rust-htslib: MUSL build fails on OSX
Hello,
I have been trying cargo build on rust-htslib:
$ git clone --recursive https://github.com/rust-bio/rust-htslib.git
$ cd rust-htslib
$ cargo build
which output a whole lot warning on the c source code and a fatal
error occurred: Command "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c" with args "cc" did not execute successfully (status code exit code: 1).
I have also tried
$ brew install FiloSottile/musl-cross/musl-cross
$ brew install bzip2 zlib xz curl-openssl
$ cross build
with the same result.
However, cross build --target x86_64-unknown-linux-musl does work.
Other info:
- OS: MacOS Catalina 10.15.6
$ cc --version
Apple clang version 12.0.0 (clang-1200.0.31.1)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
About this issue
- Original URL
- State: closed
- Created 4 years ago
- Comments: 21 (20 by maintainers)
MUSL is no longer a requirement to run lambdas an AWS thanks to the
provided.al2(Amazon Linux 2) docker/lambda environment.Feel free to reopen/inquire if MUSL is required in some other envs?: https://twitter.com/braincode/status/1412595644439490571
@sstadick See #275 for the work in progress to fix this.
Related, and unfortunately probably relevant for most (non-trivial) workflows: https://www.zdnet.com/article/google-to-github-times-up-this-unfixed-high-severity-security-bug-affects-developers/