Skip to content

mapcaller 0.9.9.41 #2254

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
BenjaminDEMAILLE wants to merge 2 commits into
base: develop
Choose a base branch
from
Open

mapcaller 0.9.9.41 #2254

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
3714fb5
mapcaller 0.9.9.41
BenjaminDEMAILLE Jul 7, 2026
56e0e95
mapcaller: depends_on zlib-ng-compat for Linux linkage
BenjaminDEMAILLE Jul 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions Formula/mapcaller.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
class Mapcaller < Formula
desc "Combined short-read alignment and variant detection"
homepage "https://github.com/hsinnan75/MapCaller"
url "https://github.com/hsinnan75/MapCaller/archive/refs/tags/v0.9.9.39.tar.gz"
sha256 "554c1d4fd1d2978ddcc657e758bc052874d31421cada2124e42f62588b527578"
url "https://github.com/hsinnan75/MapCaller/archive/refs/tags/v0.9.9.41.tar.gz"
sha256 "f1630d7c9243e70e33b244e3dfdb3ffa2a9836cea37fd2f8b49044dea029b12f"
license "MIT"

bottle do
Expand All @@ -12,12 +12,12 @@
end

depends_on "xz"
depends_on "zlib-ng-compat"

Check warning on line 15 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-26)

mapcaller: new dependency impact 

Adding `zlib-ng-compat` adds 1 new recursive dependency on arm64_tahoe (444.2KB).

Check warning on line 15 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-15)

mapcaller: new dependency impact 

Adding `zlib-ng-compat` adds 1 new recursive dependency on arm64_sequoia (445.0KB).

Check warning on line 15 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-14)

mapcaller: new dependency impact 

Adding `zlib-ng-compat` adds 1 new recursive dependency on arm64_sonoma (445.0KB).

uses_from_macos "bzip2"
uses_from_macos "curl"
uses_from_macos "zlib"

def install

Check warning on line 20 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-26)

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

ranlib libhts.a
/Applications/Xcode_26.5.app/Contents/Developer/usr/bin/make -C src
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c main.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c GetData.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c VariantCalling.cpp
clang++: error: unsupported option '-msse4.1' for target 'arm64-apple-darwin25.4.0'
make[1]: *** [GetData.o] Error 1
make[1]: *** Waiting for unfinished jobs....
clang++: error: unsupported option '-msse4.1' for target 'arm64-apple-darwin25.4.0'
make[1]: *** [main.o] Error 1
clang++: error: unsupported option '-msse4.1' for target 'arm64-apple-darwin25.4.0'
make[1]: *** [VariantCalling.o] Error 1
make: *** [MapCaller] Error 2

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/mapcaller.rb
==> Configuration
HOMEBREW_VERSION: 6.0.8-16-g8b48273
ORIGIN: https://github.com/Homebrew/brew
HEAD: 8b48273b7cc19686f3608d244958a327ab41ac1c
Last commit: 2 hours ago
Branch: main
Core tap HEAD: 907454ea24f451d2a462f6c364099277a553b866
Core tap last commit: 7 days ago
Core tap JSON: 07 Jul 12:07 UTC
Core cask tap HEAD: f5bbf0c10c7ca19568f0b4422352990b1c6dfdef
Core cask tap last commit: 7 days ago
Core cask tap JSON: 07 Jul 12:07 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/opt/zlib-ng-compat:/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/xz/lib/pkgconfig:/opt/homebrew/opt/zlib-ng-compat/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/26
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_GIT: /usr/bin/git
HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk
PATH: /opt/homebrew/Library/Homebrew/shims/mac/super/bin:/opt/homebrew/opt/xz/bin:/usr/bin:/bin:/usr/sbin:/sbin

Logs:
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/00.options.out
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/01.make.cc.log
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/01.make.log
If reporting this issue please do so at (not Homebrew/* repositories):
  https://github.com/brewsci/homebrew-bio/issues

::error::brewsci/bio/mapcaller 0.9.9.41 did not build

Check warning on line 20 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-15)

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

ranlib libhts.a
/Applications/Xcode_16.4.app/Contents/Developer/usr/bin/make -C src
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c main.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c GetData.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c VariantCalling.cpp
clang++clang++: : clang++error: : unsupported option '-msse4.1' for target 'arm64-apple-darwin24.6.0'
error: unsupported option '-msse4.1' for target 'arm64-apple-darwin24.6.0'
error: unsupported option '-msse4.1' for target 'arm64-apple-darwin24.6.0'
make[1]: *** [GetData.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [VariantCalling.o] Error 1
make[1]: *** [main.o] Error 1
make: *** [MapCaller] Error 2

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/mapcaller.rb
==> Configuration
HOMEBREW_VERSION: 6.0.8-16-g8b48273
ORIGIN: https://github.com/Homebrew/brew
HEAD: 8b48273b7cc19686f3608d244958a327ab41ac1c
Last commit: 2 hours ago
Branch: main
Core tap HEAD: d0781c070584a556f3c97a352defeb378de9c4f8
Core tap last commit: 7 days ago
Core tap JSON: 07 Jul 12:10 UTC
Core cask tap HEAD: 94bf467564ff145b8b2723ba69441c18d86ae0f4
Core cask tap last commit: 7 days ago
Core cask tap JSON: 07 Jul 12:10 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/opt/zlib-ng-compat:/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/xz/lib/pkgconfig:/opt/homebrew/opt/zlib-ng-compat/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/opt/homebrew/Library/Homebrew/os/mac/pkgconfig/15
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_GIT: /usr/bin/git
HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk
PATH: /opt/homebrew/Library/Homebrew/shims/mac/super/bin:/opt/homebrew/opt/xz/bin:/usr/bin:/bin:/usr/sbin:/sbin

Logs:
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/00.options.out
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/01.make.cc.log
     /Users/runner/work/homebrew-bio/homebrew-bio/logs/mapcaller/01.make.log
If reporting this issue please do so at (not Homebrew/* repositories):
  https://github.com/brewsci/homebrew-bio/issues

::error::brewsci/bio/mapcaller 0.9.9.41 did not build

Check warning on line 20 in Formula/mapcaller.rb

View workflow job for this annotation

GitHub Actions / build-bottles (macos-14)

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

g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c bwt_search.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c nw_alignment.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c ksw2_alignment.cpp
g++ -Wall -D NDEBUG -O3 -m64 -msse4.1 -c KmerAnalysis.cpp
In file included from ksw2_alignment.cpp:2:
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
In file included from ksw2_alignment.cpp:2:
In file included from /Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/emmintrin.h:17:
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
In file included from ksw2_alignment.cpp:2:
In file included from /Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/emmintrin.h:17:
In file included from /Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/xmmintrin.h:17:
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:37:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
    __builtin_ia32_emms();
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/math.h:507:10: note: '__builtin_isless' declared here
  return __builtin_isless((type)__x, (type)__y);
         ^
In file included from ksw2_alignment.cpp:2:
In file included from /Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/emmintrin.h:17:
In file included from /Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/xmmintrin.h:17:
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:37:25: error: too few arguments to function call, expected 2, have 0
    __builtin_ia32_emms();
    ~~~~~~~~~~~~~~~~~~~~^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:54:19: error: use of undeclared identifier '__builtin_ia32_vec_init_v2si'
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
                  ^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:71:12: error: use of undeclared identifier '__builtin_ia32_vec_ext_v2si'
    return __builtin_ia32_vec_ext_v2si((__v2si)__m, 0);
           ^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:133:19: error: use of undeclared identifier '__builtin_ia32_packsswb'
    return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
                  ^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:163:19: error: use of undeclared identifier '__builtin_ia32_packssdw'
    return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
                  ^
/Applications/Xcode_15.4.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/mmintrin.h:193:19: error: use of undeclared identifier '__builtin_ia32_packuswb'
    return (__m64)__builtin_ia32_packuswb((__v4hi)__
system "make"
bin.install "bin/MapCaller"
pkgshare.install "test"
Expand Down
Loading