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bali-phy 4.0-beta5
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@bredelings @jonchang
bredelings authored and jonchang committed Aug 4, 2023
1 parent 9e8887a commit b962f57
Showing 1 changed file with 7 additions and 5 deletions.
12 changes: 7 additions & 5 deletions Formula/bali-phy.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,9 @@ class BaliPhy < Formula
# cite Redelings_2014: "https://dx.doi.org/10.1093/molbev/msu174"
desc "Bayesian co-estimation of phylogenies and multiple alignments"
homepage "http://www.bali-phy.org/"
url "https://github.com/bredelings/BAli-Phy/archive/3.6.1.tar.gz"
sha256 "6591f39d5708f5c34fca244f20326c6cba30bb32c80b72c6ae2e7e23bafcf11a"
url "https://github.com/bredelings/BAli-Phy.git",
tag: "4.0-beta5",
revision: "8fa2cad455025e8e4f1c76b163b0f89fada4409c"
license "GPL-2.0-or-later"
head "https://github.com/bredelings/BAli-Phy.git", branch: "master"

Expand All @@ -23,14 +24,16 @@ class BaliPhy < Formula
depends_on "ninja" => :build
depends_on "pandoc" => :build
depends_on "pkg-config" => :build
depends_on "boost"
depends_on "cairo"
depends_on "gcc@9" unless OS.mac? # for C++17
depends_on "gcc" unless OS.mac? # for C++20

# C++17
# C++20
fails_with gcc: "5"
fails_with gcc: "6"
fails_with gcc: "7"
fails_with gcc: "8"
fails_with gcc: "9"

def install

Check warning on line 38 in Formula/bali-phy.rb

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GitHub Actions / build-bottles (macos-11)

`brew install --verbose --build-bottle brewsci/bio/bali-phy` failed on macOS Big Sur (11)! 

Checking for function "feenableexcept" : NO 
Configuring config.h using configuration
Compiler for C++ supports arguments -Wno-sign-compare: YES 
Compiler for C++ supports arguments -Wno-maybe-uninitialized: NO 
Compiler for C++ supports arguments -Woverloaded-virtual: YES 
Compiler for C++ supports arguments -Wstrict-aliasing: YES 
Compiler for C++ supports arguments -Wno-unknown-pragmas: YES 
Compiler for C++ supports arguments -fdiagnostics-show-template-tree: YES 
Compiler for C++ supports arguments -funroll-loops: YES 
Compiler for C++ supports arguments -fno-math-errno: YES 
Compiler for C++ supports arguments -fno-signed-zeros: YES 
Run-time dependency threads found: YES
Found pkg-config: /usr/local/Homebrew/Library/Homebrew/shims/mac/super/pkg-config (0.29.2)
Run-time dependency cairo found: YES 1.16.0
Run-time dependency Boost (found: chrono, program_options, random, system) found: YES 1.82.0 (/usr/local)
Did not find CMake 'cmake'
Found CMake: NO
Run-time dependency eigen3 found: NO (tried pkgconfig, framework and cmake)
Looking for a fallback subproject for the dependency eigen3
Downloading eigen source from https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2
Downloading file of unknown size.
Downloading eigen patch from https://wrapdb.mesonbuild.com/v2/eigen_3.4.0-2/get_patch

Executing subproject eigen 

eigen| Project name: eigen
eigen| Project version: 3.4.0
eigen| C++ compiler for the host machine: clang++ (clang 13.0.0 "Apple clang version 13.0.0 (clang-1300.0.29.30)")
eigen| C++ linker for the host machine: clang++ ld64 711
eigen| Build targets in project: 0
eigen| Subproject eigen finished.

Dependency eigen3 from subproject subprojects/eigen-3.4.0 found: YES 3.4.0
Has header "nlohmann/json.hpp" : NO 
Message: Using internal copy of <nlohman/json.hpp>.
Library dl found: YES
Has header "range/v3/view/take.hpp" : NO 
Library m found: YES
Program pandoc found: YES (/usr/local/opt/pandoc/bin/pandoc)
Program /private/tmp/bali-phy-20230804-7251-mks68x/tests/run-tests.py found: YES (/private/tmp/bali-phy-20230804-7251-mks68x/tests/run-tests.py)
Build targets in project: 124

bali-phy 4.0-beta5

  Architecture
    arch          : x86_64
    host          : darwin

  Libraries
    Eigen         : True
    nlohmann::json: internal
    range v3      : internal
    cairo         : system


  Directories
    prefix        : /usr/local/Cellar/bali-phy/4.0-beta5

  Configuration
    optimization  : 3
    debug         : False
    assertions    : disabled

  Subprojects
    eigen         : YES

  User defined options
    buildtype     : release
    prefix        : /usr/local/Cellar/bali-phy/4.0-beta5
    b_ndebug      : true

Found ninja-1.11.1 at /usr/local/Homebrew/Library/Homebrew/shims/mac/super/ninja
WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated.
==> ninja -C build install
ninja: Entering directory `build'
[1/409] Generating src/git-version.h with a custom command
[2/409] Compiling C++ object src/util/libutil.a.p/log-level.cc.o
[3/409] Compiling C++ object src/util/libutil.a.p/string_pred.cc.o
[4/409] Compiling C++ object src/util/libutil.a.p/string_strip.cc.o
[5/409] Compiling C++ object src/util/libutil.a.p/string_sanitize.cc.o
[6/409] Compiling C++ object src/util/libutil.a.p/range.cc.o
[7/409] Compiling C++ object src/util/libutil.a.p/demangle.cc.o
[8/409] Compiling C++ object src/util/libutil.a.p/io.cc.o
[9/409] Compiling C++ object src/util/libutil.a.p/mapping.cc.o
[10/409] Compiling C++ object src/util/libutil.a.p/rng.cc.o
[11/409] Compiling C++ object src/util/libutil.a.p/string_split.cc.o
[12/409] Compiling C++ object src/util/libutil.a.p/permute.cc.o
[13/409] Compiling C++ object src/util/libutil.a.p/cmdline.cc.o
[14/409] Compiling C++ object src/util/libutil.a.p/file-paths.cc.o
[15/409] Compiling C++ object src/util/libutil.a.p/graph.cc.o
[16/409] Compiling C++ object src/util/libutil.a.p/text.cc.o
[17/409] Compiling C++ obj
flags = %w[-C build install]
Expand All @@ -41,6 +44,5 @@ def install
test do
system "#{bin}/bali-phy", "--version"
system "#{bin}/bali-phy", "#{doc}/examples/sequences/5S-rRNA/5d.fasta", "--iter=150"
system "#{bin}/bp-analyze", "5d-1"
end
end

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