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Merged
YoshitakaMo merged 3 commits into from
Aug 11, 2026
Merged

coot 1.3.2 #2338

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coot 1.3.2
YoshitakaMo Aug 11, 2026
74e5b8a
coot 1.3.2
YoshitakaMo Aug 11, 2026
c6d565e
coot 1.3.2
YoshitakaMo Aug 11, 2026
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11 changes: 2 additions & 9 deletions Formula/coot.rb
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
class Coot < Formula
desc "Crystallographic Object-Oriented Toolkit"
homepage "https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"
url "https://github.com/pemsley/coot/archive/refs/tags/Release-1.3.1.tar.gz"
sha256 "39069510b2bd499a407d5cc9202d4df591b353c344dd21aaf30e2ceab8260025"
url "https://github.com/pemsley/coot/archive/refs/tags/Release-1.3.2.tar.gz"
sha256 "8bd71e6582e87a8d2959bc1b956875a7f62c575b5a93ca60f2e575eaab42ff57"
license any_of: ["GPL-3.0-only", "LGPL-3.0-only", "GPL-2.0-or-later"]
head "https://github.com/pemsley/coot.git", branch: "main"

Expand Down Expand Up @@ -89,7 +89,7 @@
"python3.14"
end

def install

Check failure on line 92 in Formula/coot.rb

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GitHub Actions / build-bottles (macos-14)

`brew install --verbose --formula --build-bottle brewsci/bio/coot` failed on macOS Sonoma (14) on Apple Silicon! 

libtool: compile:  clang++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.3.2\" "-DPACKAGE_STRING=\"coot 1.3.2\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.3.2\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_LIBM=1 -DHAVE_LIBGSLCBLAS=1 -DHAVE_LIBGSL=1 -DHAVE_PYTHON=\"3.14\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_THREAD=/**/" "-DHAVE_BOOST_PYTHON=/**/" -DHAVE_RSVG=1 -DHAVE_NETCDF=1 -I. -DUSE_PYTHON -I/opt/homebrew/Cellar/gtk4/4.22.4/include/gtk-4.0 -I/opt/homebrew/Cellar/pango/1.58.2/include/pango-1.0 -I/opt/homebrew/Cellar/fribidi/1.0.16/include/fribidi -I/opt/homebrew/Cellar/libthai/0.1.30/include -I/opt/homebrew/Cellar/libdatrie/0.2.14/include -I/opt/homebrew/Cellar/harfbuzz/14.3.0/include/harfbuzz -I/opt/homebrew/opt/graphite2/include -I/opt/homebrew/include/gdk-pixbuf-2.0 -I/opt/homebrew/opt/libtiff/include -I/opt/homebrew/opt/webp/include -I/opt/homebrew/opt/webp/include/webp -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/Cellar/xz/5.8.3/include -I/opt/homebrew/opt/jpeg-turbo/include -I/opt/homebrew/Cellar/cairo/1.18.4/include/cairo -I/opt/homebrew/Cellar/fontconfig/2.18.3/include -I/opt/homebrew/Cellar/expat/2.8.3/include -I/opt/homebrew/opt/freetype/include/freetype2 -I/opt/homebrew/opt/libpng/include/libpng16 -I/opt/homebrew/Cellar/libxext/1.3.7/include -I/opt/homebrew/Cellar/xorgproto/2025.1/include -I/opt/homebrew/Cellar/libxrender/0.9.12/include -I/opt/homebrew/Cellar/libx11/1.8.13/include -I/opt/homebrew/Cellar/libxcb/1.17.0/include -I/opt/homebrew/Cellar/libxau/1.0.12/include -I/opt/homebrew/Cellar/libxdmcp/1.1.5/include -I/opt/homebrew/Cellar/pixman/0.46.4/include/pixman-1 -I/opt/homebrew/Cellar/graphene/1.10.8/include/graphene-1.0 -I/opt/homebrew/Cellar/graphene/1.10.8/lib/graphene-1.0/include -I/opt/homebrew/Cellar/glib/2.88.3/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/ffi -I/opt/homebrew/Cellar/glib/2.88.3/include/glib-2.0 -I/opt/homebrew/Cellar/glib/2.88.3/lib/glib-2.0/include -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/Cellar/pcre2/10.47_1/include -I/opt/homebrew/opt/zlib-ng-compat/include -DWITH_GZFILEOP -I.. -I/opt/homebrew/opt/rdkit/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -I/opt/homebrew/Cellar/eigen/5.0.1/include/eigen3 -pthread -I/opt/homebrew/opt/boost/include -DMAKE_ENHANCED_LIGAND_TOOLS -I/opt/homebrew/opt/glm/include -DHAVE_SYS_STDTYPES_H=0 -DUSE_MOLECULES_TO_TRIANGLES -I/opt/homebrew/Cellar/ssm/1.4_2/include -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DHAVE_SSMLIB -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/opt/homebrew/Cellar/gsl/2.8/include -I/opt/homebrew/Cellar/clipper4coot/2.1.20180802_3/include -D_THREAD_SAFE -pthread -I/opt/homebrew/Cellar/libccp4/8.0.0/include -I/opt/homebrew/Cellar/mmdb2/2.0.22/include -DCLIPPER_HAS_TOP8000 -I/opt/homebrew/Cellar/libvorbis/1.3.7/include -I/opt/homebrew/Cellar/libogg/1.3.6/include -DWITH_SOUND -DUSE_SQLITE3 -I/opt/homebrew/opt/sqlite/include -I/opt/homebrew/opt/gemmi/include -DUSE_GEMMI=1 -DUSE_BACKWARD -I/opt/homebrew/Cellar/vte3/0.84.1/include/vte-2.91-gtk4 -I/opt/homebrew/Cellar/gtk4/4.22.4/include/gtk-4.0 -I/opt/homebrew/Cellar/pango/1.58.2/include/pango-1.0 -I/opt/homebrew/Cellar/fribidi/1.0.16/include/fribidi -I/opt/homebrew/Cellar/libthai/0.1.30/include -I/opt/homebrew/Cellar/libdatrie/0.2.14/include -I/opt/homebrew/Cellar/harfbuzz/14.3.0/include/harfbuzz -I/opt/homebrew/opt/graphite2/include -I/opt/homebrew/include/gdk-pixbuf-2.0 -I/opt/homebrew/opt/libtiff/include -I/opt/homebrew/opt/webp/include -I/opt/homebrew/opt/webp/include/webp -I/opt/homebrew/opt/zstd/include -I/opt/homebrew/Cellar/xz/5.8.3/include -I/opt/homebrew/opt/jpeg-turbo/include -I/opt/homebrew/Cellar/cairo/1.18.4/include/cairo -I/opt/homebrew/Cellar/fontconfig/2.18.3/include -I/opt/homebrew/Cellar/expat/2.8.3/include -I/opt/homebrew/
# fix issue of https://github.com/pemsley/coot/issues/335
# include DYLD_FALLBACK_LIBRARY_PATH and GI_TYPELIB_PATH
glib_opt_lib = formula_opt_lib("glib")
Expand All @@ -105,13 +105,6 @@
"\nexec_prefix="
ENV.cxx11
ENV.libcxx
# clang 15 (macOS 14) predates C++20 parenthesized aggregate initialization
# (P0960, landed in clang 16), so this `new T(str)` on the plain aggregate
# em_placement_data_t fails to compile there. Brace-initialize it instead,
# which is valid C++17 and behaves identically (obj stays value-initialized).
inreplace "src/cc-interface-map-utils.cc",
"new em_placement_data_t(em_placement_output_file_name)",
"new em_placement_data_t{em_placement_output_file_name}"
inreplace "autogen.sh", "libtool", "glibtool"
system "./autogen.sh"
if OS.mac?
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