<pre style='margin:0'>
Perry E. Metzger (pmetzger) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/3daa8e84a49ccf0cf48f6ce4f08e7167ecbee0ed">https://github.com/macports/macports-ports/commit/3daa8e84a49ccf0cf48f6ce4f08e7167ecbee0ed</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 3daa8e8 bali-phy: update to version 3.0
</span>3daa8e8 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 3daa8e84a49ccf0cf48f6ce4f08e7167ecbee0ed
</span>Author: Benjamin Redelings <benjamin.redelings@gmail.com>
AuthorDate: Thu Dec 21 21:36:39 2017 -0800
<span style='display:block; white-space:pre;color:#404040;'> bali-phy: update to version 3.0
</span>---
science/bali-phy/Portfile | 151 +++++++----------------
science/bali-phy/files/configure.patch | 42 -------
science/bali-phy/files/scripts.patch | 36 +-----
science/bali-phy/files/src-tools-draw-tree.patch | 22 ----
4 files changed, 48 insertions(+), 203 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bali-phy/Portfile b/science/bali-phy/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 122364b..34f159f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bali-phy/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bali-phy/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,110 +1,51 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> PortSystem 1.0
<span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup github 1.0
</span>
<span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup bredelings BAli-Phy 1ed068ee00
</span> name bali-phy
<span style='display:block; white-space:pre;background:#ffe0e0;'>-version 2.1.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-description Bayesian Alignment and Phylogeny estimation
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description BAli-Phy can estimate phylogenetic trees from sequence data when the alignment \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- accounts for alignment uncertainty by integrating over all alignments. \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BAli-Phy does not rely on a guide tree because the alignment and the tree are \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- co-estimated. Therefore it can construct phylogeny estimates of widely \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- divergent sequences without bias toward a guide tree.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 3.0-release
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Estimation of phylogeny and multiple alignment via MCMC
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description Estimation of phylogeny and multiple alignment via MCMC \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BAli-Phy that estimates multiple sequence alignments and \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ evolutionary trees from DNA, amino acid, or codon sequences.\
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BAli-Phy uses MCMC and Bayesian methods to estimate \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ evolutionary trees, positive selection, and branch lengths \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ while averaging over alternative alignments. \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BAli-Phy can also estimate phylogenies from a fixed \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ alignment (like MrBayes and BEAST) using substitution \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ models like GTR+gamma. BAli-Phy automatically estimates \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ relative rates for each gene.
</span> categories science
platforms darwin
<span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage http://www.biomath.ucla.edu/msuchard/bali-phy/
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites ${homepage}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums sha1 e72073a1c5b05c797668e476bfd8517594f074e6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles configure.patch scripts.patch src-tools-draw-tree.patch
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib port:gsl port:boost path:lib/pkgconfig/cairo.pc:cairo
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_build port:pkgconfig
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.args --with-system-boost --enable-cairo
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.env-append BOOST_SUFFIX=-mt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant no_cairo description {disable drawing routines} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib-delete path:lib/pkgconfig/cairo.pc:cairo
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-delete --enable-cairo
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles-delete src-tools-draw-tree.patch
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant openmpi description {enable OpenMPI parallelization} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib-append port:openmpi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-append --with-mpi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-set gcc_versions {4.3 4.4 4.5 4.6 4.7 4.8 4.9}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-set default_fortran_variant +gcc48
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-foreach ver ${gcc_versions} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set ver_no_dot [join [split ${ver} "."] ""]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set conflicts_list {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- foreach over ${gcc_versions} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {${ver} eq ${over}} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- continue
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set over_no_dot [join [split ${over} "."] ""]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- lappend conflicts_list gcc${over_no_dot}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- variant gcc${ver_no_dot} description "build with gfortran from gcc${ver_no_dot}" \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- conflicts {*}${conflicts_list} {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[variant_isset gcc${ver_no_dot}]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {${default_fortran_variant} != "+gcc${ver_no_dot}"} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set default_fortran_variant ""
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-if {${default_fortran_variant} != ""} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- default_variants-append "${default_fortran_variant}"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-foreach ver ${gcc_versions} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set ver_no_dot [join [split ${ver} "."] ""]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[variant_isset gcc${ver_no_dot}]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib-append path:lib/libgcc/libgcc_s.1.dylib:libgcc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_build-append port:gcc${ver_no_dot}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.fc ${prefix}/bin/gfortran-mp-${ver}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.f77 ${prefix}/bin/gfortran-mp-${ver}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.f90 ${prefix}/bin/gfortran-mp-${ver}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# The project doesn't even configure with clang. Based on how long it's
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# been broken, I doubt this project is even used much, so it may not be
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# worh the effort to fix
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-#
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# conftest.cpp:60:11: error: no type named 'default_name_check' in 'boost::filesystem::path'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# fs::path::default_name_check(fs::portable_posix_name);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# ~~~~~~~~~~^
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# conftest.cpp:60:34: error: definition or redeclaration of 'portable_posix_name' not allowed inside a function
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# fs::path::default_name_check(fs::portable_posix_name);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# ~~~~^
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# 2 errors generated.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-compiler.blacklist *clang*
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-platform darwin {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {${os.major} >= 13} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # TODO: Test Mavericks once the clang build failures are addressed
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_build
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pre-fetch {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ui_error "$name does not build on Mavericks or later."
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- error "unsupported platform"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.type regex
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.url ${master_sites}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.regex {BAli-Phy (\d+\.\d+\.\d+) released}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license GPL-2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers {gmail.com:benjamin.redelings @bredelings} openmaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage http://www.bali-phy.org/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles scripts.patch
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums scripts.patch \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rmd160 7a1538fa6e0f92c3d64aecde29d4bf6193fae0c4 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 2577479293668711fac962243cc7f3b28469e7660bbb243751890576a79c4aeb \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BAli-Phy-1ed068ee00.tar.gz \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rmd160 7a1538fa6e0f92c3d64aecde29d4bf6193fae0c4 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 2577479293668711fac962243cc7f3b28469e7660bbb243751890576a79c4aeb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:pkgconfig \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:automake \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:autoconf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:libtool \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:eigen3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib port:boost \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ path:lib/pkgconfig/cairo.pc:cairo
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# build in source directory until we switch to meson
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+pre-configure { system -W ${worksrcpath} "./bootstrap.sh"}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args --with-system-boost --with-system-eigen
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.env-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BOOST_SUFFIX=-mt
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bali-phy/files/configure.patch b/science/bali-phy/files/configure.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 8b4f93d..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bali-phy/files/configure.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,42 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- configure.orig 2011-08-29 16:13:55.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ configure 2011-08-29 16:19:39.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6466,7 +6466,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $as_echo_n "(cached) " >&6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ac_check_lib_save_LIBS=$LIBS
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--LIBS="-lboost_filesystem${BOOST_SUFFIX} $LIBS"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+LIBS="-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX} $LIBS"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* end confdefs.h. */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6496,10 +6496,10 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #define `$as_echo "HAVE_LIBboost_filesystem${BOOST_SUFFIX}" | $as_tr_cpp` 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- _ACEOF
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- LIBS="-lboost_filesystem${BOOST_SUFFIX} $LIBS"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ LIBS="-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX} $LIBS"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- echo "Error: I can't find the boost_filesystem library! (-lboost_filesystem${BOOST_SUFFIX})" ; exit 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ echo "Error: I can't find the boost_filesystem library! (-lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX})" ; exit 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- fi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if test "$use_mpi" != no ; then
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6591,7 +6591,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- fi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--boost_libs="-lboost_program_options${BOOST_SUFFIX} -lboost_filesystem${BOOST_SUFFIX}";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+boost_libs="-lboost_program_options${BOOST_SUFFIX} -lboost_filesystem${BOOST_SUFFIX} -lboost_system${BOOST_SUFFIX}";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- { $as_echo "$as_me:${as_lineno-$LINENO}: checking include/compile/link for the BOOST.program_options library" >&5
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $as_echo_n "checking include/compile/link for the BOOST.program_options library... " >&6; }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6681,7 +6681,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- echo " * Not using system BOOST libraries: we'll build our own."
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- boost_includes="-isystem \$(top_srcdir)/boost/include"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- boost_libs="\$(top_builddir)/boost/lib/filesystem/libboost_filesystem.a \$(top_builddir)/boost/lib/program_options/libboost_program_options.a"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ boost_libs="\$(top_builddir)/boost/lib/filesystem/libboost_filesystem.a \$(top_builddir)/boost/lib/program_options/libboost_system.a \$(top_builddir)/boost/lib/program_options/libboost_program_options.a"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CXXFLAGS="$boost_includes $CXXFLAGS"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- LIBS="$boost_libs $LIBS"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bali-phy/files/scripts.patch b/science/bali-phy/files/scripts.patch
</span><span style='display:block; white-space:pre;color:#808080;'>index 96cdf0b..2ebd2e7 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bali-phy/files/scripts.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bali-phy/files/scripts.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,40 +1,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- scripts/bp-analyze.pl 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ scripts/bp-analyze.pl 2010-07-30 20:37:50.000000000 -0400
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- scripts/bp-analyze 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ scripts/bp-analyze 2010-07-30 20:37:50.000000000 -0400
</span> @@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl -w
# TODO
<span style='display:block; white-space:pre;background:#ffe0e0;'>---- scripts/compare-runs.R 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ scripts/compare-runs.R 2010-07-30 20:38:22.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1,3 +1,5 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#!/usr/bin/env R CMD BATCH
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read filename from the command line
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- args = commandArgs(trailingOnly=T)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- filename = args[1]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- scripts/fixedpt-alignment-distances 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ scripts/fixedpt-alignment-distances 2010-07-30 20:39:19.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#!/usr/bin/perl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#!/usr/bin/env perl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # Program calculates the distance between a given (MAP) alignment and all alignments in
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- scripts/pairwise-alignment-distances 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ scripts/pairwise-alignment-distances 2010-07-30 20:39:27.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#!/usr/bin/perl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#!/usr/bin/env perl
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # Program finds the posterior sample alignment that has the minimum average distance to all other samples.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- scripts/plot-path-graph.R 2010-06-18 16:57:34.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ scripts/plot-path-graph.R 2010-07-30 20:38:41.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#!/usr/bin/R CMD BATCH
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#!/usr/bin/env R CMD BATCH
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Rreverse = function(x) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- tmp =c(1:length(x))
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bali-phy/files/src-tools-draw-tree.patch b/science/bali-phy/files/src-tools-draw-tree.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 25a0703..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bali-phy/files/src-tools-draw-tree.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,22 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/tools/draw-tree.C 2010-07-30 16:51:37.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/tools/draw-tree.C 2010-07-30 20:20:43.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2441,8 +2441,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <boost/graph/graph_traits.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <boost/graph/adjacency_list.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <boost/graph/topological_sort.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#include <boost/graph/kamada_kawai_spring_layout.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#include <boost/graph/fruchterman_reingold.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include "../../boost/include/boost/graph/kamada_kawai_spring_layout.hpp"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include "../../boost/include/boost/graph/fruchterman_reingold.hpp"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- using namespace boost;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2502,7 +2502,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- };
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#include <boost/graph/random_layout.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include "../../boost/include/boost/graph/random_layout.hpp"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <boost/random/linear_congruential.hpp>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- graph_layout fruchterman_reingold_layout(graph_layout GL, double width, double height)
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