From 153c114b4221f8f0d65da142edc44ca2755caa35 Mon Sep 17 00:00:00 2001 From: Timothy Redaelli Date: Wed, 11 Jan 2012 00:07:16 +0000 Subject: [PATCH] updated on Wed Jan 11 00:07:16 UTC 2012 --- aegisub-svn/PKGBUILD | 19 +- aegisub-svn/automation.patch | 16 - aegisub-svn/base.patch | 44 - aegisub-svn/desktop.patch | 30 - aegisub-svn/po.patch | 16 - armory-git/Makefile.patch | 2 +- armory-git/PKGBUILD | 6 +- automatic/PKGBUILD | 4 +- beagle-lib/PKGBUILD | 42 + diaspora-git/PKGBUILD | 163 ++- diaspora-git/diaspora.bashrc | 6 + diaspora-git/diaspora.bin | 12 +- diaspora-git/diaspora.install | 3 +- diaspora-git/diaspora.rc | 4 +- django-dev/PKGBUILD | 48 +- epio/PKGBUILD | 4 +- firefox-aurora-bin-it/PKGBUILD | 5 +- ghc-mod/PKGBUILD | 10 +- ginn/PKGBUILD | 2 +- java-gnome/PKGBUILD | 31 +- jsonrpc-cpp/PKGBUILD | 9 +- lib32-mesa-r600g-git/PKGBUILD | 43 +- linux-pax/PKGBUILD | 5 +- linux-pax/linux-pax-fix-permissions | 9 +- mesa-r600g-git/PKGBUILD | 50 +- mrbayes/64bit-safe.patch | 2005 ----------------------------------- mrbayes/PKGBUILD | 56 +- mrbayes/mb.1 | 31 - mrbayes/mcmcdiagnparamprint.patch | 12 - netbeans-javase/PKGBUILD | 8 +- pacmine/PKGBUILD | 4 +- perftest/PKGBUILD | 12 +- photo/PKGBUILD | 6 +- qt-static/PKGBUILD | 149 ++- ruby-commander/PKGBUILD | 26 + sunrise-commander/PKGBUILD | 4 +- theide-nogtk-svn/PKGBUILD | 2 +- theide-svn/PKGBUILD | 2 +- upp-svn/PKGBUILD | 2 +- 39 files changed, 471 insertions(+), 2431 deletions(-) delete mode 100644 aegisub-svn/automation.patch delete mode 100644 aegisub-svn/base.patch delete mode 100644 aegisub-svn/desktop.patch delete mode 100644 aegisub-svn/po.patch create mode 100644 beagle-lib/PKGBUILD create mode 100644 diaspora-git/diaspora.bashrc rewrite django-dev/PKGBUILD (93%) delete mode 100644 mrbayes/64bit-safe.patch rewrite mrbayes/PKGBUILD (63%) delete mode 100644 mrbayes/mb.1 delete mode 100644 mrbayes/mcmcdiagnparamprint.patch rewrite qt-static/PKGBUILD (61%) create mode 100644 ruby-commander/PKGBUILD diff --git a/aegisub-svn/PKGBUILD b/aegisub-svn/PKGBUILD index 50c049b30..40783d965 100755 --- a/aegisub-svn/PKGBUILD +++ b/aegisub-svn/PKGBUILD @@ -1,17 +1,16 @@ -# Maintainer : Alucryd +# Maintainer: Alucryd +# Contributor: G_Syme pkgname=aegisub-svn -pkgver=6189 +pkgver=6268 pkgrel=1 pkgdesc="A general-purpose subtitle editor with ASS/SSA support" arch=('i686' 'x86_64') url="http://www.aegisub.net" license=('GPL' 'BSD') -depends=('ffmpegsource2-svn' 'lua' 'wxgtk-2.9' 'hunspell' 'libass' 'fftw' 'hicolor-icon-theme' 'desktop-file-utils') +depends=('ffmpegsource2-svn' 'lua' 'wxgtk-2.9>=2.9.2' 'hunspell' 'libass' 'fftw' 'hicolor-icon-theme') makedepends=('imagemagick' 'subversion' 'intltool') provides=('aegisub') -conflicts=('aegisub-bin' 'aegisub-stable-svn') -source=('base.patch' 'automation.patch' 'desktop.patch' 'po.patch') -md5sums=('49672af4ccc35fe2d9514d7542ecc3b5' '3f288d301bb60bc5d0a32dd657cc671f' 'f394c239b6897f770bdc9325e1a9e2fd' '4ed1f7d183fc59d99d9a09562ab8e456') +conflicts=('aegisub' 'aegisub-bin' 'aegisub-stable-svn') install=icon.install _svntrunk=http://svn.aegisub.org/trunk/aegisub/ @@ -27,15 +26,9 @@ build() { svn co "$_svntrunk" --config-dir ./ -r "$pkgver" "$_svnmod" fi msg "SVN checkout done or server timeout" - -# Applying DESTDIR patches - patch -p0 < base.patch - patch -p0 < automation.patch - patch -p0 < desktop.patch - patch -p0 < po.patch cd "$_svnmod" - ./autogen.sh --prefix=/usr --without-{portaudio,openal,oss,pulseaudio} --with-wxdir=/usr/include/wx-2.9 --with-wx-config=/usr/bin/wx-config-2.9 + ./autogen.sh --prefix=/usr --without-{portaudio,openal,oss,libpulse} --with-wxdir=/usr/include/wx-2.9 --with-wx-config=/usr/bin/wx-config-2.9 make } diff --git a/aegisub-svn/automation.patch b/aegisub-svn/automation.patch deleted file mode 100644 index ff101abe1..000000000 --- a/aegisub-svn/automation.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- aegisub/automation/Makefile.orig 2012-01-02 15:45:19.333313444 +0100 -+++ aegisub/automation/Makefile 2012-01-02 16:20:09.306718301 +0100 -@@ -35,10 +35,10 @@ - - - install: install-share -- @$(BIN_MKDIR) -p $(addprefix $(P_DATA)/automation/, $(dir $(DATA_AUTOMATION))) -+ @$(BIN_MKDIR) -p $(addprefix $(DESTDIR)$(P_DATA)/automation/, $(dir $(DATA_AUTOMATION))) - @for i in $(DATA_AUTOMATION); do \ -- $(BIN_ECHO) "$(BIN_INSTALL) $$i $(P_DATA)/automation/$$i"; \ -- $(BIN_INSTALL) $$i $(P_DATA)/automation/$$i; \ -+ $(BIN_ECHO) "$(BIN_INSTALL) $$i $(DESTDIR)$(P_DATA)/automation/$$i"; \ -+ $(BIN_INSTALL) $$i $(DESTDIR)$(P_DATA)/automation/$$i; \ - done - - DATA_SHARE_DOC = $(DATA_GENERAL_DOC) $(DATA_AUTOMATION_DOC) diff --git a/aegisub-svn/base.patch b/aegisub-svn/base.patch deleted file mode 100644 index a4ec18748..000000000 --- a/aegisub-svn/base.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- aegisub/Makefile.target.orig 2012-01-02 15:45:24.896646968 +0100 -+++ aegisub/Makefile.target 2012-01-02 16:14:39.693373687 +0100 -@@ -66,30 +66,30 @@ - - install-program: - ifdef PROGRAM_INSTALL -- @$(BIN_MKDIR) -p $(P_BINDIR) -- @$(BIN_INSTALL) $(PROGRAM) $(P_BINDIR)/$(PROGRAM) -+ @$(BIN_MKDIR) -p $(DESTDIR)$(P_BINDIR) -+ @$(BIN_INSTALL) $(PROGRAM) $(DESTDIR)$(P_BINDIR)/$(PROGRAM) - endif - - install-lib: - ifdef LIB_SHARED_INSTALL -- $(BIN_MKDIR) -p $(P_LIB) -- $(BIN_INSTALL) $(LIB_SHARED_FULL) $(P_LIB)/$(LIB_SHARED_FULL) -- $(BIN_LN) -sf $(LIB_SHARED_FULL) $(P_LIB)/$(LIB_SHARED) -+ $(BIN_MKDIR) -p $(DESTDIR)$(P_LIB) -+ $(BIN_INSTALL) $(LIB_SHARED_FULL) $(DESTDIR)$(P_LIB)/$(LIB_SHARED_FULL) -+ $(BIN_LN) -sf $(LIB_SHARED_FULL) $(DESTDIR)$(P_LIB)/$(LIB_SHARED) - endif - - install-share: - ifdef DATA_SHARE -- @$(BIN_MKDIR) -p $(addprefix $(P_DATA)/, $(dir $(DATA_SHARE))) -+ @$(BIN_MKDIR) -p $(addprefix $(DESTDIR)$(P_DATA)/, $(dir $(DATA_SHARE))) - @for i in $(DATA_SHARE); do \ -- $(BIN_ECHO) "$(BIN_INSTALL) $$i $(P_DATA)/$$i"; \ -- $(BIN_INSTALL) $$i $(P_DATA)/$$i; \ -+ $(BIN_ECHO) "$(BIN_INSTALL) $$i $(DESTDIR)$(P_DATA)/$$i"; \ -+ $(BIN_INSTALL) $$i $(DESTDIR)$(P_DATA)/$$i; \ - done - endif - ifdef DATA_SHARE_DOC -- @$(BIN_MKDIR) -p $(addprefix $(P_DOC)/, $(dir $(DATA_SHARE_DOC))) -+ @$(BIN_MKDIR) -p $(addprefix $(DESTDIR)$(P_DOC)/, $(dir $(DATA_SHARE_DOC))) - @for i in $(DATA_SHARE_DOC); do \ -- $(BIN_ECHO) "$(BIN_INSTALL) $$i $(P_DOC)/$$i"; \ -- $(BIN_INSTALL) $$i $(P_DOC)/$$i; \ -+ $(BIN_ECHO) "$(BIN_INSTALL) $$i $(DESTDIR)$(P_DOC)/$$i"; \ -+ $(BIN_INSTALL) $$i $(DESTDIR)$(P_DOC)/$$i; \ - done - endif - diff --git a/aegisub-svn/desktop.patch b/aegisub-svn/desktop.patch deleted file mode 100644 index a4ad2d5db..000000000 --- a/aegisub-svn/desktop.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- aegisub/desktop/Makefile.orig 2012-01-02 15:45:27.000000000 +0100 -+++ aegisub/desktop/Makefile 2012-01-02 16:22:00.103388758 +0100 -@@ -31,19 +31,19 @@ - install: install-desktop install-icons - - install-desktop: -- @$(BIN_MKDIR) -p $(P_DESKTOP) -- $(BIN_INSTALL) $(DESKTOP_FILE) $(P_DESKTOP)/$(DESKTOP_FILE) -+ @$(BIN_MKDIR) -p $(DESTDIR)$(P_DESKTOP) -+ $(BIN_INSTALL) $(DESKTOP_FILE) $(DESTDIR)$(P_DESKTOP)/$(DESKTOP_FILE) - - - install-icons: -- @$(BIN_MKDIR) -p $(addprefix $(P_ICON)/hicolor/, $(dir $(ICON_HICOLOR))) -+ @$(BIN_MKDIR) -p $(addprefix $(DESTDIR)$(P_ICON)/hicolor/, $(dir $(ICON_HICOLOR))) - @for i in $(ICON_HICOLOR); do \ -- $(BIN_ECHO) "$(BIN_INSTALL) $$i $(P_ICON)/hicolor/$$i"; \ -- $(BIN_INSTALL) $$i $(P_ICON)/hicolor/$$i; \ -+ $(BIN_ECHO) "$(BIN_INSTALL) $$i $(DESTDIR)$(P_ICON)/hicolor/$$i"; \ -+ $(BIN_INSTALL) $$i $(DESTDIR)$(P_ICON)/hicolor/$$i; \ - done -- $(BIN_TOUCH) $(P_ICON)/hicolor -- $(BIN_MKDIR) -p $(P_ICON)/hicolor/scalable/apps -- $(BIN_CP) $(ICON_SCALABLE) $(P_ICON)/hicolor/$(ICON_SCALABLE) -+ $(BIN_TOUCH) $(DESTDIR)$(P_ICON)/hicolor -+ $(BIN_MKDIR) -p $(DESTDIR)$(P_ICON)/hicolor/scalable/apps -+ $(BIN_CP) $(ICON_SCALABLE) $(DESTDIR)$(P_ICON)/hicolor/$(ICON_SCALABLE) - - - CLEANFILES = aegisub.desktop diff --git a/aegisub-svn/po.patch b/aegisub-svn/po.patch deleted file mode 100644 index de5677cb5..000000000 --- a/aegisub-svn/po.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- aegisub/po/Makefile.orig 2012-01-02 15:45:30.000000000 +0100 -+++ aegisub/po/Makefile 2012-01-02 16:23:34.613391993 +0100 -@@ -35,10 +35,10 @@ - $(BIN_MSGFMT) -o $@ $< - - install: -- @$(BIN_MKDIR) -p $(addsuffix /LC_MESSAGES/, $(addprefix $(P_LOCALE)/, $(basename $(PO)))) -+ @$(BIN_MKDIR) -p $(addsuffix /LC_MESSAGES/, $(addprefix $(DESTDIR)$(P_LOCALE)/, $(basename $(PO)))) - @for i in $(basename $(PO)); do \ -- echo $(BIN_INSTALL) $$i.mo $(P_LOCALE)/$$i/LC_MESSAGES/$(GETTEXT_PACKAGE).mo; \ -- $(BIN_INSTALL) $$i.mo $(P_LOCALE)/$$i/LC_MESSAGES/$(GETTEXT_PACKAGE).mo; \ -+ echo $(BIN_INSTALL) $$i.mo $(DESTDIR)$(P_LOCALE)/$$i/LC_MESSAGES/$(GETTEXT_PACKAGE).mo; \ -+ $(BIN_INSTALL) $$i.mo $(DESTDIR)$(P_LOCALE)/$$i/LC_MESSAGES/$(GETTEXT_PACKAGE).mo; \ - done - - diff --git a/armory-git/Makefile.patch b/armory-git/Makefile.patch index dfb24d7da..9af74fede 100644 --- a/armory-git/Makefile.patch +++ b/armory-git/Makefile.patch @@ -3,4 +3,4 @@ < LIBRARY_OPTS += -lcrypto++ -lpthread --- > INCLUDE_OPTS += -I/usr/include/crypto++ -fPIC -DTEST_NETWORK -DUSE_CRYPTOPP -D__STDC_LIMIT_MACROS -Icryptopp -> LIBRARY_OPTS += -lcryptopp -lpthread -Icryptopp +> LIBRARY_OPTS += -lcryptopp -lpthread diff --git a/armory-git/PKGBUILD b/armory-git/PKGBUILD index 83fa21c30..8ba99702d 100644 --- a/armory-git/PKGBUILD +++ b/armory-git/PKGBUILD @@ -1,7 +1,7 @@ # Maintainer: Justin Gottula pkgname=armory-git -pkgver=20120109 -pkgrel=4 +pkgver=20120110 +pkgrel=1 pkgdesc="Python-Based Bitcoin Software" arch=('i686' 'x86_64') url="https://github.com/etotheipi/BitcoinArmory" @@ -18,7 +18,7 @@ install= source=('Makefile.patch' 'run-armory.sh') noextract=() -sha256sums=('3817a40d681ccee86cde141ed26f7db8e1449d5cd76489f95861fb69c43ec85a' +sha256sums=('2556f50fe8a0871895759246962aed2187fbf3445e4583431353231408e0f108' 'baa1d335273af1f1f4d12dd68f066035e5b4485b215172690c307877ac62168c') _gitroot='git://github.com/etotheipi/BitcoinArmory.git' diff --git a/automatic/PKGBUILD b/automatic/PKGBUILD index de7a33153..761c6aa59 100644 --- a/automatic/PKGBUILD +++ b/automatic/PKGBUILD @@ -1,6 +1,6 @@ # Contributor: Matias De la Puente pkgname=automatic -pkgver=0.7.0 +pkgver=0.7.1 pkgrel=1 pkgdesc="RSS downloader for Linux based systems, capable of adding downloaded torrents directly to Transmission" arch=('i686' 'x86_64') @@ -12,7 +12,7 @@ backup=('etc/conf.d/automaticd') source=(http://kylek.is-a-geek.org:31337/files/$pkgname-$pkgver-src.tar.gz automaticd.rc automaticd.conf) -sha256sums=('a33a747142ae558e163f5ba79f2030446a9f14723e64dd1017088c70b4b92e5c' +sha256sums=('7bfc5c9da80030b12a19f2b9b72dd3b9d7cc6f576ee6b3c37b7c747a23ebac8e' '6830dd6b19d233c3d7a7b83ead466b0ea2cb23ee88cd15d5aeffa50716c02d9e' 'ed4cdf8ef72840fdb57b7670d114372bb68153cdfae731d1102687b568a71940') diff --git a/beagle-lib/PKGBUILD b/beagle-lib/PKGBUILD new file mode 100644 index 000000000..d70b42e44 --- /dev/null +++ b/beagle-lib/PKGBUILD @@ -0,0 +1,42 @@ +# Maintainer: Stunts + +pkgname=beagle-lib +pkgver=1052 +pkgrel=1 +pkgdesc="A general purpose library for evaluating the likelihood of sequence evolution on trees." +arch=('i686' 'x86_64') +url="http://code.google.com/p/beagle-lib/" +license=('LGPL') +depends=('libltdl') +optdepends=('cuda-toolkit: for doing calculations on the GPU' 'openjdk6: for usage with BEAST' 'gcc-libs-multilib: for cross compiling') +makedepends=('svn') + +_svntrunk="http://beagle-lib.googlecode.com/svn/trunk/" +_svnmod="beagle-lib" + +build() { + msg "Starting SVN checkout..." + cd ${srcdir} + if [ -d $_svnmod/.svn ]; then + (cd $_svnmod && svn up -r $pkgver) + else + svn co $_svntrunk --config-dir ./ -r $pkgver $_svnmod + fi + msg "SVN checkout done or server timeout" + + msg "Creating build copy..." + if [ -d ${srcdir}/$_svnmod-build ]; then + rm -rf $_svnmod-build + fi + + cp -r $_svnmod $_svnmod-build + cd $_svnmod-build + ./autogen.sh + ./configure --prefix=/usr + make +} + +package() { + cd $_svnmod-build + make DESTDIR=${pkgdir} install +} diff --git a/diaspora-git/PKGBUILD b/diaspora-git/PKGBUILD index b15f66916..86d3dfc91 100644 --- a/diaspora-git/PKGBUILD +++ b/diaspora-git/PKGBUILD @@ -1,26 +1,36 @@ # Maintainer: fauno # Maintainer: Hilton Medeiros +# Contributor: Jonne Haß # Contributor: Splashy # After installing, see the Diaspora wiki page for more information: # https://wiki.archlinux.org/index.php/Diaspora +pkgbase=diaspora-git pkgname=diaspora-git -pkgver=20110623 +true && pkgname=('diaspora-mysql-git' 'diaspora-postgresql-git') +pkgver=20120105 pkgrel=1 pkgdesc="A privacy aware, personally controlled, do-it-all, open source social network" arch=('i686' 'x86_64') -url="http://www.joindiaspora.com/" +url="https://diasporafoundation.org/" license=('AGPL3') -depends=('ruby' 'mysql-ruby' 'redis' 'imagemagick' 'libxslt') -makedepends=('git' 'ruby-headers') +depends=('ruby' 'redis' 'imagemagick' 'libxslt' 'net-tools') +makedepends=('git' 'libmysqlclient' 'postgresql-libs') +provides=('diaspora') install=diaspora.install source=('diaspora.bin' 'diaspora.rc' 'diaspora.logrotate' - 'diaspora.pam') + 'diaspora.pam' + 'diaspora.bashrc') +md5sums=('547b0015c83da22bd739dc85fd79f9b9' + 'b7a893271d9ba778f74569eff4190c06' + '60f6b3972c73cbc6b1c9ab87c88fb655' + '96f82c38f3f540b53f3e5144900acf17' + '53867bfd389dd267eefcefb053fecc5b') -_gitroot="http://github.com/diaspora/diaspora.git" +_gitroot="git://github.com/diaspora/diaspora.git" _gitname="diaspora" build() { @@ -30,11 +40,11 @@ build() { if [[ -d $_gitname ]] ; then pushd $_gitname - git pull origin + tsocks git pull origin msg "The local files are updated." popd else - git clone $_gitroot + tsocks git clone $_gitroot msg "Git clone done." fi @@ -42,60 +52,123 @@ build() { [[ -d $_gitname-build ]] && rm -fr $_gitname-build git clone $_gitname $_gitname-build - - # Recover gems cache - rm -fr $_gitname-gems - mkdir -p $_gitname-gems - [[ -d cache ]] && mv cache $_gitname-gems - -# Include all gems - export GEM_HOME="$srcdir/$_gitname-gems" - export GEM_PATH="$srcdir/$_gitname-gems" - export PATH="${PATH}:${GEM_PATH}/bin" - - gem install bundler - - # Patch ruby_core_source to not install the headers in the system - # Remove this if you are behind a proxy and install the ruby-headers package instead -# gem install ruby_core_source -# sed -i "s@^ dest_dir.*@ dest_dir = \"$srcdir/rubyhdrs/\" + ruby_dir@" \ -# $_gitname-gems/gems/ruby_core_source*/lib/ruby_core_source.rb - - pushd $_gitname-build - bundle install --path vendor + cd ${srcdir}/${_gitname}-build + + # Symlink configs + ln -s /etc/webapps/$_gitname/application.yml config/application.yml + ln -s /etc/webapps/$_gitname/database.yml config/database.yml + ln -s /etc/webapps/$_gitname/script_server.yml config/script_server.yml + ln -s /etc/webapps/$_gitname/oauth_keys.yml config/oauth_keys.yml + + # Set version header + sed "s|git_cmd = \`git log -1 --pretty=\"format:%H %ci\"\`|git_cmd = \"$(git log -1 --pretty="format:%H %ci")\"|" \ + -i config/initializers/version_header.rb + + # Preconfigure config/script_server.yml.example + sed 's|rails_env: "development"|rails_env: "production"|' \ + -i config/script_server.yml.example + + # Preconfigure right ca_file + sed "s|ca_file: '/etc/pki/tls/certs/ca-bundle.crt' # CentOS|ca_file: '/etc/ssl/certs/ca-certificates.crt' # Arch|" \ + -i config/application.yml.example # We make this now because we do not install the git history + # Comply with AGPLv3 tar czf public/source.tar.gz `git ls-tree -r master | awk '{print $4}'` + # Remove git repo rm -fr .git - popd - # Keep the gems cache - mv $_gitname-gems/cache "$srcdir" + # Create gem cache + mkdir -p ${srcdir}/gem-cache } -package() { - cd "$srcdir" - options=(!strip) +# Helper +_package() { + cd "${srcdir}" - usrdir="$pkgdir/usr/share/webapps" + usrdir="${pkgdir}/usr/share/webapps" - install -d "$usrdir" - cp -r $_gitname-build "$usrdir/$_gitname" - #cp -r $_gitname-gems "$usrdir/" - find "$usrdir/$_gitname-gems" \ - -type d -name ".git" -exec rm -fr '{}' \; &>/dev/null || true + install -d "${usrdir}" + cp -a ${_gitname}-build "${usrdir}/${_gitname}" install -Dm755 $_gitname.bin "$pkgdir/usr/bin/$_gitname" install -Dm755 $_gitname.rc "$pkgdir/etc/rc.d/$_gitname" install -Dm644 $_gitname.logrotate "$pkgdir/etc/logrotate.d/$_gitname" install -Dm644 $_gitname.pam "$pkgdir/etc/pam.d/$_gitname" + install -Dm644 $_gitname.bashrc "$usrdir/$_gitname/.bashrc" + +# Set the DB in the environment + sed -i "s/-DB-/$DB/g" "$usrdir/$_gitname/.bashrc" + sed -i "s/-DB-/$_db_rc/g" "$pkgdir/etc/rc.d/$_gitname" + + install -Dm644 $_gitname-build/config/application.yml.example "$pkgdir/etc/webapps/$_gitname/application.yml" + install -Dm644 $_gitname-build/config/database.yml.example "$pkgdir/etc/webapps/$_gitname/database.yml" + install -Dm644 $_gitname-build/config/script_server.yml.example "$pkgdir/etc/webapps/$_gitname/script_server.yml" + install -Dm644 $_gitname-build/config/oauth_keys.yml.example "$pkgdir/etc/webapps/$_gitname/oauth_keys.yml" + + # Include all gems + cd "${usrdir}/${_gitname}" + mkdir -p ${usrdir}/${_gitname}/vendor/ruby/1.9.1/ + ln -s ${srcdir}/gem-cache ${usrdir}/${_gitname}/vendor/cache + ln -s ${srcdir}/gem-cache ${usrdir}/${_gitname}/vendor/ruby/1.9.1/cache + + export GEM_HOME="${PWD}/vendor" + export GEM_PATH="${PWD}/vendor" + export PATH="${GEM_PATH}/bin:${PATH}" + +# TODO extract mysql2 version from Gemfile + case $DB in + mysql) + tsocks gem install mysql2 -v "0.2.17" -- --with-mysql-config=/usr/bin/mysql_config + + ;; + posgres) + tsocks gem install pg -- --with-pg-config=/usr/bin/pg_config + + # Preconfigure right subsection in database.yml.example + sed -e "s/<<: \*mysql/#<<: \*mysql/" \ + -e "s/#<<: \*postgres/<<: \*postgres/" \ + -i $_gitname-build/config/database.yml.example + + # Preconfigure right db in script_server.yml + sed "s/db: \"mysql\"/db: \"postgres\"/" \ + -i $_gitname-build/config/script_server.yml.example + + esac + + tsocks gem install bundler + tsocks bundle install --path ${GEM_PATH} --without development test heroku install -d $pkgdir/usr/share/licenses/$_gitname/ install -Dm644 ${srcdir}/$_gitname-build/{AUTHORS,COPYRIGHT,GNU-AGPL-3.0} \ $pkgdir/usr/share/licenses/$_gitname/ + + msg "Removing gem cache" + rm -vr ${usrdir}/${_gitname}/vendor/{,ruby/1.9.1/}cache } -md5sums=('7e7402127f9a05bc58aff0adc5057d1c' - '7bffaaee41b515247ba19a19c77dc5bf' - '60f6b3972c73cbc6b1c9ab87c88fb655' - '96f82c38f3f540b53f3e5144900acf17') + +package_diaspora-mysql-git() { + pkgdesc="A privacy aware, personally controlled, do-it-all, open source social network (MySQL version)" + provides=('diaspora-mysql' 'diaspora') + depends=('ruby' 'redis' 'imagemagick' 'libxslt' 'net-tools' 'mysql' 'libmysqlclient') + options=(!strip) + + export DB="mysql" + export _db_rc="mysqld" + + _package +} + +package_diaspora-postgresql-git() { + pkgdesc="A privacy aware, personally controlled, do-it-all, open source social network (PostgreSQL version)" + provides=('diaspora-postgresql' 'diaspora') + depends=('ruby' 'redis' 'imagemagick' 'libxslt' 'net-tools' 'postgresql') + options=(!strip) + + export DB="postgres" + export _db_rc="postgresql" + + _package +} +pkgdesc="A privacy aware, personally controlled, do-it-all, open source social network" diff --git a/diaspora-git/diaspora.bashrc b/diaspora-git/diaspora.bashrc new file mode 100644 index 000000000..b694ca0b0 --- /dev/null +++ b/diaspora-git/diaspora.bashrc @@ -0,0 +1,6 @@ +export GEM_HOME="${HOME}/.gems" +export GEM_PATH="${HOME}/.gems" +export PATH="${GEM_PATH}/bin:${PATH}" +export RAILS_ENV="production" +export DB="-DB-" + diff --git a/diaspora-git/diaspora.bin b/diaspora-git/diaspora.bin index d18a40014..dfd0d026f 100644 --- a/diaspora-git/diaspora.bin +++ b/diaspora-git/diaspora.bin @@ -1,3 +1,9 @@ -cd /usr/share/webapps/diaspora -export GEM_HOME=/usr/share/webapps/diaspora-gems/ -./script/server &>>/var/log/diaspora.log +#!/bin/sh + +if [ "$(whoami)" == "diaspora" ]; then + cd /usr/share/webapps/diaspora + source ./.bashrc + ./script/server &>>/var/log/diaspora.log +else + echo 'Please run this as the "diaspora" user!' +fi diff --git a/diaspora-git/diaspora.install b/diaspora-git/diaspora.install index faf2cb78f..7833be058 100644 --- a/diaspora-git/diaspora.install +++ b/diaspora-git/diaspora.install @@ -1,12 +1,11 @@ dusr=diaspora dhome=/usr/share/webapps/diaspora -dgems=/usr/share/webapps/diaspora-gems dlog=/var/log/diaspora.log post_install() { getent passwd $dusr &>/dev/null || useradd -r -d $dhome -s /bin/bash $dusr &>/dev/null - chown -R $dusr:$dusr $dhome $dgems &>/dev/null + chown -R $dusr:$dusr $dhome &>/dev/null [[ -f $dlog ]] && chown $dusr:$dusr $dlog } diff --git a/diaspora-git/diaspora.rc b/diaspora-git/diaspora.rc index bd79237ee..8464f3947 100644 --- a/diaspora-git/diaspora.rc +++ b/diaspora-git/diaspora.rc @@ -10,8 +10,8 @@ PID=`pgrep -u $daemon_name` case "$1" in start) - #Check if mysqld and redis are running, start them if not - ck_daemon mysqld && /etc/rc.d/mysqld start + #Check if db and redis are running, start them if not + ck_daemon -DB- && /etc/rc.d/-DB- start ck_daemon redis && /etc/rc.d/redis start if [ ! -e /var/log/$daemon_name.log ]; then diff --git a/django-dev/PKGBUILD b/django-dev/PKGBUILD dissimilarity index 93% index 023f2464c..17e9f30c9 100644 --- a/django-dev/PKGBUILD +++ b/django-dev/PKGBUILD @@ -1,21 +1,27 @@ -# $Id$ -# Packager: Viktor Semykin - -pkgname=django-dev -pkgver=1.1 -pkgrel=1 -pkgdesc="Development version of a high-level Python Web framework." -arch=(any) -license=('BSD') -url="http://www.djangoproject.com" -provides=('django') -conflicts=('django') -depends=('setuptools') -source=(http://media.djangoproject.com/releases/1.1/Django-$pkgver-beta-1.tar.gz) -md5sums=('0a95c73ea5d46a75d1592984ad197dbd') - -build() { - cd $startdir/src/Django-$pkgver-beta-1 - python setup.py install --root=$startdir/pkg || return 1 - install -D -m644 LICENSE $startdir/pkg/usr/share/licenses/$pkgname/LICENSE - } +# Contributor: Viktor Semykin +pkgname=django-dev +pkgver=1.4alpha1 +pkgrel=1 +pkgdesc="Django framework development version." +arch=(any) +url="http://djangoproject.com" +license=(BSD) +groups=() +depends=(python2) +makedepends=() +provides=(django) +conflicts=(django) +replaces=() +backup=() +options=(!emptydirs) +install= +source=(https://www.djangoproject.com/m/releases/1.4/Django-1.4-alpha-1.tar.gz) +md5sums=(7a2e42bccb63f41a2c6931ddc36f46bf) + +package() { + cd "$srcdir/Django-1.4-alpha-1" + python2 setup.py install --root="$pkgdir/" --optimize=1 + install -D -m644 LICENSE $startdir/pkg/usr/share/licenses/$pkgname/LICENSE +} + +# vim:set ts=2 sw=2 et: diff --git a/epio/PKGBUILD b/epio/PKGBUILD index f97210933..790cf751e 100644 --- a/epio/PKGBUILD +++ b/epio/PKGBUILD @@ -5,7 +5,7 @@ pkgrel=1 pkgdesc="The command-line client for the ep.io service" arch=(any) url="https://www.ep.io/docs/client/" -license=(GPL) +license=(unknown) groups=() depends=(python2-httplib2) makedepends=() @@ -15,7 +15,7 @@ replaces=() backup=() options=(!emptydirs) install= -source=(http://pypi.python.org/packages/source/e/epio/epio-0.3.1.tar.gz) +source=(http://pypi.python.org/packages/source/e/epio/epio-$pkgver.tar.gz) md5sums=(0edec64e5ea1b90d31a22b25d587b3c0) package() { diff --git a/firefox-aurora-bin-it/PKGBUILD b/firefox-aurora-bin-it/PKGBUILD index 9c7272260..b462042a8 100644 --- a/firefox-aurora-bin-it/PKGBUILD +++ b/firefox-aurora-bin-it/PKGBUILD @@ -5,7 +5,7 @@ _mypkgn=firefox-aurora pkgdesc='Standalone web browser from mozilla.org (Italian version from Aurora channel)' url='http://www.mozilla.com/firefox/channel/' pkgver=11.0a2 -pkgrel=1 +pkgrel=2 arch=('i686' 'x86_64') license=('MPL' 'GPL' 'LGPL') depends=('desktop-file-utils' 'xulrunner' 'gnome-vfs' 'orbit2') @@ -25,14 +25,13 @@ sha512sums=('0597c08fec67e1755e8bfee89e82e5f44ce53ccab9529111a1ee7ccabb62cd078b9 $_ffsha512) package() { - mkdir -p ${pkgdir}/usr/{lib,bin} + mkdir -p ${pkgdir}/usr/{lib,bin,share/{applications,pixmaps}} cp -r firefox "${pkgdir}/usr/lib/${_mypkgn}" ln -s /usr/lib/libnotify.so ${pkgdir}/usr/lib/${_mypkgn}/libnotify.so.1 ln -s /usr/lib/${_mypkgn}/firefox ${pkgdir}/usr/bin/firefox-aurora - mkdir -p $pkgdir/usr/share/{applications,pixmaps} install -m644 {firefox-aurora.desktop,firefox-aurora-safe.desktop} ${pkgdir}/usr/share/applications/ install -m644 firefox/icons/mozicon128.png ${pkgdir}/usr/share/pixmaps/${_mypkgn}-icon.png } diff --git a/ghc-mod/PKGBUILD b/ghc-mod/PKGBUILD index e73b1b752..5a0189f3e 100644 --- a/ghc-mod/PKGBUILD +++ b/ghc-mod/PKGBUILD @@ -4,11 +4,11 @@ _licensefile=LICENSE # PKGBUILD options/directives pkgname=ghc-mod -pkgver=0.6.2 -pkgrel=6 +pkgver=1.0.2 +pkgrel=1 pkgdesc="Happy Haskell programming on Emacs" url="http://www.mew.org/~kazu/proj/ghc-mod/" -license=("BSD3") +license=('custom:BSD') arch=('i686' 'x86_64') makedepends=("ghc" "haskell-attoparsec" @@ -20,7 +20,7 @@ makedepends=("ghc" depends=() options=('strip') source=("http://hackage.haskell.org/packages/archive/${_hkgname}/${pkgver}/${_hkgname}-${pkgver}.tar.gz") -sha256sums=('99733b2deace5e04632b4e7bdda5b9edc3a34540dfaf91f65dc6b9831aa551ab') +sha256sums=('fa851743278e369aea617bc05c42cbd38130bffccb45d51b178333b0257a6900') # PKGBUILD functions @@ -38,4 +38,6 @@ package() { make install -d ${pkgdir}/usr/share/emacs/site-lisp cp *.elc *.el ${pkgdir}/usr/share/emacs/site-lisp + install -Dm644 ${srcdir}/${_hkgname}-${pkgver}/LICENSE \ + ${pkgdir}/usr/share/licenses/$pkgname/LICENSE } diff --git a/ginn/PKGBUILD b/ginn/PKGBUILD index 13e64ed48..934425a90 100644 --- a/ginn/PKGBUILD +++ b/ginn/PKGBUILD @@ -3,7 +3,7 @@ pkgname=ginn pkgver=0.2.5 pkgrel=2 -pkgdesc="" +pkgdesc="A deamon with jinn-like wish-granting capabilities: it gives applications the ability to support a subset of multi-touch gestures without having to integrate uTouch-GEIS or multi-touch GTK/Qt libs." url="http://launchpad.net/ginn" arch=('i686' 'x86_64') license=('GPL') diff --git a/java-gnome/PKGBUILD b/java-gnome/PKGBUILD index 1cdf9f9be..9f7216b33 100644 --- a/java-gnome/PKGBUILD +++ b/java-gnome/PKGBUILD @@ -1,23 +1,23 @@ -# Maintainer : Ionut Biru +# Maintainer: György Balló +# Contributor: Ionut Biru # Contributor: Timm Preetz pkgname=java-gnome -pkgver=4.0.17 +pkgver=4.1.1 pkgrel=1 pkgdesc="Java bindings to the GNOME platform (including gtk, glib and glade)" arch=('i686' 'x86_64') url="http://java-gnome.sourceforge.net" license=('GPL') -depends=('gtksourceview2' 'libnotify' 'libunique' 'gtkspell' 'libglade' 'java-runtime') +depends=('java-runtime' 'gtksourceview3' 'librsvg' 'libunique3' 'libnotify' 'enchant') makedepends=('java-environment' 'junit' 'python2') -options=(!libtool) -source=(http://ftp.gnome.org/pub/gnome/sources/${pkgname}/4.0/${pkgname}-${pkgver}.tar.bz2) -sha256sums=('350cd6c4d75995c309785794b8e216bf5c09568e52975f26ff0be7d79bb2a422') +source=(http://ftp.gnome.org/pub/gnome/sources/$pkgname/4.1/$pkgname-$pkgver.tar.xz) +sha256sums=('b013020d3da99740bae17e60f29b94c1d999183128612eac1f19a4570b045db2') build() { - cd ${srcdir}/${pkgname}-${pkgver} + cd "$srcdir/$pkgname-$pkgver" + #python2 - sed -i "s|env python|env python2|" build/faster - sed -i "s|env python|env python2|" src/util/demux/demux.py + sed -i 's@^#!.*python$@#!/usr/bin/python2@' build/faster src/util/demux/demux.py # adapt to the new build-system unset CLASSPATH @@ -27,9 +27,14 @@ build() { ./configure fi make - DISPLAY= make -j1 doc - make -j1 DESTDIR=${pkgdir} install + DISPLAY= make doc +} + +package() { + cd "$srcdir/$pkgname-$pkgver" + + make DESTDIR=$pkgdir install - install -d ${pkgdir}/usr/share/gtk-doc/html/java-gnome - cp -R ${srcdir}/java-gnome-${pkgver}/doc/api/* ${pkgdir}/usr/share/gtk-doc/html/java-gnome + install -d "$pkgdir/usr/share/gtk-doc/html/$pkgname" + cp -R "$srcdir"/$pkgname-$pkgver/doc/api/* "$pkgdir/usr/share/gtk-doc/html/$pkgname" } diff --git a/jsonrpc-cpp/PKGBUILD b/jsonrpc-cpp/PKGBUILD index 0c7686107..13930b13c 100644 --- a/jsonrpc-cpp/PKGBUILD +++ b/jsonrpc-cpp/PKGBUILD @@ -1,7 +1,7 @@ # Author: Jonahtan Schaeffer pkgname=jsonrpc-cpp -pkgver=0.2 +pkgver=0.3 pkgrel=1 pkgdesc="A C++ implementation of JSONRPC v2 protocol" url="http://jsonrpc-cpp.sourceforge.net/" @@ -9,11 +9,12 @@ license="GPL3" arch=('i686' 'x86_64') depends=('jsoncpp') makedepends=('scons' 'gcc') -source=("http://sourceforge.net/projects/jsonrpc-cpp/files/jsonrpc-cpp/jsonrpc-cpp-0.2/${pkgname}-${pkgver}.tar.bz2/download") -md5sums=('028a566d3123a864a15a1a8af7cbce46') +#source=("http://sourceforge.net/projects/jsonrpc-cpp/files/jsonrpc-cpp/jsonrpc-cpp-2/${pkgname}-${pkgver}.tar.bz2/download") +source=("http://downloads.sourceforge.net/project/jsonrpc-cpp/jsonrpc-cpp/jsonrcp-cpp-0.3.tar.bz2") +md5sums=('c64a5de3dc7b16ee22ae31ff61b3477d') build(){ - cd ${startdir}/src/${pkgname}-${pkgver} + cd ${startdir}/src/jsonrcp-cpp-0.3 scons scons install -Q prefix=${pkgdir}/usr } diff --git a/lib32-mesa-r600g-git/PKGBUILD b/lib32-mesa-r600g-git/PKGBUILD index 739b3a155..220a19532 100644 --- a/lib32-mesa-r600g-git/PKGBUILD +++ b/lib32-mesa-r600g-git/PKGBUILD @@ -3,18 +3,18 @@ # Maintainer: Lone_Wolf pkgname=lib32-mesa-r600g-git -pkgver=20111101 +pkgver=20120111 pkgrel=1 _realver=7.12 -pkgdesc="LIB32 Mesa R600 gallium - git version.If you live in the US, you should delete --enable-texture-float \ line." +pkgdesc="LIB32 Mesa R300 & R600 gallium - git version.If you live in the US, you should delete --enable-texture-float \ line." arch=('x86_64') -depends=('lib32-libxt' 'lib32-libxxf86vm' 'lib32-libxdamage' 'lib32-libffi' 'lib32-libxv' 'gcc-multilib' 'xorg-server' 'lib32-udev') +depends=('lib32-libxt' 'lib32-libxxf86vm' 'lib32-libxdamage' 'lib32-libffi' 'lib32-libxv' 'gcc-multilib' 'xorg-server' 'lib32-udev' 'mesa-r600g-git') makedepends=('pkgconfig' 'python2' 'talloc' 'libxml2' 'imake' 'git' 'glproto' 'dri2proto>=2.6' 'lib32-llvm' 'lib32-libxvmc' 'lib32-libvdpau' 'xorg-server-devel') optdepends=('lib32-libtxc_dxtn: S3TC support' 'lib32-mesa-demos: glxinfo and glxgears') -provides=(lib32-mesa=${_realver} lib32-libgl=${_realver} lib32-ati-dri=${_realver} lib32-libglapi=${_realver}) -replaces=(lib32-mesa lib32-libgl lib32-ati-dri lib32-libglapi) -conflicts=('xf86-video-ati<6.9.0-6' lib32-mesa lib32-libgl lib32-ati-dri lib32-libglapi) +provides=(lib32-mesa=${_realver} lib32-libgl=${_realver} lib32-ati-dri=${_realver} lib32-libglapi=${_realver} lib32-libegl=${_realver} ) +replaces=(lib32-mesa lib32-libgl lib32-ati-dri lib32-libglapi lib32-libegl) +conflicts=('xf86-video-ati<6.9.0-6' lib32-mesa lib32-libgl lib32-ati-dri lib32-libglapi lib32-libegl) url="http://mesa3d.sourceforge.net" license=(custom) source=(LICENSE) @@ -26,9 +26,9 @@ _gitname='mesa' build() { msg 'Connecting to git.freedesktop.org GIT server....' if [ -d ${_gitname} ] ; then - cd ${_gitname} && git pull origin --depth=1 + cd ${_gitname} && git pull origin else - git clone ${_gitroot} --depth=1 + git clone ${_gitroot} fi msg 'GIT checkout done or server timeout' msg 'Starting make...' @@ -50,7 +50,6 @@ build() { --with-dri-drivers=swrast \ --enable-texture-float \ --enable-glx-tls \ - --enable-xcb \ --enable-shared-dricore \ --enable-gbm \ --enable-gallium-gbm \ @@ -61,7 +60,8 @@ build() { --enable-32-bit \ --libdir=/usr/lib32 \ --enable-osmesa \ - --enable-xorg + --enable-xorg \ + --enable-gallium-egl \ # left out compile flags # default = auto # --enable-64-bit build 64-bit libraries [default=auto] @@ -90,30 +90,26 @@ build() { # --enable-d3d1x enable support for Direct3D 10 & 11 low-level API [default=no] # --enable-xa enable build of the XA X Acceleration API [default=no] # --enable-xlib-glx make GLX library Xlib-based instead of DRI-based [default=disable] -# --enable-gallium-egl enable optional EGL state tracker -# (not required for EGL support in Gallium with OpenGL and OpenGL ES) -# [default=disable] make } package() { -# Mesa +# lib32-Mesa cd "${srcdir}/build" make DESTDIR="${pkgdir}" install - rm -f "${pkgdir}/usr/lib32/libGL.so"* rm -f "${pkgdir}/usr/lib32/libGLESv"* rm -f "${pkgdir}/usr/lib32/libEGL"* rm -rf "${pkgdir}/usr/lib32/egl" - rm -f ${pkgdir}/usr/lib32/pkgconfig/{glesv1_cm.pc,glesv2.pc,egl.pc} + rm -f ${pkgdir}/usr/lib32/pkgconfig/{glesv1_cm.pc,glesv2.pc} rm -rf "${pkgdir}/usr/lib32/xorg" rm -f "${pkgdir}/usr/include/GL/glew.h" rm -f "${pkgdir}/usr/include/GL/glxew.h" rm -f "${pkgdir}/usr/include/GL/wglew.h" rm -f "${pkgdir}/usr/include/GL/glut.h" - rm -rf ${pkgdir}/usr/include/{GLES,GLES2,EGL,KHR} -# libgl + rm -rf ${pkgdir}/usr/include/{GLES,GLES2,KHR} +# lib32-libgl cd "${srcdir}/build" install -m755 -d "${pkgdir}/usr/lib32" install -m755 -d "${pkgdir}/usr/lib32/xorg/modules/extensions" @@ -123,7 +119,16 @@ package() { make -C ${srcdir}/build/src/gallium/targets/dri-swrast DESTDIR="${pkgdir}" install ln -s libglx.xorg "${pkgdir}/usr/lib32/xorg/modules/extensions/libglx.so" rm -rf "${pkgdir}"/usr/{include,share,bin} -# ati-dri +# lib32-libegl + cd "${srcdir}/build" + make -C src/gallium/targets/egl-static DESTDIR="${pkgdir}" install + install -m755 -d "${pkgdir}/usr/lib32" + install -m755 -d "${pkgdir}/usr/lib32/pkgconfig" + install -m755 -d "${pkgdir}/usr/lib32/egl" + bin/minstall lib32/libEGL.so* "${pkgdir}/usr/lib32/" + bin/minstall lib32/egl/* "${pkgdir}/usr/lib32/egl/" + bin/minstall src/egl/main/egl.pc "${pkgdir}/usr/lib32/pkgconfig/" +# lib32-ati-dri cd "${srcdir}/build/src/mesa/drivers/dri" make -C ${srcdir}/build/src/gallium/targets/dri-r300 DESTDIR="${pkgdir}" install make -C ${srcdir}/build/src/gallium/targets/dri-r600 DESTDIR="${pkgdir}" install diff --git a/linux-pax/PKGBUILD b/linux-pax/PKGBUILD index 9d73b926c..4a94addf0 100644 --- a/linux-pax/PKGBUILD +++ b/linux-pax/PKGBUILD @@ -9,7 +9,7 @@ _kernelname=${pkgname#linux} _basekernel=3.2 _paxver=test3 pkgver=${_basekernel} -pkgrel=2 +pkgrel=3 arch=(i686 x86_64) url="http://www.kernel.org/" license=(GPL2) @@ -45,7 +45,7 @@ md5sums=( f26cdeeb12f10b251d20a777203b0afc c792439f6f6c0dcedd1c71af63673d30 5d29c2995ffa1ac918dd6b269ec09ecc - b477a139f8fc66f4d72952f37d3565bf + d50670fac5d343d50e19ceb6e86dcd35 ) build() { @@ -152,4 +152,3 @@ package() { install -D -m755 $srcdir/$pkgname-fix-permissions \ $pkgdir/usr/bin/$pkgname-fix-permissions } - diff --git a/linux-pax/linux-pax-fix-permissions b/linux-pax/linux-pax-fix-permissions index c78cac38c..ca4cb99d0 100755 --- a/linux-pax/linux-pax-fix-permissions +++ b/linux-pax/linux-pax-fix-permissions @@ -10,6 +10,13 @@ perms=( /usr/lib/firefox/plugin-container /usr/lib/thunderbird/thunderbird-bin ' + # PAGEEXEC and MPROTECT off + ['pSmXER']=' + /opt/Osmos/Osmos.bin32 + /opt/Osmos/Osmos.bin64 + /usr/share/worldofgoo/WorldOfGoo.bin32 + /usr/share/worldofgoo/WorldOfGoo.bin64 + ' # MPROTECT off ['PSmXER']=' /usr/bin/glxgears @@ -39,7 +46,7 @@ for perm in ${!perms[@]}; do done echo -echo -n Continue writing PaX headers? \[Y/n\] +echo Continue writing PaX headers? \[Y/n\] read a diff --git a/mesa-r600g-git/PKGBUILD b/mesa-r600g-git/PKGBUILD index 9694d97bb..2642849b8 100644 --- a/mesa-r600g-git/PKGBUILD +++ b/mesa-r600g-git/PKGBUILD @@ -4,18 +4,18 @@ # Adapted from offical archlinux mesa package pkgname=mesa-r600g-git -pkgver=20111101 +pkgver=20120110 pkgrel=1 _realver=7.12 -pkgdesc="Mesa R600 gallium for Radeon HD 2xxx and later - git version.If you live in the US, you should delete --enable-texture-float \ line." +pkgdesc="Mesa for R300 & R600 chipsets - git version. If you live in the US, you should delete --enable-texture-float \ line." arch=('x86_64') -depends=('libxt' 'libxxf86vm' 'libxdamage' 'xorg-server' 'libffi' 'libxv') -makedepends=('pkgconfig' 'python2' 'talloc' 'libxml2' 'imake' 'git' 'glproto' 'dri2proto>=2.6' 'llvm' 'xorg-server-devel' 'libxvmc' 'libvdpau') +depends=('libxt' 'libxxf86vm' 'libxdamage' 'xorg-server' 'libxv' 'libffi') +makedepends=('pkgconfig' 'python2' 'talloc' 'libxml2' 'imake' 'git' 'glproto' 'dri2proto>=2.6' 'llvm>=3.0' 'xorg-server-devel' 'libxvmc' 'libvdpau') optdepends=('libtxc_dxtn: S3TC support' - 'mesa-demos: glxinfo and glxgears') -provides=(mesa=${_realver} libgl=${_realver} ati-dri=${_realver} libglapi=${_realver}) -replaces=(mesa libgl ati-dri libglapi) -conflicts=('xf86-video-ati<6.9.0-6' mesa libgl ati-dri libglapi) + 'mesa-demos-git: glxinfo and glxgears') +provides=(mesa=${_realver} libgl=${_realver} ati-dri=${_realver} libglapi=${_realver} libegl=${_realver} khrplatform-devel=${_realver}) +replaces=(mesa libgl ati-dri libglapi libegl khrplatform-devel) +conflicts=('xf86-video-ati<6.9.0-6' mesa libgl ati-dri libglapi libegl khrplatform-devel) url="http://mesa3d.sourceforge.net" license=(custom) source=(LICENSE) @@ -46,7 +46,6 @@ build() { --with-dri-drivers=swrast \ --enable-texture-float \ --enable-glx-tls \ - --enable-xcb \ --enable-shared-dricore \ --enable-gbm \ --enable-gallium-gbm \ @@ -56,6 +55,7 @@ build() { --enable-shared-glapi \ --enable-osmesa \ --enable-xorg \ + --enable-gallium-egl \ # left out compile flags # default = auto # --enable-32-bit build 32-bit libraries [default=auto] @@ -86,9 +86,6 @@ build() { # --enable-d3d1x enable support for Direct3D 10 & 11 low-level API [default=no] # --enable-xa enable build of the XA X Acceleration API [default=no] # --enable-xlib-glx make GLX library Xlib-based instead of DRI-based [default=disable] -# --enable-gallium-egl enable optional EGL state tracker -# (not required for EGL support in Gallium with OpenGL and OpenGL ES) -# [default=disable] make } @@ -102,13 +99,13 @@ package() { rm -f "${pkgdir}/usr/lib/libGLESv"* rm -f "${pkgdir}/usr/lib/libEGL"* rm -rf "${pkgdir}/usr/lib/egl" - rm -f ${pkgdir}/usr/lib/pkgconfig/{glesv1_cm.pc,glesv2.pc,egl.pc} + rm -f ${pkgdir}/usr/lib/pkgconfig/{glesv1_cm.pc,glesv2.pc} rm -rf "${pkgdir}/usr/lib/xorg" rm -f "${pkgdir}/usr/include/GL/glew.h" rm -f "${pkgdir}/usr/include/GL/glxew.h" rm -f "${pkgdir}/usr/include/GL/wglew.h" rm -f "${pkgdir}/usr/include/GL/glut.h" - rm -rf ${pkgdir}/usr/include/{GLES,GLES2,EGL,KHR} + rm -rf ${pkgdir}/usr/include/{GLES,GLES2} # libgl cd "${srcdir}/build" install -m755 -d "${pkgdir}/usr/lib" @@ -119,6 +116,31 @@ package() { cd src/mesa/drivers/dri make -C ${srcdir}/build/src/gallium/targets/dri-swrast DESTDIR="${pkgdir}" install ln -s libglx.xorg "${pkgdir}/usr/lib/xorg/modules/extensions/libglx.so" +# libglapi + cd "${srcdir}/build" + install -m755 -d "${pkgdir}/usr/lib" + bin/minstall lib/libglapi.so* "${pkgdir}/usr/lib/" +# libegl + cd "${srcdir}/build" + make -C src/gallium/targets/egl-static DESTDIR="${pkgdir}" install + install -m755 -d "${pkgdir}/usr/lib" + install -m755 -d "${pkgdir}/usr/lib/pkgconfig" + install -m755 -d "${pkgdir}/usr/include" + install -m755 -d "${pkgdir}/usr/include/" + install -m755 -d "${pkgdir}/usr/include/EGL" + install -m755 -d "${pkgdir}/usr/share" + install -m755 -d "${pkgdir}/usr/share/doc" + install -m755 -d "${pkgdir}/usr/share/doc/libegl" + bin/minstall lib/libEGL.so* "${pkgdir}/usr/lib/" + install -m755 -d "${pkgdir}/usr/lib/egl" + bin/minstall lib/egl/* "${pkgdir}/usr/lib/egl/" + bin/minstall src/egl/main/egl.pc "${pkgdir}/usr/lib/pkgconfig/" + bin/minstall include/EGL/* "${pkgdir}/usr/include/EGL/" + bin/minstall docs/egl.html "${pkgdir}/usr/share/doc/libegl/" +# khrplatform-devel + cd "${srcdir}/build" + install -m755 -d "${pkgdir}/usr/include/KHR" + bin/minstall include/KHR/khrplatform.h "${pkgdir}/usr/include/KHR/" # ati-dri cd "${srcdir}/build/src/mesa/drivers/dri" make -C ${srcdir}/build/src/gallium/targets/dri-r300 DESTDIR="${pkgdir}" install diff --git a/mrbayes/64bit-safe.patch b/mrbayes/64bit-safe.patch deleted file mode 100644 index c3f123eed..000000000 --- a/mrbayes/64bit-safe.patch +++ /dev/null @@ -1,2005 +0,0 @@ -diff -ur mrbayes-3.1.2.new/Makefile mrbayes-3.1.2/Makefile ---- mrbayes-3.1.2.new/Makefile 2006-08-08 16:26:36.000000000 +0200 -+++ mrbayes-3.1.2/Makefile 2005-12-22 17:13:06.000000000 +0100 -@@ -6,7 +6,6 @@ - # Set MPI=yes for the parallel version - MPI ?= no - --_64BIT ?= no - # Set DEBUG=yes for a debug version of mrbayes, otherwise set OPTFLAGS - # to the desired optimization level (e.g. -O2 -fomit-frame-pointer for - # less aggressive optimization than the default -O3) -@@ -64,10 +63,6 @@ - CFLAGS += $(OPTFLAGS) - endif - --ifeq ($(strip $(_64BIT)), yes) -- CFLAGS += -D_64BIT --endif -- - CFLAGS += -Wall - - LIBS += -lm -diff -ur mrbayes-3.1.2.new/bayes.c mrbayes-3.1.2/bayes.c ---- mrbayes-3.1.2.new/bayes.c 2006-08-08 16:01:52.000000000 +0200 -+++ mrbayes-3.1.2/bayes.c 2005-12-23 17:26:28.000000000 +0100 -@@ -81,11 +81,11 @@ - int defPairs; /* flag for whether pairs are read */ - Doublet doublet[16]; /* holds information on states for doublets */ - int fileNameChanged; /* has file name been changed ? */ --safeLong globalSeed; /* seed that is initialized at start up */ --int nBitsInALong; /* number of bits in a safeLong */ -+long int globalSeed; /* seed that is initialized at start up */ -+int nBitsInALong; /* number of bits in a long */ - int readWord; /* should we read word next ? */ --safeLong runIDSeed; /* seed used only for determining run ID [stamp] */ --safeLong swapSeed; /* seed used only for determining which to swap */ -+long int runIDSeed; /* seed used only for determining run ID [stamp] */ -+long int swapSeed; /* seed used only for determining which to swap */ - int userLevel; /* user level */ - - # if defined (MPI_ENABLED) -@@ -143,7 +143,7 @@ - # endif - /*mtrace();*/ - /* calculate the size of a long - used by bit manipulation functions */ -- nBitsInALong = sizeof(safeLong) * 8; -+ nBitsInALong = sizeof(long) * 8; - if (nBitsInALong > 32) /* Do not use more than 32 bits until we */ - nBitsInALong = 32; /* understand how 64-bit longs are handled. */ - -@@ -401,7 +401,7 @@ - if (proc_id == 0) - { - curTime = time(NULL); -- globalSeed = (safeLong)curTime; -+ globalSeed = (long int)curTime; - if (globalSeed < 0) - globalSeed = -globalSeed; - } -@@ -414,7 +414,7 @@ - if (proc_id == 0) - { - curTime = time(NULL); -- swapSeed = (safeLong)curTime; -+ swapSeed = (long int)curTime; - if (swapSeed < 0) - swapSeed = -swapSeed; - } -@@ -427,7 +427,7 @@ - if (proc_id == 0) - { - curTime = time(NULL); -- runIDSeed = (safeLong)curTime; -+ runIDSeed = (long int)curTime; - if (runIDSeed < 0) - runIDSeed = -runIDSeed; - } -@@ -439,17 +439,17 @@ - - # else - curTime = time(NULL); -- globalSeed = (safeLong)curTime; -+ globalSeed = (long int)curTime; - if (globalSeed < 0) - globalSeed = -globalSeed; - - curTime = time(NULL); -- swapSeed = (safeLong)curTime; -+ swapSeed = (long int)curTime; - if (swapSeed < 0) - swapSeed = -swapSeed; - - curTime = time(NULL); -- runIDSeed = (safeLong)curTime; -+ runIDSeed = (long int)curTime; - if (runIDSeed < 0) - runIDSeed = -globalSeed; - -@@ -473,7 +473,7 @@ - readWord = NO; /* should we read a word next ? */ - fileNameChanged = NO; /* has the file name been changed ? */ - echoMB = YES; /* flag used by Manual to control printing */ -- longIntegerSize = sizeof(safeLong); /* size of an safeLong */ -+ longIntegerSize = sizeof(long int); /* size of an long integer */ - - # if defined (MPI_ENABLED) - sprintf(manFileName, "commref_mb%sp.txt", VERSION_NUMBER); /* name of command reference file */ -diff -ur mrbayes-3.1.2.new/command.c mrbayes-3.1.2/command.c ---- mrbayes-3.1.2.new/command.c 2006-08-08 16:03:50.000000000 +0200 -+++ mrbayes-3.1.2/command.c 2005-12-23 17:53:30.000000000 +0100 -@@ -142,7 +142,7 @@ - int StateCode_AA (int n); - int StateCode_NUC4 (int n); - int StateCode_Std (int n); --void WhatVariableExp (unignedSafeLong exp, char *st); -+void WhatVariableExp (unsigned long int exp, char *st); - char WhichAA (int x); - MrBFlt WhichCont (int x); - char WhichRes (int x); -@@ -161,7 +161,7 @@ - char *constraintNames; /* holds names of constraints */ - int dataType; /* type of data */ - int echoMB; /* flag used by Manual to prevent echoing */ --unignedSafeLong expecting; /* variable denoting expected token type */ -+unsigned long int expecting; /* variable denoting expected token type */ - int foundNewLine; /* whether a new line has been found */ - int inComment; /* flag for whether input stream is commented */ - int inferAncStates; /* should ancestral states be inferred (y/n) */ -@@ -7348,13 +7348,13 @@ - - - --unignedSafeLong Expecting (int y) -+unsigned long int Expecting (int y) - - { - -- unignedSafeLong x; -+ unsigned long int x; - -- x = (unignedSafeLong)pow(2.0, (MrBFlt)y); -+ x = (unsigned long int)pow(2.0, (MrBFlt)y); - - return (x); - -@@ -12200,7 +12200,7 @@ - - - --void WhatVariableExp (unignedSafeLong exp, char *st) -+void WhatVariableExp (unsigned long int exp, char *st) - - { - -diff -ur mrbayes-3.1.2.new/command.h mrbayes-3.1.2/command.h ---- mrbayes-3.1.2.new/command.h 2006-08-08 16:03:50.000000000 +0200 -+++ mrbayes-3.1.2/command.h 2005-03-09 04:01:30.000000000 +0100 -@@ -1,7 +1,7 @@ - - - extern int AddToString (char *s1, char *s2, int *x); --extern unignedSafeLong Expecting (int y); -+extern unsigned long int Expecting (int y); - extern int CheckString (char *s1, char *s2, int *x); - extern int CheckStringValidity (char *s); - extern int DerootUserTree (TreeNode *p); -diff -ur mrbayes-3.1.2.new/globals.h mrbayes-3.1.2/globals.h ---- mrbayes-3.1.2.new/globals.h 2006-08-08 16:03:51.000000000 +0200 -+++ mrbayes-3.1.2/globals.h 2005-12-22 22:34:40.000000000 +0100 -@@ -17,11 +17,11 @@ - extern int defTaxa; /* flag for whether number of taxa is known */ - extern Doublet doublet[16]; /* holds information on states for doublets */ - extern int echoMB; /* flag used by Manual to prevent echoing */ --extern unignedSafeLong expecting; /* variable denoting expected token type */ -+extern long unsigned int expecting; /* variable denoting expected token type */ - extern int fileNameChanged; /* has file name been changed? */ - extern int foundNewLine; /* whether a new line has been found */ - extern char gapId; /* gap character Id */ --extern safeLong globalSeed; /* seed that is initialized at start up */ -+extern long int globalSeed; /* seed that is initialized at start up */ - extern char *headerNames; /* string to hold headers in sump and plot */ - extern int inComment; /* flag for whether input stream is commented */ - extern int inferAncStates; /* should ancestral states be inferred (y/n) */ -@@ -75,9 +75,9 @@ - extern ReassembleInfo reassembleParams; /* holds parameters for reassemble command */ - extern MrBFlt relConstraintProbs[30]; /* relative probs. of trees with constraint */ - extern int replaceLogFile; /* should logfile be replace/appended to */ --extern safeLong runIDSeed; /* seed used only for generating run ID [stamp] */ -+extern long int runIDSeed; /* seed used only for generating run ID [stamp] */ - extern char spacer[10]; /* holds blanks for printing indentations */ --extern safeLong swapSeed; /* seed used only for determining which to swap */ -+extern long int swapSeed; /* seed used only for determining which to swap */ - extern Sump sumpParams; /* holds parameters for sump command */ - extern Sumt sumtParams; /* holds parameters for sumt command */ - extern char stamp[11]; /* holds a unique identifier for each analysis */ -@@ -88,7 +88,7 @@ - extern int theAmbigChar; /* int containing ambiguous character */ - extern char *transFrom; /* translation block information */ - extern char *transTo; /* translation block information */ --extern int longIntegerSize; /* size of an safeLong */ -+extern int longIntegerSize; /* size of an long integer */ - extern int userBrlensDef; /* are the branch lengths on user tree defined */ - extern int userLevel; /* the level of the user */ - extern Tree *userTree; /* user tree */ -diff -ur mrbayes-3.1.2.new/mb.h mrbayes-3.1.2/mb.h ---- mrbayes-3.1.2.new/mb.h 2006-08-08 16:03:51.000000000 +0200 -+++ mrbayes-3.1.2/mb.h 2005-12-23 17:26:28.000000000 +0100 -@@ -6,22 +6,6 @@ - #endif - #endif - --/* found out that mrbayes crashes on 64 bit platform -- especially in sumt function. If every long is substituted with -- an int, it works. I'm going to define a safeLong and a unsigned -- safeLong for 64 bit platforms... -- Davide Cittaro - daweonline(at)gmail.com --*/ -- --#ifdef _64BIT --typedef int safeLong; --typedef unsigned int unignedSafeLong; --#else --typedef long safeLong; --typedef long unsigned int unignedSafeLong; --#endif -- -- - /* definition of UNIX_VERSION, WIN_VERSION or MAC_VERSION is now set in the - Makefile file; for compilers not using a project file or Makefile, use the #defines above to select version */ - -@@ -370,8 +354,8 @@ - struct node *left, *right, *anc; - int memoryIndex, index, upDateCl, upDateTi, marked, x, y, - scalerNode, isLocked, lockID, uL, dL, mL, isDated; -- safeLong scalersSet[MAX_NUM_DIV_LONGS], clSpace[MAX_NUM_DIV_LONGS], tiSpace[MAX_NUM_DIV_LONGS]; -- safeLong *partition; -+ long int scalersSet[MAX_NUM_DIV_LONGS], clSpace[MAX_NUM_DIV_LONGS], tiSpace[MAX_NUM_DIV_LONGS]; -+ long int *partition; - char label[100]; - MrBFlt length, nodeDepth, d, age; - Calibration *calibration; -@@ -405,7 +389,7 @@ - int x, y, mark, index, memoryIndex, isLocked, lockID, isDated; - MrBFlt length, support, f, age; - char label[100]; -- safeLong *partition; -+ long int *partition; - Calibration *calibration; - } - PolyNode; -@@ -561,7 +545,7 @@ - #define OMEGA_10FFF 108 - - /* typedef for a MoveFxn */ --typedef int (MoveFxn)(Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+typedef int (MoveFxn)(Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); - - /* struct holding info on each move type that the program handles */ - typedef struct -@@ -788,7 +772,7 @@ - int numStartPerts; /* number of perturbations to starting tree */ - char chainStartTree[100]; /* starting tree for chain (random/user) */ - int saveBrlens; /* should branch lengths be saved */ -- safeLong chainSeed; /* random seed for chain */ -+ long int chainSeed; /* random seed for chain */ - MrBFlt weightScheme[3]; /* percent chars to increase/decrease in weight */ - int calcPbf; /* should we calculate the pseudo Bayes factor */ - int pbfInitBurnin; /* initial burnin when calculating pseudo BF */ -@@ -963,12 +947,12 @@ - - typedef struct doublet - { -- safeLong first, second; -+ long int first, second; - } Doublet; - - typedef struct matrix - { -- safeLong *origin; -+ long *origin; - int rowSize; - int nRows; - int column; -diff -ur mrbayes-3.1.2.new/mbmath.c mrbayes-3.1.2/mbmath.c ---- mrbayes-3.1.2.new/mbmath.c 2006-08-08 16:01:53.000000000 +0200 -+++ mrbayes-3.1.2/mbmath.c 2005-12-23 17:26:28.000000000 +0100 -@@ -90,7 +90,7 @@ - void Exchange (int j, int k, int l, int m, int n, MrBFlt **a, MrBFlt *scale); - MrBFlt Factorial (int x); - void ForwardSubstitutionRow (int dim, MrBFlt **L, MrBFlt *b); --MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, safeLong *seed); -+MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, long int *seed); - void GaussianElimination (int dim, MrBFlt **a, MrBFlt **bMat, MrBFlt **xMat); - int Hqr2 (int dim, int low, int high, MrBFlt **h, MrBFlt *wr, MrBFlt *wi, MrBFlt **z); - MrBFlt IncompleteBetaFunction (MrBFlt alpha, MrBFlt beta, MrBFlt x); -@@ -108,9 +108,9 @@ - void PrintSquareDoubleMatrix (int dim, MrBFlt **matrix); - void PrintSquareIntegerMatrix (int dim, int **matrix); - complex ProductOfRealAndComplex (MrBFlt a, complex b); --MrBFlt RndGamma (MrBFlt s, safeLong *seed); --MrBFlt RndGamma1 (MrBFlt s, safeLong *seed); --MrBFlt RndGamma2 (MrBFlt s, safeLong *seed); -+MrBFlt RndGamma (MrBFlt s, long int *seed); -+MrBFlt RndGamma1 (MrBFlt s, long int *seed); -+MrBFlt RndGamma2 (MrBFlt s, long int *seed); - int SetQvalue (MrBFlt tol); - void SetToIdentity (int dim, MrBFlt **matrix); - MrBFlt Tha (MrBFlt h1, MrBFlt h2, MrBFlt a1, MrBFlt a2); -@@ -1910,7 +1910,7 @@ - | in the vector z. - | - ---------------------------------------------------------------------------------*/ --void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, safeLong *seed) -+void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, long int *seed) - - { - -@@ -2578,7 +2578,7 @@ - | a and b. The mean is E(X) = a / b and the variance is Var(X) = a / b^2. - | - ---------------------------------------------------------------------------------*/ --MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, safeLong *seed) -+MrBFlt GammaRandomVariable (MrBFlt a, MrBFlt b, long int *seed) - - { - -@@ -4746,11 +4746,11 @@ - | ones are hard to find. Communications of the ACM, 31(10):1192-1201. - | - ---------------------------------------------------------------------------------*/ --MrBFlt RandomNumber (safeLong *seed) -+MrBFlt RandomNumber (long int *seed) - - { - -- safeLong lo, hi, test; -+ long int lo, hi, test; - - hi = (*seed) / 127773; - lo = (*seed) % 127773; -@@ -4772,7 +4772,7 @@ - | RndGamma - | - ---------------------------------------------------------------------------------*/ --MrBFlt RndGamma (MrBFlt s, safeLong *seed) -+MrBFlt RndGamma (MrBFlt s, long int *seed) - - { - -@@ -4800,7 +4800,7 @@ - | RndGamma1 - | - ---------------------------------------------------------------------------------*/ --MrBFlt RndGamma1 (MrBFlt s, safeLong *seed) -+MrBFlt RndGamma1 (MrBFlt s, long int *seed) - - { - -@@ -4844,7 +4844,7 @@ - | RndGamma2 - | - ---------------------------------------------------------------------------------*/ --MrBFlt RndGamma2 (MrBFlt s, safeLong *seed) -+MrBFlt RndGamma2 (MrBFlt s, long int *seed) - - { - -diff -ur mrbayes-3.1.2.new/mbmath.h mrbayes-3.1.2/mbmath.h ---- mrbayes-3.1.2.new/mbmath.h 2006-08-08 16:01:53.000000000 +0200 -+++ mrbayes-3.1.2/mbmath.h 2005-03-09 04:01:30.000000000 +0100 -@@ -15,7 +15,7 @@ - void CalcCijk (int dim, MrBFlt *c_ijk, MrBFlt **u, MrBFlt **v); - void CopyComplexMatrices (int dim, complex **from, complex **to); - void CopyDoubleMatrices (int dim, MrBFlt **from, MrBFlt **to); --void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, safeLong *seed); -+void DirichletRandomVariable (MrBFlt *alp, MrBFlt *z, int n, long int *seed); - int DiscreteGamma (MrBFlt *rK, MrBFlt alfa, MrBFlt beta, int K, int median); - void FreeSquareComplexMatrix (complex **m); - void FreeSquareDoubleMatrix (MrBFlt **m); -@@ -25,4 +25,4 @@ - void MultiplyMatrices (int dim, MrBFlt **a, MrBFlt **b, MrBFlt **result); - int MultiplyMatrixNTimes (int dim, MrBFlt **Mat, int power, MrBFlt **Result); - MrBFlt QuantileGamma (MrBFlt x, MrBFlt alfa, MrBFlt beta); --MrBFlt RandomNumber (safeLong *seed); -+MrBFlt RandomNumber (long int *seed); -diff -ur mrbayes-3.1.2.new/mcmc.c mrbayes-3.1.2/mcmc.c ---- mrbayes-3.1.2.new/mcmc.c 2006-08-08 16:01:53.000000000 +0200 -+++ mrbayes-3.1.2/mcmc.c 2005-12-23 17:26:28.000000000 +0100 -@@ -139,21 +139,21 @@ - struct pfnode *left; - struct pfnode *right; - int *count; -- safeLong *partition; -+ long *partition; - } PFNODE; - - /* local prototypes */ - int AddDummyChars (void); - int AddTreeSamples (int from, int to); --PFNODE *AddPartition (PFNODE *r, safeLong *p, int runId); -+PFNODE *AddPartition (PFNODE *r, long *p, int runId); - int AddToPrintString (char *tempStr); - int AddTreeToPartitionCounters (Tree *tree, int treeId, int runId); - Tree *AllocateTree (int numTaxa, int isTreeRooted); --int AttemptSwap (int swapA, int swapB, safeLong *seed); --int Bit (int n, safeLong *p); -+int AttemptSwap (int swapA, int swapB, long int *seed); -+int Bit (int n, long *p); - int BuildConstraintTree (Tree *t, PolyTree *pt); - void BuildExhaustiveSearchTree (Tree *t, int chain, int nTaxInTree, TreeInfo *tInfo); --int BuildStartTree (Tree *t, safeLong *seed); -+int BuildStartTree (Tree *t, long int *seed); - int CalcLike_Adgamma (int d, Param *param, int chain, MrBFlt *lnL); - void CalcPartFreqStats (PFNODE *p, STATS *stat); - void CalculateTopConvDiagn (int numSamples); -@@ -214,12 +214,12 @@ - # endif - int ExhaustiveParsimonySearch (Tree *t, int chain, TreeInfo *tInfo); - int ExtendChainQuery (); --int FillNormalParams (safeLong *seed); -+int FillNormalParams (long int *seed); - int FillNumSitesOfPat (void); - int FillRelPartsString (Param *p, char relPartString[100]); --int FillTreeParams (safeLong *seed); -+int FillTreeParams (long int *seed); - int Flip01 (int x); --void FlipOneBit (int n, safeLong *p); -+void FlipOneBit (int n, long *p); - void FreeChainMemory (void); - void FreeTree (Tree *t); - void GetChainIds (void); -@@ -237,7 +237,7 @@ - void GetPossibleAAs (int aaCode, int aa[]); - void GetPossibleNucs (int nucCode, int nuc[]); - void GetPossibleRestrictionSites (int resSiteCode, int *sites); --int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, safeLong *seed, int *nEmbeddedTrees); -+int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, long *seed, int *nEmbeddedTrees); - MrBFlt GetRate (int division, int chain); - void GetSprParsimonyLengths (int chain, int nNodes1, int nNodes2, TreeNode **subTree1DP, TreeNode **subTree2DP, TreeNode *root2, MrBFlt *pLengths); - void GetStamp (void); -@@ -253,13 +253,13 @@ - int InitSprParsSets (void); - int InitTermCondLikes (void); - void InitTreeNode (TreeNode *p); --int IsBitSet (int i, safeLong *bits); -+int IsBitSet (int i, long *bits); - int IsClockSatisfied (Tree *t, MrBFlt tol); - int IsCalibratedClockSatisfied (Tree *t, MrBFlt tol); - int IsPFNodeEmpty (PFNODE *p); - void JukesCantor (MrBFlt *tiP, MrBFlt length); - PFNODE *LargestNonemptyPFNode (PFNODE *p, int *i, int j); --safeLong LastBlock (FILE *fp, char *lineBuf, int longestLine); -+long LastBlock (FILE *fp, char *lineBuf, int longestLine); - int Likelihood_Adgamma (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); - int Likelihood_Gen (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); - int Likelihood_NUC4 (TreeNode *p, int division, int chain, MrBFlt *lnL, int whichSitePats); -@@ -279,62 +279,62 @@ - void MarkClsBelow (TreeNode *p); - MrBFlt MaximumValue (MrBFlt x, MrBFlt y); - MrBFlt MinimumValue (MrBFlt x, MrBFlt y); --int Move_Aamodel (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Adgamma (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Beta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Beta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_BiasedSpr (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_BrLen (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Extinction (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Extinction_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtSPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtSS (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtTBR (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtTBR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtTBR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtTBR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ExtTBR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_GammaShape_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Growth (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Local (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_LocalClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_NNI (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_NNI_Hetero (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_NodeSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_NodeSliderClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Omega (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Omega_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaBeta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaCat (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaGamma_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaNeu (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaPos (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_OmegaPur (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_ParsEraser1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Pinvar (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_RanSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_RanSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_RanSPR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_RanSPR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_RateMult_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Revmat_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Speciation (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Speciation_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_SPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Statefreqs (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_StatefreqsSymDirMultistate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_SwitchRate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_SwitchRate_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Theta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_Tratio_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_TreeHeight (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); --int Move_UnrootedSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Aamodel (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Adgamma (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Beta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Beta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_BiasedSpr (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_BrLen (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Extinction (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Extinction_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtSPR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtSPR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtSPRClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtSS (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtTBR (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtTBR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtTBR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtTBR3 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ExtTBR4 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_GammaShape_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Growth (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Local (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_LocalClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_NNI (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_NNI_Hetero (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_NodeSlider (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_NodeSliderClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Omega (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Omega_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaBeta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaCat (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaGamma_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaNeu (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaPos (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_OmegaPur (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_ParsEraser1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Pinvar (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_RanSPR1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_RanSPR2 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_RanSPR3 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_RanSPR4 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_RateMult_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Revmat_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Speciation (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Speciation_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_SPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Statefreqs (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_StatefreqsSymDirMultistate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_SwitchRate (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_SwitchRate_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Theta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_Tratio_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_TreeHeight (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); -+int Move_UnrootedSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp); - void NodeToNodeDistances (Tree *t, TreeNode *fromNode); - int NumNonExcludedChar (void); - int NumNonExcludedTaxa (void); --int PickProposal (safeLong *seed); -+int PickProposal (long int *seed); - int PosSelProbs (TreeNode *p, int division, int chain); - int PreparePrintFiles (void); - int PrintAncStates_Bin (TreeNode *p, int division, int chain); -@@ -361,19 +361,19 @@ - int PrintTree (int curGen, Tree *tree); - int ProcessStdChars (void); - int PruneTree (Tree *t); --int RandResolve (Tree *destination, PolyTree *t, safeLong *seed); -+int RandResolve (Tree *destination, PolyTree *t, long *seed); - # if defined (MPI_ENABLED) - int ReassembleMoveInfo (void); - int ReassembleSwapInfo (void); - # endif - int RecreateTree (Tree *t, char *s); --int RemovePartition (PFNODE *r, safeLong *p, int runId); -+int RemovePartition (PFNODE *r, long *p, int runId); - int RemoveTreeFromPartitionCounters (Tree *tree, int treeId, int runId); - int RemoveTreeSamples (int from, int to); - int ReopenMBPrintFiles (void); - int RequestAbortRun(void); - int ResetScalers (void); --int RunChain (safeLong *seed); -+int RunChain (long int *seed); - int SaveSprintf(char **target, int *targetLen, char *fmt, ...); - int SetAARates (void); - int SetChainParams (void); -@@ -454,9 +454,9 @@ - int *compColPos; /* column position in compressed matrix */ - int *termState = NULL; /* index to terminal state ti:s */ - int *isPartAmbig = NULL; /* does terminal taxon have partial ambiguity */ --safeLong *compMatrix; /* compressed character matrix */ --safeLong *parsMatrix = NULL; /* parsimony (bitset) matrix for terminals */ --safeLong *parsSets = NULL; /* parsimony (bitset) matrix for int nodes */ -+long int *compMatrix; /* compressed character matrix */ -+long int *parsMatrix = NULL; /* parsimony (bitset) matrix for terminals */ -+long int *parsSets = NULL; /* parsimony (bitset) matrix for int nodes */ - CLFlt *numSitesOfPat; /* no. sites of each pattern */ - CLFlt *termCondLikes = NULL; /* cond likes for terminals */ - CLFlt *chainCondLikes; /* cond likes for chains */ -@@ -473,16 +473,16 @@ - int *nAccepted; /* counter of accepted moves */ - CLFlt **chainCLPtrSpace; /* space holding pointers to cond likes */ - CLFlt ***condLikePtr; /* pointers to cond likes for chain and node */ --safeLong **parsPtrSpace = NULL; /* space holding pointers to parsimony sets */ --safeLong ***parsPtr = NULL; /* pointers to pars state sets for chain & node */ -+long **parsPtrSpace = NULL; /* space holding pointers to parsimony sets */ -+long ***parsPtr = NULL; /* pointers to pars state sets for chain & node */ - CLFlt *parsNodeLengthSpace = NULL; /* space for parsimony node lengths */ - CLFlt **parsNodeLen = NULL; /* pointers to pars node lengths for chains */ - char *printString; /* string for printing to a file */ - size_t printStringSize; /* length of printString */ --safeLong *sprParsMatrix; /* SPR parsimony (bitset) matrix for terminals */ --safeLong *sprParsSets; /* SPR parsimony (bitset) matrix for all nodes */ --safeLong **sprParsPtrSpace; /* space holding pointers to SPR parsimony sets */ --safeLong ***sprParsPtr; /* ptrs to SPR pars state sets for chain & node */ -+long int *sprParsMatrix; /* SPR parsimony (bitset) matrix for terminals */ -+long int *sprParsSets; /* SPR parsimony (bitset) matrix for all nodes */ -+long **sprParsPtrSpace; /* space holding pointers to SPR parsimony sets */ -+long ***sprParsPtr; /* ptrs to SPR pars state sets for chain & node */ - int sprParsMatrixRowSize; /* row size of SPR parsimony matrix */ - CLFlt *treeScalerSpace; /* space holding tree scalers */ - CLFlt **treeScaler; /* pointers to tree scalers for each chain */ -@@ -535,7 +535,7 @@ - /*MrBFlt*/int abortMove; /* flag determining whether to abort move */ - PFNODE **partFreqTreeRoot; /* root of tree(s) holding partition freqs */ - int nLongsNeeded; /* number of longs needed for partitions */ --safeLong **partition; /* matrix holding partitions */ -+long **partition; /* matrix holding partitions */ - MrBFlt *maxLnL0 = NULL; /* maximum likelihood */ - FILE *fpMcmc = NULL; /* pointer to .mcmc file */ - FILE **fpParm = NULL; /* pointer to .p file(s) */ -@@ -561,7 +561,7 @@ - int i, j, k, d, numIncompatible, numDeleted, numStdChars, oldRowSize, - newRowSize, numDummyChars, newColumn, newChar, oldColumn, oldChar, - isCompat, *tempChar, numIncompatibleChars; -- safeLong *tempMatrix; -+ long *tempMatrix; - CLFlt *tempSitesOfPat; - ModelInfo *m; - ModelParams *mp; -@@ -626,7 +626,7 @@ - numCompressedChars += numDummyChars; - - /* allocate space for new data */ -- tempMatrix = (safeLong *) calloc (numLocalTaxa * newRowSize, sizeof(safeLong)); -+ tempMatrix = (long *) calloc (numLocalTaxa * newRowSize, sizeof(long)); - tempSitesOfPat = (CLFlt *) calloc (numCompressedChars, sizeof(CLFlt)); - tempChar = (int *) calloc (compMatrixRowSize, sizeof(int)); - if (!tempMatrix || !tempSitesOfPat || !tempChar) -@@ -838,7 +838,7 @@ - - - /* AddPartition: Add a partition to the tree keeping track of partition frequencies */ --PFNODE *AddPartition (PFNODE *r, safeLong *p, int runId) -+PFNODE *AddPartition (PFNODE *r, long *p, int runId) - { - int i, comp; - -@@ -935,7 +935,7 @@ - int AddTreeSamples (int from, int to) - { - int i, j, k, longestLine; -- safeLong lastBlock; -+ long lastBlock; - char *word, *s, *lineBuf; - FILE *fp; - Tree *t; -@@ -1115,7 +1115,7 @@ - - - --int AttemptSwap (int swapA, int swapB, safeLong *seed) -+int AttemptSwap (int swapA, int swapB, long int *seed) - - { - -@@ -1583,15 +1583,15 @@ - - /*---------------------------------------------------------------- - | --| Bit: return 1 if bit n is set in safeLong *p -+| Bit: return 1 if bit n is set in long *p - | else return 0 - | - -----------------------------------------------------------------*/ --int Bit (int n, safeLong *p) -+int Bit (int n, long *p) - - { - -- safeLong x; -+ long x; - - p += n / nBitsInALong; - x = 1 << (n % nBitsInALong); -@@ -1617,11 +1617,11 @@ - { - - int i, j, k, k1, nLongsNeeded, nextNode, nextActiveConstraint; -- safeLong *constraintPartition, *mask; -+ long int *constraintPartition, *mask; - PolyNode *pp, *qq, *rr, *ss, *tt; - - nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; -- constraintPartition = (safeLong *) calloc (2*nLongsNeeded, sizeof(safeLong)); -+ constraintPartition = (long int *) calloc (2*nLongsNeeded, sizeof(long int)); - if (!constraintPartition) - { - MrBayesPrint ("%s Problems allocating constraintPartition in BuildConstraintTree", spacer); -@@ -1898,7 +1898,7 @@ - | BuildStartTree: Build one starting tree - | - ----------------------------------------------------------------*/ --int BuildStartTree (Tree *t, safeLong *seed) -+int BuildStartTree (Tree *t, long int *seed) - - { - -@@ -1909,7 +1909,7 @@ - PolyTree constraintTree; - Tree *tempTree; - char tempName[100]; -- safeLong *bitsets; -+ long int *bitsets; - - /* set pointers allocated locally to NULL for correct exit on error */ - tempNums = NULL; -@@ -1955,7 +1955,7 @@ - /* make random tree consistent with constraints */ - /* first allocate space for partition specifiers and polytomous tree */ - nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; -- bitsets = (safeLong *) calloc (2*numLocalTaxa*nLongsNeeded, sizeof(safeLong)); -+ bitsets = (long int *) calloc (2*numLocalTaxa*nLongsNeeded, sizeof(long int)); - if (bitsets == NULL) - { - MrBayesPrint ("%s Problem allocating space for bitsets in BuildStartTree", spacer); -@@ -2595,7 +2595,7 @@ - - { - int c, i, j, nRates, posit; -- safeLong inHMM; -+ long int inHMM; - MrBFlt logScaler, max, prob, *F, - *oldF, *tempF, fSpace[2][MAX_GAMMA_CATS]; - MrBFlt *rP; -@@ -3054,15 +3054,15 @@ - { - - int a, b, i, j, k, nLongsNeeded; -- safeLong *constraintPartition, *mask, *bitsets; -+ long int *constraintPartition, *mask, *bitsets; - TreeNode *p=NULL; - - /* allocate space */ - nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; - -- bitsets = (safeLong *) calloc ((t->nNodes + 1)*nLongsNeeded + /*1*/ -+ bitsets = (long int *) calloc ((t->nNodes + 1)*nLongsNeeded + /*1*/ - 1+numLocalTaxa/nBitsInALong+1, -- sizeof(safeLong)); -+ sizeof(long int)); - - if (!bitsets) - { -@@ -3494,12 +3494,12 @@ - { - - int a, b, i, j, k, nLongsNeeded, foundIt, nextActiveConstraint; -- safeLong *constraintPartition, *mask, *bitsets; -+ long int *constraintPartition, *mask, *bitsets; - TreeNode *p; - - /* allocate space */ - nLongsNeeded = (numLocalTaxa / nBitsInALong) + 1; -- bitsets = (safeLong *) calloc (2*nLongsNeeded*numLocalTaxa + 2, sizeof(safeLong)); -+ bitsets = (long int *) calloc (2*nLongsNeeded*numLocalTaxa + 2, sizeof(long int)); - if (!bitsets) - { - MrBayesPrint ("%s Problems allocating bitsets in CheckSetConstraints", spacer); -@@ -3730,7 +3730,7 @@ - - int a, c, d, i, j, k, t, col[3], isSame, newRow, newColumn, - *isTaken, *tempSitesOfPat, *tempChar; -- safeLong *tempMatrix; -+ long *tempMatrix; - ModelInfo *m; - ModelParams *mp; - -@@ -3780,7 +3780,7 @@ - /* allocate space for temporary matrix, tempSitesOfPat, */ - /* vector keeping track of whether a character has been compressed, */ - /* and vector indexing first original char for each compressed char */ -- tempMatrix = (safeLong *) calloc (numLocalTaxa * numLocalChar, sizeof(safeLong)); -+ tempMatrix = (long *) calloc (numLocalTaxa * numLocalChar, sizeof(long)); - tempSitesOfPat = (int *) calloc (numLocalChar, sizeof(int)); - isTaken = (int *) calloc (numChar, sizeof(int)); - tempChar = (int *) calloc (numLocalChar, sizeof(int)); -@@ -3967,10 +3967,10 @@ - MrBayesPrint ("%s compMatrix not free in CompressData\n", spacer); - goto errorExit; - } -- compMatrix = (safeLong *) calloc (compMatrixRowSize * numLocalTaxa, sizeof(safeLong)); -+ compMatrix = (long *) calloc (compMatrixRowSize * numLocalTaxa, sizeof(long)); - if (!compMatrix) - { -- MrBayesPrint ("%s Problem allocating compMatrix (%d)\n", spacer, compMatrixRowSize * numLocalTaxa * sizeof(safeLong)); -+ MrBayesPrint ("%s Problem allocating compMatrix (%d)\n", spacer, compMatrixRowSize * numLocalTaxa * sizeof(long)); - goto errorExit; - } - memAllocs[ALLOC_COMPMATRIX] = YES; -@@ -6913,7 +6913,7 @@ - - int i, j, k, d, nParsStatesForCont, nuc1, nuc2, nuc3, newColumn, - codingNucCode, allNucCode, allAmbig; -- safeLong x, x1, x2, x3, *longPtr; -+ long x, x1, x2, x3, *longPtr; - ModelInfo *m; - ModelParams *mp; - -@@ -6932,7 +6932,7 @@ - mp = &modelParams[d]; - m->parsMatrixStart = parsMatrixRowSize; - -- /* find how many parsimony ints (safeLong) are needed for each model site */ -+ /* find how many parsimony ints (long) are needed for each model site */ - if (mp->dataType == CONTINUOUS) - { - /* scale continuous characters down to an ordered parsimony character */ -@@ -6953,7 +6953,7 @@ - MrBayesPrint ("%s parsMatrix not free in CreateParsMatrix\n", spacer); - return (ERROR); - } -- parsMatrix = (safeLong *) calloc (parsMatrixRowSize * numLocalTaxa, sizeof(safeLong)); -+ parsMatrix = (long *) calloc (parsMatrixRowSize * numLocalTaxa, sizeof(long)); - if (!parsMatrix) - { - MrBayesPrint ("%s Problem allocating parsMatrix\n", spacer); -@@ -7227,7 +7227,7 @@ - - { - -- safeLong seed, numGlobalChains; -+ long int seed, numGlobalChains; - int rc; - - # if defined (MPI_ENABLED) -@@ -8662,7 +8662,7 @@ - | FillNormalParams: Allocate and fill in non-tree parameters - | - -------------------------------------------------------------------------*/ --int FillNormalParams (safeLong *seed) -+int FillNormalParams (long int *seed) - - { - -@@ -9559,7 +9559,7 @@ - | FillTreeParams: Fill in trees and branch lengths - | - ------------------------------------------------------------------*/ --int FillTreeParams (safeLong *seed) -+int FillTreeParams (long int *seed) - - { - -@@ -9894,14 +9894,14 @@ - - /*----------------------------------------------------------------- - | --| FlipOneBit: flip bit n in safeLong *p -+| FlipOneBit: flip bit n in long *p - | - ------------------------------------------------------------------*/ --void FlipOneBit (int n, safeLong *p) -+void FlipOneBit (int n, long *p) - - { - -- safeLong x; -+ long x; - - p += n/nBitsInALong; - x = 1 << (n % nBitsInALong); -@@ -10562,7 +10562,7 @@ - { - - int c, i, n, division; -- safeLong *pL, *pR, *pP, *pA, x; -+ long *pL, *pR, *pP, *pA, x; - CLFlt *nSitesOfPat; - TreeNode *p; - ModelInfo *m; -@@ -10635,7 +10635,7 @@ - { - - int c, i, n, division; -- safeLong *pL, *pR, *pP, x; -+ long *pL, *pR, *pP, x; - CLFlt *nSitesOfPat; - TreeNode *p; - ModelInfo *m; -@@ -10684,7 +10684,7 @@ - { - - int c, i, n, division; -- safeLong *pL, *pR, *pP, *pA, x; -+ long *pL, *pR, *pP, *pA, x; - CLFlt *nSitesOfPat; - MrBFlt length; - TreeNode *p; -@@ -10759,7 +10759,7 @@ - { - - int c, i, n, division; -- safeLong *pD, *pP, *pA, x; -+ long *pD, *pP, *pA, x; - TreeNode *p; - ModelInfo *m; - -@@ -10994,7 +10994,7 @@ - - - --int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, safeLong *seed, int *nEmbeddedTrees) -+int GetRandomEmbeddedSubtree (Tree *t, int nTerminals, long *seed, int *nEmbeddedTrees) - - { - -@@ -11142,7 +11142,7 @@ - { - - int i, j, c, d; -- safeLong *cl, *clL, *clR, *clA, *clU, *clM, x, y, z; -+ long *cl, *clL, *clR, *clA, *clU, *clM, x, y, z; - CLFlt temp1, temp2=0.0; - CLFlt *nSitesOfPat; - TreeNode *p, *q; -@@ -11506,7 +11506,7 @@ - - int i, j, k, n, c, d, s, chain, nObs, chosen, oneMatSize, nNodes, - nScalerNodes, numReps; -- safeLong *charBits; -+ long *charBits; - ModelInfo *m; - ModelParams *mp; - CLFlt *clPtr; -@@ -12232,7 +12232,7 @@ - { - - int c, d, i, s, invCondLikeSize, isConstant; -- safeLong *charBits; -+ long int *charBits; - MrBFlt *cI; - ModelInfo *m; - ModelParams *mp; -@@ -12384,7 +12384,7 @@ - { - - int i, j, k, d, chain, nIntNodes, nNodes, nParsSets; -- safeLong *ptr; -+ long *ptr; - ModelInfo *m; - - /* Calculate number of nodes and number of internal nodes for rooted tree (worst case) */ -@@ -12417,9 +12417,9 @@ - MrBayesPrint ("%s Space for parsimony state sets not free in InitParsSets\n", spacer); - return ERROR; - } -- parsSets = (safeLong *) calloc (numLocalChains * nIntNodes * nParsSets * 2, sizeof(safeLong)); -- parsPtrSpace = (safeLong **) SafeMalloc (numLocalChains * nNodes * sizeof(safeLong *)); -- parsPtr = (safeLong ***) SafeMalloc (numLocalChains * sizeof(safeLong **)); -+ parsSets = (long *) calloc (numLocalChains * nIntNodes * nParsSets * 2, sizeof(long)); -+ parsPtrSpace = (long **) SafeMalloc (numLocalChains * nNodes * sizeof(long *)); -+ parsPtr = (long ***) SafeMalloc (numLocalChains * sizeof(long **)); - parsNodeLengthSpace = (CLFlt *) calloc (numLocalChains * parsNodeLenRowSize * 2, sizeof (CLFlt)); - parsNodeLen = (CLFlt **) SafeMalloc (numLocalChains * sizeof(CLFlt *)); - if (!parsSets || !parsPtrSpace || !parsPtr || !parsNodeLengthSpace || !parsNodeLen) -@@ -12520,7 +12520,7 @@ - { - - int c, i, j, d, chain, nIntNodes, nNodes; -- safeLong *ptr, x; -+ long *ptr, x; - ModelInfo *m; - - /* Calculate number of nodes and number of internal nodes for rooted tree (worst case) */ -@@ -12537,10 +12537,10 @@ - MrBayesPrint ("%s Space for SPR parsimony state sets not free in InitSprParsSets\n", spacer); - return ERROR; - } -- sprParsMatrix = (safeLong *) calloc (sprParsMatrixRowSize * numLocalTaxa, sizeof(safeLong)); -- sprParsSets = (safeLong *) calloc (numLocalChains * nNodes * sprParsMatrixRowSize * 3, sizeof(safeLong)); -- sprParsPtrSpace = (safeLong **) SafeMalloc (numLocalChains * nNodes * sizeof(safeLong *)); -- sprParsPtr = (safeLong ***) SafeMalloc (numLocalChains * sizeof(safeLong **)); -+ sprParsMatrix = (long *) calloc (sprParsMatrixRowSize * numLocalTaxa, sizeof(long)); -+ sprParsSets = (long *) calloc (numLocalChains * nNodes * sprParsMatrixRowSize * 3, sizeof(long)); -+ sprParsPtrSpace = (long **) SafeMalloc (numLocalChains * nNodes * sizeof(long *)); -+ sprParsPtr = (long ***) SafeMalloc (numLocalChains * sizeof(long **)); - if (!sprParsMatrix || !sprParsSets || !sprParsPtrSpace || !sprParsPtr) - { - if (sprParsMatrix) -@@ -12653,7 +12653,7 @@ - - int c, d, i, j, k, s, maxRates, numReps, oneMatSize, - corrModel[MAX_NUM_DIVS]; -- safeLong *charBits; -+ long int *charBits; - CLFlt *cL; - ModelInfo *m; - ModelParams *mp=NULL; -@@ -12970,11 +12970,11 @@ - - - --int IsBitSet (int i, safeLong *bits) -+int IsBitSet (int i, long *bits) - - { - -- safeLong x; -+ long x; - - bits += i / nBitsInALong; - -@@ -13341,9 +13341,9 @@ - - - /* LastBlock: Return file position of last block in file */ --safeLong LastBlock (FILE *fp, char *lineBuf, int longestLine) -+long LastBlock (FILE *fp, char *lineBuf, int longestLine) - { -- safeLong lastBlock; -+ long lastBlock; - char *word; - - lastBlock = 0L; -@@ -14085,7 +14085,7 @@ - { - - int c, i, nStates; -- safeLong done, *pL, *pR, *pP, *pA, *oldpP, x; -+ long done, *pL, *pR, *pP, *pA, *oldpP, x; - CLFlt nParsChars, treeLength; - CLFlt length, *nSitesOfPat, *newNodeLength, oldNodeLength; - Tree *t; -@@ -14266,7 +14266,7 @@ - { - - int c, i, *nStates; -- safeLong *pL, *pR, *pP, *pA, *oldpP, x; -+ long *pL, *pR, *pP, *pA, *oldpP, x; - CLFlt *treeLength; - CLFlt *nSitesOfPat; - Tree *t; -@@ -15095,7 +15095,7 @@ - - - --int Move_Aamodel (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Aamodel (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -15212,7 +15212,7 @@ - - - --int Move_Adgamma (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Adgamma (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -15280,7 +15280,7 @@ - - - --int Move_Beta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Beta (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -15411,7 +15411,7 @@ - | TODO: Smart update of tiprobs, rnd insert both ends of - | the moved branch on attachment branch - ----------------------------------------------------------------*/ --int Move_BiasedSpr (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_BiasedSpr (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -16013,7 +16013,7 @@ - - - --int Move_BrLen (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_BrLen (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -16095,7 +16095,7 @@ - - - --int Move_TreeHeight (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_TreeHeight (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -16294,7 +16294,7 @@ - - - --int Move_Extinction (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Extinction (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -16389,7 +16389,7 @@ - - - --int Move_Extinction_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Extinction_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -16484,7 +16484,7 @@ - - - --int Move_ExtSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtSPR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -17020,7 +17020,7 @@ - - - --int Move_ExtSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtSPR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -17562,7 +17562,7 @@ - - - --int Move_ExtSPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtSPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -17927,7 +17927,7 @@ - - - --int Move_ExtSS (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtSS (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -18471,7 +18471,7 @@ - - - --int Move_ExtTBR (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtTBR (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -18934,7 +18934,7 @@ - - - --int Move_ExtTBR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtTBR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -19456,7 +19456,7 @@ - - - --int Move_ExtTBR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtTBR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -20032,7 +20032,7 @@ - - - --int Move_ExtTBR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtTBR3 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -20648,7 +20648,7 @@ - - - --int Move_ExtTBR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ExtTBR4 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -21171,7 +21171,7 @@ - - - --int Move_GammaShape_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_GammaShape_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -21261,7 +21261,7 @@ - - - --int Move_Growth (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Growth (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -21382,7 +21382,7 @@ - | the boundary conditions into account - | - ----------------------------------------------------------------*/ --int Move_Local (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Local (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -21699,7 +21699,7 @@ - | does not change tree height. - | - ----------------------------------------------------------------*/ --int Move_LocalClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_LocalClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -22186,7 +22186,7 @@ - - - /* change topology using NNI */ --int Move_NNI (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_NNI (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -22259,7 +22259,7 @@ - - - /* change topology with unlinked brlens using NNI */ --int Move_NNI_Hetero (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_NNI_Hetero (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -22465,7 +22465,7 @@ - | - -------------------------------------------------------------------------------------*/ - --int Move_NodeSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_NodeSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - MrBFlt tuning, maxV, minV, oldM, newM, brlensPrExp=0.0, newMin, newMax, oldMin, oldMax; -@@ -22558,7 +22558,7 @@ - | - -------------------------------------------------------------------------------------*/ - --int Move_NodeSliderClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_NodeSliderClock (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - MrBFlt window, minV, minDepth, maxDepth, oldDepth, newDepth, oldLnPrior, newLnPrior, theta=0.0, growth=0.0, sR=0.0, eR=0.0, sF=0.0; -@@ -22772,7 +22772,7 @@ - | Note that this is appropriate when omegavar=equal - | - ----------------------------------------------------------------*/ --int Move_Omega (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Omega (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -22854,7 +22854,7 @@ - | omegavar=equal - | - ----------------------------------------------------------------*/ --int Move_Omega_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Omega_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -22937,7 +22937,7 @@ - | appropriate whenomegavar=M10 - | - ----------------------------------------------------------------*/ --int Move_OmegaBeta_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaBeta_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23025,7 +23025,7 @@ - | appropriate whenomegavar=M10 - | - ----------------------------------------------------------------*/ --int Move_OmegaGamma_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaGamma_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23120,7 +23120,7 @@ - - - #undef DO_DIR_CAT_PROP --int Move_OmegaCat (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaCat (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23288,7 +23288,7 @@ - | for neutral sites - | - ----------------------------------------------------------------*/ --int Move_OmegaNeu (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaNeu (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23371,7 +23371,7 @@ - | for positively selected sites - | - ----------------------------------------------------------------*/ --int Move_OmegaPos (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaPos (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23477,7 +23477,7 @@ - | for purifying selection sites - | - ----------------------------------------------------------------*/ --int Move_OmegaPur (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_OmegaPur (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23569,7 +23569,7 @@ - | Programmed by FR 2004-10-23-- - | - ----------------------------------------------------------------*/ --int Move_ParsEraser1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_ParsEraser1 (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23854,7 +23854,7 @@ - - - --int Move_Pinvar (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Pinvar (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -23918,7 +23918,7 @@ - - - --int Move_RanSPR1 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_RanSPR1 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -24486,7 +24486,7 @@ - - - --int Move_RanSPR2 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_RanSPR2 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -25066,7 +25066,7 @@ - - - --int Move_RanSPR3 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_RanSPR3 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -25714,7 +25714,7 @@ - - - --int Move_RanSPR4 (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_RanSPR4 (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -26416,7 +26416,7 @@ - | proposal. - | - ----------------------------------------------------------------*/ --int Move_RateMult_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_RateMult_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -26531,7 +26531,7 @@ - | mechanism. - | - ----------------------------------------------------------------*/ --int Move_Revmat_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Revmat_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -26632,7 +26632,7 @@ - - - --int Move_Speciation (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Speciation (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -26726,7 +26726,7 @@ - - - --int Move_Speciation_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Speciation_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -26829,7 +26829,7 @@ - | Programmed by JH 2002-11-18 - | - ----------------------------------------------------------------*/ --int Move_SPRClock (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_SPRClock (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27474,7 +27474,7 @@ - - - --int Move_Statefreqs (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Statefreqs (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27560,7 +27560,7 @@ - - - --int Move_StatefreqsSymDirMultistate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_StatefreqsSymDirMultistate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27653,7 +27653,7 @@ - - - --int Move_SwitchRate (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_SwitchRate (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27742,7 +27742,7 @@ - - - --int Move_SwitchRate_M (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_SwitchRate_M (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27831,7 +27831,7 @@ - - - --int Move_Theta (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Theta (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -27917,7 +27917,7 @@ - - - --int Move_Tratio_Dir (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_Tratio_Dir (Param *param, int chain, long int *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -28017,7 +28017,7 @@ - | Programmed by JH 2003-08-13 - | - ----------------------------------------------------------------*/ --int Move_UnrootedSlider (Param *param, int chain, safeLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) -+int Move_UnrootedSlider (Param *param, int chain, long *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp) - - { - -@@ -28979,7 +28979,7 @@ - - - --int PickProposal (safeLong *seed) -+int PickProposal (long int *seed) - - { - -@@ -30162,7 +30162,7 @@ - { - - int i, j=0, k, c, d, printWidth, nextColumn, nChars, inputChar; -- safeLong x, y; -+ long x, y; - char ch, tempName[200]; - ModelInfo *m; - ModelParams *mp; -@@ -32379,7 +32379,7 @@ - | RandResolve: Randomly resolve a polytomous tree - | - ---------------------------------------------------------------------*/ --int RandResolve (Tree *destination, PolyTree *t, safeLong *seed) -+int RandResolve (Tree *destination, PolyTree *t, long *seed) - - { - -@@ -32646,7 +32646,7 @@ - - - /* RemovePartition: Remove a partition from the tree keeping track of partition frequencies */ --int RemovePartition (PFNODE *r, safeLong *p, int runId) -+int RemovePartition (PFNODE *r, long *p, int runId) - { - int i, comp; - -@@ -32728,7 +32728,7 @@ - int RemoveTreeSamples (int from, int to) - { - int i, j, k, longestLine; -- safeLong lastBlock; -+ long lastBlock; - char *word, *s, *lineBuf=0; - FILE *fp; - Tree *t; -@@ -33079,7 +33079,7 @@ - - - --int RunChain (safeLong *seed) -+int RunChain (long int *seed) - - { - -@@ -35289,10 +35289,10 @@ - - - --void SetBit (int i, safeLong *bits) -+void SetBit (int i, long int *bits) - - { -- safeLong x; -+ long x; - - bits += i / nBitsInALong; - -@@ -39329,13 +39329,13 @@ - MrBayesPrint ("%s ERROR: pfcounters not free in SetUpPartitionCounters\n", spacer); - return ERROR; - } -- partition = (safeLong **) calloc (2*numLocalTaxa, sizeof (safeLong *)); -+ partition = (long **) calloc (2*numLocalTaxa, sizeof (long *)); - if (partition == NULL) - { - MrBayesPrint ("%s Failed to allocate partition in SetUpPartitionCounters\n", spacer); - return ERROR; - } -- partition[0] = (safeLong *) calloc (2*numLocalTaxa * nLongsNeeded, sizeof(safeLong)); -+ partition[0] = (long *) calloc (2*numLocalTaxa * nLongsNeeded, sizeof(long)); - if (partition[0] == NULL) - { - free (partition); -@@ -39381,7 +39381,7 @@ - { - - int i, j, k, n, c, d, x=0, nReps; -- safeLong *p; -+ long int *p; - ModelInfo *m; - ModelParams *mp; - -@@ -39859,7 +39859,7 @@ - if (temp == NULL) - return NULL; - -- temp->partition = (safeLong *) calloc (nLongsNeeded, sizeof (safeLong)); -+ temp->partition = (long *) calloc (nLongsNeeded, sizeof (long)); - if (temp->partition == NULL) - { - free (temp); -diff -ur mrbayes-3.1.2.new/mcmc.h mrbayes-3.1.2/mcmc.h ---- mrbayes-3.1.2.new/mcmc.h 2006-08-08 16:01:53.000000000 +0200 -+++ mrbayes-3.1.2/mcmc.h 2005-12-22 22:34:40.000000000 +0100 -@@ -10,5 +10,5 @@ - int MoveCalculationRoot (Tree *t, int outgroup); - FILE *OpenNewMBPrintFile (char *fileName); - int RootTree (Tree *t); --void SetBit (int i, safeLong *bits); -+void SetBit (int i, long *bits); - void SetUpMoveTypes (void); -diff -ur mrbayes-3.1.2.new/sumt.c mrbayes-3.1.2/sumt.c ---- mrbayes-3.1.2.new/sumt.c 2006-08-08 16:01:53.000000000 +0200 -+++ mrbayes-3.1.2/sumt.c 2005-12-23 17:26:29.000000000 +0100 -@@ -51,7 +51,7 @@ - struct stnode *left, *right, *anc; - int memoryIndex, index, upDateCl, upDateTi, marked, x, y, - scalerNode, taxonName; -- safeLong scalersSet, clSpace, tiSpace; -+ long scalersSet, clSpace, tiSpace; - char label[100]; - MrBFlt length; - } -@@ -66,8 +66,8 @@ - /* local prototypes */ - int AddTreeToList (int whichList); - int AllocBits (int n); --void AssignIntPart (safeLong *lft, safeLong *rht, safeLong *p); --void AssignTipPart (int n, safeLong *p); -+void AssignIntPart (long *lft, long *rht, long *p); -+void AssignTipPart (int n, long *p); - int BrlensVals (int treeNo, char *s, int longestLineLength, int lastTreeBlockBegin, int lastTreeBlockEnd); - void CalculateTreeToTreeDistance (int *lst[2], MrBFlt *lngs[2], int nnds, int hasBrlens, MrBFlt *d1, MrBFlt *d2, MrBFlt *d3); - int CheckSumtSpecies (void); -@@ -76,7 +76,7 @@ - int FindParts (void); - int FindTree (void); - void FinishSumtTree (SumtNode *p, int *i, int isThisTreeRooted); --int FirstTaxonInPartition (safeLong *partition, int length); -+int FirstTaxonInPartition (long *partition, int length); - int FreeBits (void); - void GetConDownPass (PolyNode **downPass, PolyNode *p, int *i); - int GetPartitions (void); -@@ -85,20 +85,20 @@ - int OpenBrlensFile (int treeNo); - int OpenComptFiles (void); - int OpenSumtFiles (int treeNo); --int PartFinder (safeLong *p, MrBFlt bl, int *partID); -+int PartFinder (long *p, MrBFlt bl, int *partID); - int PrintBrlensToFile (void); --void PrintParts (FILE *fp, safeLong *p, int nTaxaToShow); -+void PrintParts (FILE *fp, long *p, int nTaxaToShow); - int PruneSumt (void); - int RealloateBits (void); - int RealloateFullCompTrees (int whichList); - int RealloateFullTrees (void); - int ReorderParts (void); - int RootSumtTree (SumtNode *p, int n, int out); --void ShowBits (safeLong *p, int nBitsToShow); -+void ShowBits (long *p, int nBitsToShow); - void ShowConNodes (int nNodes, PolyNode *root); - int ShowConTree (FILE *fp, int nNodes, PolyNode *root, int screenWidth, int showSupport); - int ShowConPhylogram (FILE *fp, int nNodes, PolyNode *root, int screenWidth); --void ShowParts (safeLong *p, int nTaxaToShow); -+void ShowParts (long *p, int nTaxaToShow); - void ShowSumtNodes (SumtNode *p, int indent, int isThisTreeRooted); - void SortIndParts (int *item, MrBFlt *assoc, int count, int descendingOrder); - void SortIndParts2 (int *item, MrBFlt *assoc, int left, int right, int descendingOrder); -@@ -122,7 +122,7 @@ - *prunedTaxa, *absentTaxa, *firstPrunedTaxa, *firstAbsentTaxa, comparingFiles, fileNum, numCompTrees[2], numCompTreesSampled[2], - numFullCompTreesFound[2], numFullCompTreesAllocated[2], *fullCompTreePartIds1, *fullCompTreePartIds2, - numBrlens, printingBrlens, runIndex; --safeLong *treeBits, *treePartsFound, *taxonMask; -+long int *treeBits, *treePartsFound, *taxonMask; - MrBFlt *aBrlens, *sBrlens, *treePartLengths, *fullCompTreePartLengths1, *fullCompTreePartLengths2, - *brlens, *aWithinBrlens, *sWithinBrlens, *sumB, *sumsqB; - SumtNode *pSumtPtr, *qSumtPtr, *sumtRoot, *sumtNodes; -@@ -185,11 +185,11 @@ - { - - int i, j, offSet; -- safeLong x, y; -+ long x, y; - - /* decide how many unsigned ints are going to be needed to - represent a taxon number */ -- taxonLongsNeeded = (n / (sizeof(safeLong)*8)) + 1; -+ taxonLongsNeeded = (n / (sizeof(long int)*8)) + 1; - - /* how many partitions have been allocated */ - numPartsAllocated = MAX_PARTITIONS; -@@ -208,11 +208,11 @@ - treeBits = NULL; - treePartNums = NULL; - treePartLengths = NULL; -- treeBits = (safeLong *)SafeMalloc((size_t) (2 * n * taxonLongsNeeded * sizeof(safeLong))); -+ treeBits = (long *)SafeMalloc((size_t) (2 * n * taxonLongsNeeded * sizeof(long))); - treePartNums = (int *)SafeMalloc((size_t) (2 * n * sizeof(int))); - if (!treeBits || !treePartNums) - { -- MrBayesPrint ("%s Problem allocating treeBits (%d)\n", spacer, 2 * n * taxonLongsNeeded * sizeof(safeLong)); -+ MrBayesPrint ("%s Problem allocating treeBits (%d)\n", spacer, 2 * n * taxonLongsNeeded * sizeof(long)); - goto errorExit; - } - treePartLengths = (MrBFlt *)SafeMalloc((size_t) (2 * n * sizeof(MrBFlt))); -@@ -249,10 +249,10 @@ - goto errorExit; - } - treePartsFound = NULL; -- treePartsFound = (safeLong *)SafeMalloc((size_t) (taxonLongsNeeded * MAX_PARTITIONS * sizeof(safeLong))); -+ treePartsFound = (long *)SafeMalloc((size_t) (taxonLongsNeeded * MAX_PARTITIONS * sizeof(long))); - if (!treePartsFound) - { -- MrBayesPrint ("%s Problem allocating treePartsFound (%d)\n", spacer, taxonLongsNeeded * MAX_PARTITIONS * sizeof(safeLong)); -+ MrBayesPrint ("%s Problem allocating treePartsFound (%d)\n", spacer, taxonLongsNeeded * MAX_PARTITIONS * sizeof(long)); - goto errorExit; - } - memAllocs[ALLOC_TREEPARTS] = YES; -@@ -457,10 +457,10 @@ - goto errorExit; - } - taxonMask = NULL; -- taxonMask = (safeLong *)SafeMalloc((size_t) (taxonLongsNeeded * sizeof(safeLong))); -+ taxonMask = (long *)SafeMalloc((size_t) (taxonLongsNeeded * sizeof(long))); - if (!taxonMask) - { -- MrBayesPrint ("%s Problem allocating taxonMask (%d)\n", spacer, taxonLongsNeeded * sizeof(safeLong)); -+ MrBayesPrint ("%s Problem allocating taxonMask (%d)\n", spacer, taxonLongsNeeded * sizeof(long)); - goto errorExit; - } - memAllocs[ALLOC_TAXONMASK] = YES; -@@ -478,7 +478,7 @@ - prunedTaxa = (int *)SafeMalloc((size_t) (i * sizeof(int))); - if (!prunedTaxa) - { -- MrBayesPrint ("%s Problem allocating prunedTaxa (%d)\n", spacer, i * sizeof(safeLong)); -+ MrBayesPrint ("%s Problem allocating prunedTaxa (%d)\n", spacer, i * sizeof(long)); - goto errorExit; - } - absentTaxa = prunedTaxa + numTaxa; -@@ -579,11 +579,11 @@ - - - --void AssignTipPart (int n, safeLong *p) -+void AssignTipPart (int n, long *p) - - { - -- safeLong x; -+ long x; - - p += n / nBitsInALong; - x = 1 << (n % nBitsInALong); -@@ -595,7 +595,7 @@ - - - --void AssignIntPart (safeLong *lft, safeLong *rht, safeLong *p) -+void AssignIntPart (long *lft, long *rht, long *p) - - { - -@@ -992,7 +992,7 @@ - { - - int i, j, targetNode, nBits, nextConNode, isCompat, localOutgroupNum, numTerminalsEncountered; -- safeLong x, *mask = NULL, *partition = NULL, *ingroupPartition = NULL, *outgroupPartition = NULL; -+ long x, *mask = NULL, *partition = NULL, *ingroupPartition = NULL, *outgroupPartition = NULL; - MrBFlt freq; - char tempName[100]; - PolyNode *cp, *q, *r, *ql, *rl, *pl, **downPass = NULL; -@@ -1054,7 +1054,7 @@ - MrBayesPrint ("%s outgroupPartition is already allocated\n", spacer); - goto errorExit; - } -- outgroupPartition = (safeLong *) calloc (3 * taxonLongsNeeded, sizeof(safeLong)); -+ outgroupPartition = (long *) calloc (3 * taxonLongsNeeded, sizeof(long)); - if (!outgroupPartition) - { - MrBayesPrint ("%s Could not allocate outgroupPartition\n", spacer); -@@ -1687,8 +1687,8 @@ - longestLineLength1, longestLineLength2, xaxis, yaxis, starHolder[80], *treePartList[2], minNumTrees, - screenWidth, screenHeigth, numY[60], nSamples, nCompPartitions, numIncludedTaxa1, numIncludedTaxa2, - oldSumtBrlensDef, brlensDef; -- safeLong temporarySeed, len; -- safeLong *x; -+ long int temporarySeed, len; -+ long *x; - MrBFlt xProb, yProb, xInc, yInc, xUpper, xLower, yUpper, yLower, *treeLengthList[2], *dT1=NULL, *dT2=NULL, *dT3=NULL, d1, d2, d3, - meanY[60], xVal, yVal, minX, minY, maxX, maxY, sums[3]; - char *s=NULL, tempStr[100], tempName[100], prCh; -@@ -2725,7 +2725,7 @@ - - /* calculate average tree-to-tree distances */ - curTime = time(NULL); -- temporarySeed = (safeLong)curTime; -+ temporarySeed = (long int)curTime; - if (temporarySeed < 0) - temporarySeed = -temporarySeed; - sums[0] = sums[1] = sums[2] = 0.0; -@@ -2937,7 +2937,7 @@ - maxWidthNumberPartitions, tableWidth, unreliable, oneUnreliable, firstSumtBrlensDef=0, - numTotalTreesSampled; - MrBFlt var=0.0, f, var_s, sum_s, stddev_s=0.0, sumsq_s, varB, varW=0.0, sqrt_R=0.0; -- safeLong *x; -+ long *x; - char *s=NULL, tempName[100], tempStr[100], fileName[100]; - FILE *fp; - -@@ -5187,14 +5187,14 @@ - - - --int FirstTaxonInPartition (safeLong *partition, int length) -+int FirstTaxonInPartition (long *partition, int length) - - { - - int i, j, nBits, taxon; -- safeLong x; -+ long x; - -- nBits = sizeof(safeLong) * 8; -+ nBits = sizeof(long) * 8; - - for (i=taxon=0; i -# Maintainer: Stunts -pkgname=mrbayes -pkgver=3.1.2 -pkgrel=2 -pkgdesc="A program for the Bayesian estimation of phylogeny" -arch=('i686' 'x86_64') -license=('GPL') -url="http://mrbayes.csit.fsu.edu" -depends=('readline') -source=(http://downloads.sourceforge.net/mrbayes/${pkgname}-${pkgver}.tar.gz mb.1 mcmcdiagnparamprint.patch 64bit-safe.patch) -md5sums=('942e4e0a90fa23481bb1f2e0fa0e0d66' - 'f7148b480f1c0c4d7be73c5c4d84a194' - '71456a25cab345bd4686b050a5468cb2' - '6b62ab2b01e20d52e4b12f7ea8a4ba23') - -build() { - cd ${srcdir}/${pkgname}-${pkgver} - patch -p1 < ../../mcmcdiagnparamprint.patch - [ "$CARCH" = "i686" ] && make - [ "$CARCH" = "x86_64" ] && patch -R -p1 < ../../64bit-safe.patch - [ "$CARCH" = "x86_64" ] && OBJECT_MODE=64 make _64BIT=yes - install -D -m755 mb ${pkgdir}/usr/bin/mb - install -D -m644 ../mb.1 ${pkgdir}/usr/share/man/man1/mb.1 -} +# Original: Abhishek Dasgupta +# Maintainer: Stunts +pkgname=mrbayes +pkgver=3.2.0 +pkgrel=1 +pkgdesc="A program for the Bayesian estimation of phylogeny" +arch=('i686' 'x86_64') +license=('GPL') +url="http://mrbayes.csit.fsu.edu" +depends=('readline') +optdepends=('beagle-lib: for using GPU calculations among other enhancements - rebuild package after installing this dep') +source=(http://downloads.sourceforge.net/mrbayes/${pkgname}-${pkgver}.tar.gz) +md5sums=('e08c6728da2c711848902dca5832410a') + +build() { + #MrBayes requires specific LDFLAGS specified in the makefile. Thus we unset our own. + unset LDFLAGS + cd ${srcdir}/${pkgname}_${pkgver}/src + autoconf + #Build with beagle-lib support if available: + if [ pacman -Q beagle-lib |grep -v error] + then + ./configure --with-beagle=/usr + else + ./configure --with-beagle=no + fi + make +} +package() { + install -D -m755 ${srcdir}/${pkgname}_${pkgver}/src/mb ${pkgdir}/usr/bin/mb +} diff --git a/mrbayes/mb.1 b/mrbayes/mb.1 deleted file mode 100644 index 558353887..000000000 --- a/mrbayes/mb.1 +++ /dev/null @@ -1,31 +0,0 @@ -.TH mrbayes "1" "May 2008" "mrbayes 3.1.2" "User Commands" -.SH NAME -mb \- A program for the Bayesian estimation of phylogeny -.SH SYNOPSIS -.B mb [OPTION]... [FILE]... -.SH DESCRIPTION -A program for the Bayesian estimation of phylogeny. - -MrBayes is a program for the Bayesian estimation of -phylogeny. Bayesian inference of phylogeny is based upon a quantity -called the posterior probability distribution of trees, which is the -probability of a tree conditioned on the observations. The -conditioning is accomplished using Bayes's theorem. The posterior -probability distribution of trees is impossible to calculate -analytically; instead, MrBayes uses a simulation technique called -Markov chain Monte Carlo (or MCMC) to approximate the posterior -probabilities of trees. - -You can get a full manual in PDF format at their website. The URL is -http://mrbayes.csit.fsu.edu/mb3.1_manual.pdf - -.SH OPTIONS -.B \-i -interactive mode - -.SH AUTHORS - -This manual page has been written by Abhishek Dasgupta - for Archlinux since the original package did not -provide a manual page. It is based upon some slight additions and -alterations to the Ubuntu manual page for the same package. diff --git a/mrbayes/mcmcdiagnparamprint.patch b/mrbayes/mcmcdiagnparamprint.patch deleted file mode 100644 index a89507eb9..000000000 --- a/mrbayes/mcmcdiagnparamprint.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ur mrbayes-3.1.2.orig/mcmc.c mrbayes-3.1.2/mcmc.c ---- mrbayes-3.1.2.orig/mcmc.c 2005-12-24 05:26:28.000000000 +1300 -+++ mrbayes-3.1.2/mcmc.c 2007-08-17 11:58:14.858900600 +1200 -@@ -7871,7 +7871,7 @@ - free(tempStr); - return (ERROR); - } -- if (chainParams.saveBrlens == YES) -+ if (chainParams.mcmcDiagn == YES) - MrBayesPrint ("%s Calculating MCMC diagnostics\n", spacer); - else - MrBayesPrint ("%s Not calculating MCMC diagnostics\n", spacer); diff --git a/netbeans-javase/PKGBUILD b/netbeans-javase/PKGBUILD index b0ca4b752..fdfd50d64 100644 --- a/netbeans-javase/PKGBUILD +++ b/netbeans-javase/PKGBUILD @@ -5,10 +5,10 @@ basename=netbeans edname=javase pkgname=${basename}-${edname} -pkgver=7.0.1 -pkgdate=201107282000 +pkgver=7.1 +pkgdate=201112071828 pkgrel=1 -pkgdesc="A Java (SE) IDE" +pkgdesc="Oracle's Java (SE) IDE" arch=("any") url="http://${basename}.org" license=("CDDL") @@ -35,4 +35,4 @@ package() { install -D -m644 "${startdir}"/${basename}.desktop "${pkgdir}"/usr/share/applications/${basename}.desktop } -sha1sums=('8cc0b030e1adc5bb5b965fcdbffa0569fc5db9f8') +sha1sums=('edbc740eaa0093e8e3fd1078080f54cc0fd1ec78') diff --git a/pacmine/PKGBUILD b/pacmine/PKGBUILD index 516b7e477..4b0ccb02a 100644 --- a/pacmine/PKGBUILD +++ b/pacmine/PKGBUILD @@ -1,7 +1,7 @@ # Maintainer: Peter Richard Lewis pkgname=pacmine -pkgver=0.0.1 +pkgver=0.1.0 pkgrel=1 pkgdesc="A tool to get a list of someone's packages from archlinux.org" arch=(any) @@ -11,7 +11,7 @@ depends=('ruby' 'ruby-commander' 'ruby-hpricot') makedepends=(rubygems) source=(http://rubygems.org/downloads/$pkgname-$pkgver.gem) noextract=($pkgname-$pkgver.gem) -sha256sums=('9d7e306d7a187ee1a3980b6463c0051690b8053d3d071a179fa38e1ccd069f14') +sha256sums=('fc17f88f6e533d7783fe4375e2f50caaa88998acb5018f1329efc049d4fb6dc0') build() { cd $srcdir diff --git a/perftest/PKGBUILD b/perftest/PKGBUILD index ad779ddd0..8698a1538 100644 --- a/perftest/PKGBUILD +++ b/perftest/PKGBUILD @@ -2,9 +2,9 @@ # https://github.com/twinshadow/abs-ofed pkgname=perftest pkgver=1.3.0 -_subver=0.56 -_commit=gd6f6093 -pkgrel=1 +_subver=0.58 +_commit=g8f82435 +pkgrel=2 pkgdesc="InfiniBand performance tests" groups=('ofed') url="http://www.openfabrics.org" @@ -12,8 +12,8 @@ arch=('x86_64' 'i686') license=('GPL2' 'custom:"Open Fabrics Alliance BSD"') depends=('bash' 'libibumad' 'librdmacm') source=("http://www.openfabrics.org/downloads/${pkgname}/${pkgname}-${pkgver}-${_subver}.${_commit}.tar.gz") -md5sums=('9ab9f1ca36dd47eb184196c552dd2587') -sha512sums=('257696eeef4e32584b0f6e89405446d0496035a13765ec916406bec6e33e6f737f1ad27bd0eebfd25dc5e54718559fe130f225deea332584b0d614e85375dd4e') +md5sums=('5ac59f07e39ffe9726ceb10c3e32ba8e') +sha512sums=('ad7c1e09d22f65c1ee82da13b90e29b9b0d633878b4fc146b35555bb6554e228358e5354a57307bd5e78ede554f4e58cbe5a4d210bc96cd1efb8bf196e2dc9c4') build() { cd "${srcdir}/${pkgname}-${pkgver}" @@ -23,7 +23,7 @@ build() { package() { cd "${srcdir}/${pkgname}-${pkgver}" mkdir -p "${pkgdir}/usr/bin" - cp ib_* rdma_bw rdma_lat "${pkgdir}/usr/bin" + install -Dm755 ib_* rdma_bw rdma_lat "${pkgdir}/usr/bin" install -Dm755 runme "${pkgdir}/usr/share/${pkgname}/runme" install -Dm644 README "${pkgdir}/usr/share/${pkgname}/README" install -Dm644 COPYING "${pkgdir}/usr/share/licenses/${pkgname}/COPYING" diff --git a/photo/PKGBUILD b/photo/PKGBUILD index 64c1cd6fe..dcfa87de4 100755 --- a/photo/PKGBUILD +++ b/photo/PKGBUILD @@ -1,15 +1,15 @@ # Maintainer: archtux pkgname=photo -pkgver=0.3.0.1 -pkgrel=2 +pkgver=0.4 +pkgrel=1 pkgdesc="A fast, simple, good looking, yet powerfull and highly configurable image viewer." arch=('i686' 'x86_64') url="http://qt-apps.org/content/show.php/Photo?content=147453" license='GPL' depends=('qt>4.4') source=(http://qt-apps.org/CONTENT/content-files/147453-$pkgname-$pkgver.tar.gz) -md5sums='3664d72073611fe130fcd6e6a1370f68' +md5sums='262e0122be7779a22d267d9980645918' build() { cd $srcdir/$pkgname-$pkgver diff --git a/qt-static/PKGBUILD b/qt-static/PKGBUILD dissimilarity index 61% index 730a2c839..c4fd97a41 100644 --- a/qt-static/PKGBUILD +++ b/qt-static/PKGBUILD @@ -1,76 +1,73 @@ -# Maintainer: Sven-Hendrik Haase -# Contributor: Andrea Scarpino -# Contributor: Pierre Schmitz - -pkgname=qt-static -pkgver=4.8.0 -pkgrel=2 -pkgdesc='A cross-platform application and UI framework (static)' -arch=('i686' 'x86_64') -url='http://qt.nokia.com/' -license=('GPL3' 'LGPL') -options=('!libtool') -depends=() -makedepends=('mesa') -_pkgfqn="qt-everywhere-opensource-src-${pkgver}" -source=("ftp://ftp.qt.nokia.com/qt/source/${_pkgfqn}.tar.gz" - "qmake-static") -md5sums=('e8a5fdbeba2927c948d9f477a6abe904' - 'ea0914ee23bfd2f461d4fc8655a1db92') - -build() { - unset QMAKESPEC - export QT4DIR=$srcdir/$_pkgfqn - export PATH=${QT4DIR}/bin:${PATH} - export LD_LIBRARY_PATH=${QT4DIR}/lib:${LD_LIBRARY_PATH} - - cd $srcdir/$_pkgfqn - - sed -i "s|-O2|$CXXFLAGS|" mkspecs/common/g++.conf - sed -i "/^QMAKE_RPATH/s| -Wl,-rpath,||g" mkspecs/common/gcc-base-unix.conf - sed -i "/^QMAKE_LFLAGS\s/s|+=|+= $LDFLAGS|g" mkspecs/common/gcc-base.conf - - ./configure -confirm-license -opensource \ - -prefix /opt/qt-static \ - -largefile \ - -qt-sql-sqlite \ - -no-phonon \ - -no-phonon-backend \ - -no-webkit \ - -graphicssystem raster \ - -qt-zlib \ - -qt-libtiff \ - -qt-libpng \ - -qt-libmng \ - -qt-libjpeg \ - -nomake demos \ - -nomake examples \ - -nomake docs \ - -nomake tools \ - -nomake translations \ - -no-rpath \ - -openssl \ - -silent \ - -optimized-qmake \ - -dbus \ - -reduce-relocations \ - -no-gtkstyle \ - -no-opengl \ - -no-openvg \ - -no-glib \ - -static \ - -qpa - make -} - -package() { - cd $srcdir/$_pkgfqn - - make INSTALL_ROOT=$pkgdir install - - # Fix wrong path in prl files - find ${pkgdir}/opt/qt-static/lib -type f -name '*.prl' \ - -exec sed -i -e '/^QMAKE_PRL_BUILD_DIR/d;s/\(QMAKE_PRL_LIBS =\).*/\1/' {} \; - - install -Dm755 $srcdir/qmake-static $pkgdir/usr/bin/qmake-static -} +# Maintainer: Sven-Hendrik Haase +# Contributor: Andrea Scarpino +# Contributor: Pierre Schmitz + +pkgname=qt-static +pkgver=4.8.0 +pkgrel=3 +pkgdesc='A cross-platform application and UI framework (static)' +arch=('i686' 'x86_64') +url='http://qt.nokia.com/' +license=('GPL3' 'LGPL') +options=('!libtool') +depends=() +makedepends=('mesa') +_pkgfqn="qt-everywhere-opensource-src-${pkgver}" +source=("ftp://ftp.qt.nokia.com/qt/source/${_pkgfqn}.tar.gz" + "qmake-static") +md5sums=('e8a5fdbeba2927c948d9f477a6abe904' + 'ea0914ee23bfd2f461d4fc8655a1db92') + +build() { + cd "${srcdir}"/${_pkgfqn} + + export QT4DIR="${srcdir}"/${_pkgfqn} + export LD_LIBRARY_PATH=${QT4DIR}/lib:${LD_LIBRARY_PATH} + + sed -i "s|-O2|${CXXFLAGS}|" mkspecs/common/g++-base.conf + sed -i "/^QMAKE_LFLAGS_RPATH/s| -Wl,-rpath,||g" mkspecs/common/gcc-base-unix.conf + sed -i "/^QMAKE_LFLAGS\s/s|+=|+= ${LDFLAGS}|g" mkspecs/common/gcc-base.conf + + ./configure -confirm-license -opensource \ + -prefix /opt/qt-static \ + -qt-sql-sqlite \ + -no-phonon \ + -no-phonon-backend \ + -no-webkit \ + -graphicssystem raster \ + -qt-zlib \ + -qt-libtiff \ + -qt-libpng \ + -qt-libmng \ + -qt-libjpeg \ + -nomake demos \ + -nomake examples \ + -nomake docs \ + -nomake tools \ + -nomake translations \ + -openssl \ + -silent \ + -no-rpath \ + -optimized-qmake \ + -dbus \ + -reduce-relocations \ + -no-gtkstyle \ + -no-opengl \ + -no-openvg \ + -no-glib \ + -static \ + -qpa + make +} + +package() { + cd "${srcdir}"/${_pkgfqn} + + make INSTALL_ROOT="${pkgdir}" install + + # Fix wrong path in prl files + find "${pkgdir}/opt/qt-static/lib" -type f -name '*.prl' \ + -exec sed -i -e '/^QMAKE_PRL_BUILD_DIR/d;s/\(QMAKE_PRL_LIBS =\).*/\1/' {} \; + + install -Dm755 $srcdir/qmake-static $pkgdir/usr/bin/qmake-static +} diff --git a/ruby-commander/PKGBUILD b/ruby-commander/PKGBUILD new file mode 100644 index 000000000..427790802 --- /dev/null +++ b/ruby-commander/PKGBUILD @@ -0,0 +1,26 @@ +# Maintainer: Peter Richard Lewis +_gemname=commander +pkgname=ruby-$_gemname +pkgver=4.0.6 +pkgrel=1 +pkgdesc="The complete solution for Ruby command-line executables." +arch=(any) +url="http://visionmedia.github.com/commander/" +license=('MIT') +depends=('ruby' 'ruby-highline') # Full dependency information is available in the yaml specification +makedepends=('rubygems') +source=("http://gems.rubyforge.org/gems/$_gemname-$pkgver.gem") +noextract=($_gemname-$pkgver.gem) +sha256sums=('05449fbdb3e6beddca3b86d08709c3198f73df1194ed06f7a7be01defd94ce09') + +package() { + cd "$srcdir" + # _gemdir is defined inside package() because if ruby[gems] is not installed on + # the system, makepkg will exit with an error when sourcing the PKGBUILD. + local _gemdir="$(ruby -rubygems -e'puts Gem.default_dir')" + + gem install --ignore-dependencies -i "$pkgdir$_gemdir" -n "$pkgdir/usr/bin" \ + "$_gemname-$pkgver.gem" +} + +# vim:set ts=2 sw=2 et: diff --git a/sunrise-commander/PKGBUILD b/sunrise-commander/PKGBUILD index f37853a14..9f05595b9 100644 --- a/sunrise-commander/PKGBUILD +++ b/sunrise-commander/PKGBUILD @@ -1,6 +1,6 @@ # Maintainer: Stefan Husmann pkgname=sunrise-commander -pkgver=5r399 +pkgver=5r404 pkgrel=1 pkgdesc="a two panel filemanager for emacs" arch=('any') @@ -9,7 +9,7 @@ license=('GPL') depends=('emacs' 'avfs' 'fuse') optdepends=('zip: support for zip files' 'unzip: support for zip files') source=(http://www.emacswiki.org/emacs/download/sunrise-commander.el) -md5sums=('3069a0436d58a8f3104c7494c3188b9a') +md5sums=('7d54f2a4c169a85d9e126fe3086e0592') build() { cd "$srcdir" diff --git a/theide-nogtk-svn/PKGBUILD b/theide-nogtk-svn/PKGBUILD index 09d82ef1d..568c97431 100644 --- a/theide-nogtk-svn/PKGBUILD +++ b/theide-nogtk-svn/PKGBUILD @@ -1,7 +1,7 @@ # Maintainer: Jan Dolinar pkgname=theide-nogtk-svn -pkgver=4382 +pkgver=4392 pkgrel=1 pkgdesc="Modern IDE designed for developping large U++/C++ applications (nogtk version)" arch=('i686' 'x86_64') diff --git a/theide-svn/PKGBUILD b/theide-svn/PKGBUILD index fb3139b02..4fd0fa3bd 100644 --- a/theide-svn/PKGBUILD +++ b/theide-svn/PKGBUILD @@ -1,7 +1,7 @@ # Maintainer: Jan Dolinar pkgname=theide-svn -pkgver=4382 +pkgver=4392 pkgrel=1 pkgdesc="Modern IDE designed for developping large U++/C++ applications" arch=('i686' 'x86_64') diff --git a/upp-svn/PKGBUILD b/upp-svn/PKGBUILD index 6e18cede5..06f6c4c00 100644 --- a/upp-svn/PKGBUILD +++ b/upp-svn/PKGBUILD @@ -1,7 +1,7 @@ # Maintainer: Jan Dolinar pkgname=upp-svn -pkgver=4387 +pkgver=4396 pkgrel=1 pkgdesc="Radical and innovative multiplatform C++ framework (known as U++)" arch=('any') -- 2.11.4.GIT