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bcalm 2.2.3 #2297

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4fa79ed
bcalm 2.2.3
BenjaminDEMAILLE Jul 7, 2026
d2aa0bd
bcalm: fix CI (set CMAKE_POLICY_VERSION_MINIMUM=3.5)
BenjaminDEMAILLE Jul 8, 2026
dddd341
bcalm: fix CI (scrub Homebrew shim path from bin/bcalm on Linux)
BenjaminDEMAILLE Jul 10, 2026
d3f2ca0
bcalm: strip compiler path from bundled HDF5 build banner too
BenjaminDEMAILLE Jul 11, 2026
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18 changes: 16 additions & 2 deletions Formula/bcalm.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
desc "De Bruijn graph compaction in low memory"
homepage "https://github.com/GATB/bcalm"
url "https://github.com/GATB/bcalm.git",
tag: "v2.2.2",
revision: "febf79a3b9e334962902b5f920114b7cc7e91881"
tag: "v2.2.3",
revision: "1f8a8b15e84f6bcaf47296eb3eb381288131b203"
license "MIT"

bottle do
Expand All @@ -17,7 +17,21 @@

uses_from_macos "zlib"

def install

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GitHub Actions / build-bottles (macos-14)

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

-- Check size of __uint128_t
-- Check size of __uint128_t - done
-------------------------------------------------------------------------------------
-- WARNING !!! YOU USE AN UNKNOWN COMPILER...
-------------------------------------------------------------------------------------
CMake Error at gatb-core/gatb-core/CMakeLists.txt:151 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


CMake Error at gatb-core/gatb-core/CMakeLists.txt:153 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


-- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof
-- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation
-- SOVERSION: 103.1.0
-- SOVERSION_TOOLS: 100.1.2
-- SOVERSION_CXX: 103.1.0
-- SOVERSION_F: 102.0.0
-- SOVERSION_HL: 100.1.2
-- SOVERSION_HL_CXX: 100.1.3
-- SOVERSION_HL_F: 100.0.4
-- SOVERSION_JAVA: 100.4.0
-- Looking for include file sys/file.h
-- Looking for include file sys/file.h - found
-- Looking for include files sys/file.h, sys/ioctl.h
-- Looking for include files sys/file.h, sys/ioctl.h - found
-- Looking for 3 include files sys/file.h, ..., sys/resource.h
-- Looking for 3 include files sys/file.h, ..., sys/resource.h - found
-- Looking for 4 include files sys/file.h, ..., sys/socket.h
-- Looking for 4 include files sys/file.h, ..., sys/socket.h - found
-- Looking for 5 include files sys/file.h, ..., sys/stat.h
-- Looking for 5 include files sys/file.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/file.h, ..., sys/time.h
-- Looking for 6 include files sys/file.h, ..., sys/time.h - found
-- Looking for 7 include files sys/file.h, ..., sys/types.h
-- Looking for 7 include files sys/file.h, ..., sys/types.h - found
-- Looking for 8 include files sys/file.h, ..., features.h
-- Looking for 8 include files sys/file.h, ..., features.h - not found
-- Looking for 8 include files sys/file.h, ..., dirent.h
-- Looking for 8 include files sys/file.h, ..., dirent.h - found
-- Looking for 9 include files sys/file.h, ..., setjmp.h
-- Looking for 9 include files sys/file.h, ..., setjmp.h - found
-- Looking for 10 include files sys/file.h, ..., stddef.h
-- Looking for 10 include files sys/file.h, ..., stddef.h - found
-- Looking for 11 include files sys/file.h, ..., stdint.h
-- Looking for 11 include files sys/file.h, ..., stdint.h - found
-- Looking for 12 include files sys/file.h, ..., unistd.h
-- Looking for 12 include files sys/file.h, ..., unistd.h - found
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h - found
-- Looking for 14 include files sys/file.h, ..., io.h
-- Looking for 14 include files sys/file.h, ..., io.h - not found
-- Looking for 14 include files sys/file.h, ..., winsock2.h
-- Looking for 14 include files sys/file.h, ..., winsock2.h - not found
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h - found
-- Looking for 15 include files sys/file.h, ..., globus/common.h
-- Looking for 15 include files sys/file.h, ..., globus/common.h - not found
-- Looking for 15 include files sys/file.h, ..., pdb.h
-- Looking for 15 include files sys/file.h, ..., pdb.h - not found
-- Looking for 15 include files sys/file.h, ..., pthread.h
-- Looking for 15 include files sys/file.h, ..., pthread.h - found
-- Looking for 16 include files sys/file.h, ..., srbclient.h
-- Looking for 16 include files sys/file.h, ..., srbclient.h - not found
-- Looking for 16 include files sys/file.h, ..., string.h
-- Looking for 16 include files sys/file.h, ..., string.h - found
-- Looking for 17 include files sys/file.h, ..., strings.h
-- Looking for 17 include files sys/file.h, ..., strings.h - found
-- Looking for 18 include files sys/file.h, ..., stdlib.h
-- Looking for 18 include files sys/file.h, ..., stdlib.h - fo

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GitHub Actions / build-bottles (macos-15)

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

-- Check size of __uint128_t
-- Check size of __uint128_t - done
-------------------------------------------------------------------------------------
-- WARNING !!! YOU USE AN UNKNOWN COMPILER...
-------------------------------------------------------------------------------------
CMake Error at gatb-core/gatb-core/CMakeLists.txt:151 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


CMake Error at gatb-core/gatb-core/CMakeLists.txt:153 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


-- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof
-- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation
-- SOVERSION: 103.1.0
-- SOVERSION_TOOLS: 100.1.2
-- SOVERSION_CXX: 103.1.0
-- SOVERSION_F: 102.0.0
-- SOVERSION_HL: 100.1.2
-- SOVERSION_HL_CXX: 100.1.3
-- SOVERSION_HL_F: 100.0.4
-- SOVERSION_JAVA: 100.4.0
-- Looking for include file sys/file.h
-- Looking for include file sys/file.h - found
-- Looking for include files sys/file.h, sys/ioctl.h
-- Looking for include files sys/file.h, sys/ioctl.h - found
-- Looking for 3 include files sys/file.h, ..., sys/resource.h
-- Looking for 3 include files sys/file.h, ..., sys/resource.h - found
-- Looking for 4 include files sys/file.h, ..., sys/socket.h
-- Looking for 4 include files sys/file.h, ..., sys/socket.h - found
-- Looking for 5 include files sys/file.h, ..., sys/stat.h
-- Looking for 5 include files sys/file.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/file.h, ..., sys/time.h
-- Looking for 6 include files sys/file.h, ..., sys/time.h - found
-- Looking for 7 include files sys/file.h, ..., sys/types.h
-- Looking for 7 include files sys/file.h, ..., sys/types.h - found
-- Looking for 8 include files sys/file.h, ..., features.h
-- Looking for 8 include files sys/file.h, ..., features.h - not found
-- Looking for 8 include files sys/file.h, ..., dirent.h
-- Looking for 8 include files sys/file.h, ..., dirent.h - found
-- Looking for 9 include files sys/file.h, ..., setjmp.h
-- Looking for 9 include files sys/file.h, ..., setjmp.h - found
-- Looking for 10 include files sys/file.h, ..., stddef.h
-- Looking for 10 include files sys/file.h, ..., stddef.h - found
-- Looking for 11 include files sys/file.h, ..., stdint.h
-- Looking for 11 include files sys/file.h, ..., stdint.h - found
-- Looking for 12 include files sys/file.h, ..., unistd.h
-- Looking for 12 include files sys/file.h, ..., unistd.h - found
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h - found
-- Looking for 14 include files sys/file.h, ..., io.h
-- Looking for 14 include files sys/file.h, ..., io.h - not found
-- Looking for 14 include files sys/file.h, ..., winsock2.h
-- Looking for 14 include files sys/file.h, ..., winsock2.h - not found
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h - found
-- Looking for 15 include files sys/file.h, ..., globus/common.h
-- Looking for 15 include files sys/file.h, ..., globus/common.h - not found
-- Looking for 15 include files sys/file.h, ..., pdb.h
-- Looking for 15 include files sys/file.h, ..., pdb.h - not found
-- Looking for 15 include files sys/file.h, ..., pthread.h
-- Looking for 15 include files sys/file.h, ..., pthread.h - found
-- Looking for 16 include files sys/file.h, ..., srbclient.h
-- Looking for 16 include files sys/file.h, ..., srbclient.h - not found
-- Looking for 16 include files sys/file.h, ..., string.h
-- Looking for 16 include files sys/file.h, ..., string.h - found
-- Looking for 17 include files sys/file.h, ..., strings.h
-- Looking for 17 include files sys/file.h, ..., strings.h - found
-- Looking for 18 include files sys/file.h, ..., stdlib.h
-- Looking for 18 include files sys/file.h, ..., stdlib.h - fo

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GitHub Actions / build-bottles (macos-26)

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

-- Check size of __uint128_t
-- Check size of __uint128_t - done
-------------------------------------------------------------------------------------
-- WARNING !!! YOU USE AN UNKNOWN COMPILER...
-------------------------------------------------------------------------------------
CMake Error at gatb-core/gatb-core/CMakeLists.txt:151 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


CMake Error at gatb-core/gatb-core/CMakeLists.txt:153 (STRING):
  STRING sub-command REGEX, mode REPLACE needs at least 6 arguments total to
  command.


-- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof
-- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation
-- SOVERSION: 103.1.0
-- SOVERSION_TOOLS: 100.1.2
-- SOVERSION_CXX: 103.1.0
-- SOVERSION_F: 102.0.0
-- SOVERSION_HL: 100.1.2
-- SOVERSION_HL_CXX: 100.1.3
-- SOVERSION_HL_F: 100.0.4
-- SOVERSION_JAVA: 100.4.0
-- Looking for include file sys/file.h
-- Looking for include file sys/file.h - found
-- Looking for include files sys/file.h, sys/ioctl.h
-- Looking for include files sys/file.h, sys/ioctl.h - found
-- Looking for 3 include files sys/file.h, ..., sys/resource.h
-- Looking for 3 include files sys/file.h, ..., sys/resource.h - found
-- Looking for 4 include files sys/file.h, ..., sys/socket.h
-- Looking for 4 include files sys/file.h, ..., sys/socket.h - found
-- Looking for 5 include files sys/file.h, ..., sys/stat.h
-- Looking for 5 include files sys/file.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/file.h, ..., sys/time.h
-- Looking for 6 include files sys/file.h, ..., sys/time.h - found
-- Looking for 7 include files sys/file.h, ..., sys/types.h
-- Looking for 7 include files sys/file.h, ..., sys/types.h - found
-- Looking for 8 include files sys/file.h, ..., features.h
-- Looking for 8 include files sys/file.h, ..., features.h - not found
-- Looking for 8 include files sys/file.h, ..., dirent.h
-- Looking for 8 include files sys/file.h, ..., dirent.h - found
-- Looking for 9 include files sys/file.h, ..., setjmp.h
-- Looking for 9 include files sys/file.h, ..., setjmp.h - found
-- Looking for 10 include files sys/file.h, ..., stddef.h
-- Looking for 10 include files sys/file.h, ..., stddef.h - found
-- Looking for 11 include files sys/file.h, ..., stdint.h
-- Looking for 11 include files sys/file.h, ..., stdint.h - found
-- Looking for 12 include files sys/file.h, ..., unistd.h
-- Looking for 12 include files sys/file.h, ..., unistd.h - found
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/file.h, ..., mach/mach_time.h - found
-- Looking for 14 include files sys/file.h, ..., io.h
-- Looking for 14 include files sys/file.h, ..., io.h - not found
-- Looking for 14 include files sys/file.h, ..., winsock2.h
-- Looking for 14 include files sys/file.h, ..., winsock2.h - not found
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h
-- Looking for 14 include files sys/file.h, ..., sys/timeb.h - found
-- Looking for 15 include files sys/file.h, ..., globus/common.h
-- Looking for 15 include files sys/file.h, ..., globus/common.h - not found
-- Looking for 15 include files sys/file.h, ..., pdb.h
-- Looking for 15 include files sys/file.h, ..., pdb.h - not found
-- Looking for 15 include files sys/file.h, ..., pthread.h
-- Looking for 15 include files sys/file.h, ..., pthread.h - found
-- Looking for 16 include files sys/file.h, ..., srbclient.h
-- Looking for 16 include files sys/file.h, ..., srbclient.h - not found
-- Looking for 16 include files sys/file.h, ..., string.h
-- Looking for 16 include files sys/file.h, ..., string.h - found
-- Looking for 17 include files sys/file.h, ..., strings.h
-- Looking for 17 include files sys/file.h, ..., strings.h - found
-- Looking for 18 include files sys/file.h, ..., stdlib.h
-- Looking for 18 include files sys/file.h, ..., stdlib.h - fo
# bcalm and its gatb-core submodule request an ancient CMake policy version
ENV["CMAKE_POLICY_VERSION_MINIMUM"] = "3.5"

# gatb-core and its bundled HDF5 bake the compiler path (Homebrew's shim
# wrapper on Linux) into bin/bcalm via generated build banners, which trips
# brew audit's check for references to the Homebrew shims directory. Drop
# the compiler-path substitutions from the source templates so nothing
# references the shim directory.
inreplace "gatb-core/gatb-core/src/gatb/system/api/build_info.hpp.in",
"${CMAKE_C_COMPILER}", "cc"
hdf5_settings = "gatb-core/gatb-core/thirdparty/hdf5/config/cmake/libhdf5.settings.cmake.in"
inreplace hdf5_settings, "@CMAKE_C_COMPILER@", "cc"
inreplace hdf5_settings, "@CMAKE_CXX_COMPILER@", "c++"

mkdir "build" do
system "cmake", "..", *std_cmake_args
system "make"
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