm.o --- In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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 --- UnRootedClusterTree.o --- In file included from clustalW/tree/../alignment/../general/clustalw.h:44:0, from clustalW/tree/../alignment/../general/Utility.h:15, from clustalW/tree/../alignment/../general/utils.h:8, from clustalW/tree/../alignment/../general/UserParameters.h:22, from clustalW/tree/../alignment/../general/userparams.h:8, from clustalW/tree/../alignment/Sequence.h:20, from clustalW/tree/../alignment/Alignment.h:41, from clustalW/tree/ClusterTree.h:20, from clustalW/tree/UnRootedClusterTree.h:8, from clustalW/tree/UnRootedClusterTree.cpp:9: clustalW/tree/../alignment/../general/SymMatrix.h: In member function 'void clustalw::UnRootedClusterTree::treeFromDistMatrix(clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)': clustalW/tree/../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ --- RootedClusterTree.o --- In file included from clustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:0, from clustalW/tree/UPGMA/../../alignment/../general/Utility.h:15, from clustalW/tree/UPGMA/../../alignment/../general/utils.h:8, from clustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22, from clustalW/tree/UPGMA/../../alignment/../general/userparams.h:8, from clustalW/tree/UPGMA/../../alignment/Sequence.h:20, from clustalW/tree/UPGMA/../../alignment/Alignment.h:41, 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/../general/SymMatrix.h: In member function 'std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::__cxx11::string&)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ --- RootedTreeOutput.o --- In file included from clustalW/tree/UPGMA/../../alignment/../general/clustalw.h:44:0, from clustalW/tree/UPGMA/../../alignment/../general/Utility.h:15, from clustalW/tree/UPGMA/../../alignment/../general/utils.h:8, from clustalW/tree/UPGMA/../../alignment/../general/UserParameters.h:22, from clustalW/tree/UPGMA/../../alignment/../general/userparams.h:8, from clustalW/tree/UPGMA/../../alignment/Sequence.h:20, from clustalW/tree/UPGMA/../../alignment/Alignment.h:41, 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/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printPhylipTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h: In member function 'void clustalw::RootedTreeOutput::printNexusTree(clustalw::RootedGuideTree*, std::ofstream*, clustalw::Alignment*, clustalw::DistMatrix*)': clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ clustalW/tree/UPGMA/../../alignment/../general/SymMatrix.h:183:13: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] if (_i > _j) ^ --- 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_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_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_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_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 --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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_AlignmentWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentWidget.h:41, from moc_AlignmentWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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_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_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_AlignmentViewerWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from AlignmentViewerWidget.h:36, from moc_AlignmentViewerWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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_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_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_SeqNameWidget.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from SeqNameWidget.h:41, from moc_SeqNameWidget.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- moc_BootstrapTreeDialog.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- moc_ColorFileXmlParser.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from 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_PSPrinter.o --- --- moc_mainwindow.o --- --- 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 --- 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_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 --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from TreeOutputFileNames.h:10, from moc_TreeOutputFileNames.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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_AlignOutputFileNames.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from 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_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_SaveSeqFile.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from SaveSeqFile.h:9, from moc_SaveSeqFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- moc_PSPrinter.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from 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:8:0, from clustalW/alignment/Alignment.h:42, from ClustalQtParams.h:13, from WritePostscriptFile.h:10, from moc_WritePostscriptFile.cpp:9: clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- moc_mainwindow.o --- In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8:0, 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: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printInFormat(vector& temp, char* name = "tempfile.out"); ^ clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] void printVectorToFile(vector& temp, char* name = "tempfile.out"); ^ --- 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: Thursday, 30 AUG 2018 at 13:03:46 UTC Duration: 00:01:37