Closed alexreg closed 2 years ago
Looks like you are trying to compile for ARM, emmintrin.h is header file for SSE2 intrinsics, SSE2 is an instruction set on Intel/x86-64 CPUs. If you feel competent you can try to replace emmintrin.h with sse2neon (sse2neon.h).
@th-of Thanks. Upstream or in the cask, you mean?
You would have to download and compile the source. But that seems impossible at the moment, just forget my comment.
Why impossible, may I ask?
I can't get it to compile here. First error: fatal error: 'tabix.hpp' file not found This is supposed to fix it: https://github.com/Niema-Docker/freebayes/blob/main/Dockerfile#L8-L28 But I can't compile that either: fatal error: 'lzma.h' file not found Even though all all the dependencies are correctly installed.
Okay, I've got everything building nicely on my end. (N.B., This uses brew's version of htslib rather than the bundled one, which I think is the intention.)
First, apply this patch.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8ec8f9c..f5ad5a8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -52,6 +52,9 @@ endif(GPROF)
# ---- Include files
+include_directories(/opt/homebrew/include /usr/local/include)
+link_directories(/opt/homebrew/lib /usr/local/lib)
+
include_directories(include)
include_directories(fastahack)
include_directories(intervaltree)
Then to build, run this script which should be placed in the root dir of the vcflib repo.
#!/bin/bash
mkdir -p build &&
cd build &&
{ rm -Rf tabixpp; true; } &&
git clone https://github.com/ekg/tabixpp.git --branch v1.1.0 &&
cd tabixpp &&
make INCLUDES=-I/opt/homebrew/include LIBPATH="-L. -L/opt/homebrew/lib" HTS_HEADERS= HTS_LIB= &&
g++ -g -Wall -O2 -fPIC -I/opt/homebrew/include -L. -L/opt/homebrew/lib -lhts -lpthread -lm -lbz2 -llzma -lz tabix.o -shared -o libtabixpp.so &&
sudo install -p -m 644 libtabixpp.so /usr/local/lib &&
sudo install -p -m 644 tabix.hpp /usr/local/include &&
cd .. &&
cmake .. &&
cmake --build . &&
sudo cmake --install . &&
exit 0
FYI, seems that emmintrin.h
is bundled with clang on my system.
/opt/homebrew//Cellar/llvm/13.0.0_2/lib/clang/13.0.0/include/emmintrin.h
Not sure we can have the formula build using brew's llvm though...
brew install
ing one, specific formula and not every time you runbrew
? If it's a generalbrew
problem please file this issue at https://github.com/Homebrew/brew/issues/new.brew update
and retried your prior step?brew doctor
, fixed all issues and retried your prior step?brew gist-logs <formula>
(where<formula>
is the name of the formula that failed) and included the output link?brew gist-logs
didn't work: ranbrew config
andbrew doctor
and included their output with your issue?Output of
brew install brewsci/bio/vcflib
is the following.From the build output file, it looks like this is the problem.
Full Logs