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r2r 1.0.7 #2271

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r2r 1.0.7
BenjaminDEMAILLE Jul 7, 2026
847646c
r2r: fix CI (move R2R_Stockholm.pm out of bin)
BenjaminDEMAILLE Jul 8, 2026
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8 changes: 6 additions & 2 deletions Formula/r2r.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@
# cite Weinberg_2011: "https://doi.org/10.1186/1471-2105-12-3"
desc "Software to speed depiction of aesthetic consensus RNA secondary structures"
homepage "https://sourceforge.net/projects/weinberg-r2r/"
url "https://downloads.sourceforge.net/project/weinberg-r2r/R2R-1.0.6.tgz"
sha256 "1ba8f51db92866ebe1aeb3c056f17489bceefe2f67c5c0bbdfbddc0eee17743d"
url "https://downloads.sourceforge.net/project/weinberg-r2r/R2R-1.0.7.tgz"
sha256 "b18d26e27b84d022a59bb5cb33d0670fb5cc6245ce40808b2ef2fc9f8e968b61"

bottle do
root_url "https://ghcr.io/v2/brewsci/bio"
Expand All @@ -13,12 +13,16 @@

depends_on "nlopt"

def install

Check warning on line 16 in Formula/r2r.rb

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GitHub Actions / build-bottles (macos-15)

`brew install --verbose --formula --build-bottle brewsci/bio/r2r` failed on macOS Sequoia (15) on Apple Silicon! 

clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-12711-cktv4v/R2R-1.0.7\"" -c -o AdobeGraphics.o AdobeGraphics.cpp
clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-12711-cktv4v/R2R-1.0.7\"" -c -o AdobeGraphicsLayout.o AdobeGraphicsLayout.cpp
clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-12711-cktv4v/R2R-1.0.7\"" -c -o AdobeGraphicsPdfLike.o AdobeGraphicsPdfLike.cpp
In file included from AdobeGraphicsLayout.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
In file included from AdobeGraphicsPdfLike.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
In file included from AdobeGraphics.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
1 error generated.
make[1]: *** [AdobeGraphics.o] Error 1
make[1]: *** Waiting for unfinished jobs....
1 error generated.
make[1]: *** [AdobeGraphicsPdfLike.o] Error 1
1 error generated.
make[1]: *** [AdobeGraphicsLayout.o] Error 1
make: *** [install-recursive] Error 1

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/r2r.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-14-g3d58a45
ORIGIN: https://github.com/Homebrew/brew
HEAD: 3d58a45b3fee3f284c6926f286fcf6ac0d8eb30d
Last commit: 3 hours ago
Branch: main
Core tap HEAD: d0781c070584a556f3c97a352defeb378de9c4f8
Core tap last commit: 9 days ago
Core tap JSON: 08 Jul 21:15 UTC
Core cask tap HEAD: 94bf467564ff145b8b2723ba69441c18d86ae0f4
Core cask tap last commit: 9 days ago
Core cask tap JSON: 08 Jul 21:15 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 6
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 17.0.0 build 1700
Git: 2.39.5 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.7.7-arm64
CLT: 16.4.0.0.1.1747106510
Xcode: 16.4 => /Applications/Xcode_16.4.app/Contents/Developer
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /opt/homebrew/opt/nlopt/lib/pkgconfig
PKG_CONFIG_LIB

Check warning on line 16 in Formula/r2r.rb

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GitHub Actions / build-bottles (macos-26)

`brew install --verbose --formula --build-bottle brewsci/bio/r2r` failed on macOS Tahoe (26) on Apple Silicon! 

clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-8180-593whu/R2R-1.0.7\"" -c -o AdobeGraphics.o AdobeGraphics.cpp
clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-8180-593whu/R2R-1.0.7\"" -c -o AdobeGraphicsLayout.o AdobeGraphicsLayout.cpp
clang++ -DHAVE_CONFIG_H -I../NotByZasha/cfsqp -I../NotByZasha/infernal-0.7/squid     -g -O2 -DINKSCAPE_HELVETICA_FONTNAME="\"Bitstream Vera Sans\"" -DDISTRIBUTION -DDISABLE_CFSQP  -DR2R -Dabs_top_srcdir="\"/private/tmp/r2r-20260708-8180-593whu/R2R-1.0.7\"" -c -o AdobeGraphicsPdfLike.o AdobeGraphicsPdfLike.cpp
In file included from AdobeGraphics.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
In file included from AdobeGraphicsLayout.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
In file included from AdobeGraphicsPdfLike.cpp:1:
In file included from ./stdafx.h:48:
./multiDimVector.h:232:9: error: no member named 'Load' in 'MultiplyArray3d<T>'
  232 |                 this->Load(_s1,_s2,_s3);
      |                 ~~~~  ^
1 error generated.
make[1]: *** [AdobeGraphics.o] Error 1
make[1]: *** Waiting for unfinished jobs....
1 error generated.
make[1]: *** [AdobeGraphicsPdfLike.o] Error 1
1 error generated.
make[1]: *** [AdobeGraphicsLayout.o] Error 1
make: *** [install-recursive] Error 1

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/r2r.rb
==> Configuration
HOMEBREW_VERSION: 6.0.9-14-g3d58a45
ORIGIN: https://github.com/Homebrew/brew
HEAD: 3d58a45b3fee3f284c6926f286fcf6ac0d8eb30d
Last commit: 3 hours ago
Branch: main
Core tap HEAD: 907454ea24f451d2a462f6c364099277a553b866
Core tap last commit: 9 days ago
Core tap JSON: 08 Jul 21:29 UTC
Core cask tap HEAD: f5bbf0c10c7ca19568f0b4422352990b1c6dfdef
Core cask tap last commit: 9 days ago
Core cask tap JSON: 08 Jul 21:29 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_DOWNLOAD_CONCURRENCY: 6
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: 1589480+BrewTestBot@users.noreply.github.com
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 21.0.0 build 2100
Git: 2.50.1 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.4-arm64
CLT: 26.6.0.0.1781586589
Xcode: 26.5 => /Applications/Xcode_26.5.app/Contents/Developer
Metal Toolchain: 17.0 (17F42)
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/Library/Homebrew/shims/mac/super:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /opt/homebrew/opt/nlopt/lib/p
system "./configure", "--enable-nlopt",
"--disable-dependency-tracking",
"--prefix=#{prefix}"
system "make", "install"
doc.install "R2R-manual.pdf"
# R2R_Stockholm.pm is a Perl module, not an executable; keep it out of bin
libexec.install bin/"R2R_Stockholm.pm"
inreplace bin/"SelectSubFamilyFromStockholm.pl",
"use lib $Bin;", "use lib \"#{libexec}\";"
end

test do
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