Compile errors

[jdidion]

MacBook M1 Max Pro

Dockerfile:

FROM ubuntu:focal as build

ARG MUDSKIPPER_VERSION

ENV DEBIAN_FRONTEND=noninteractive
ENV PATH=/root/.cargo/bin:$PATH

ADD https://github.com/OceanGenomics/mudskipper/archive/refs/tags/v${MUDSKIPPER_VERSION}.tar.gz mudskipper.tgz

RUN apt update \
    && apt install -y curl build-essential cmake \
    && curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y \
    && mkdir mudskipper \
    && tar -C mudskipper --strip-components=1 -xzf mudskipper.tgz \
    && cd mudskipper \
    && cargo build --release \
    && mv target/release/mudskipper /usr/local/bin

FROM ubuntu:focal

COPY --from=build /usr/local/bin/mudskipper /usr/local/bin/mudskipper

Docker command: docker build -f Dockerfile.mudskipper -t mudskipper --build-arg MUDSKIPPER_VERSION=0.1.0 .

Errors:

#0 131.0 error[E0308]: mismatched types
#0 131.0    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:152:16
#0 131.0     |
#0 131.0 152 |             s: sam_copy.as_ptr() as *mut i8,
#0 131.0     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.0     |
#0 131.0     = note: expected raw pointer `*mut u8`
#0 131.0                found raw pointer `*mut i8`
#0 131.0 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:583:17
#0 131.1     |
#0 131.1 583 |                 c_str.as_ptr() as *mut i8,
#0 131.1     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:678:49
#0 131.1     |
#0 131.1 678 |                 let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::<i8>());
#0 131.1     |                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*const i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:798:21
#0 131.1     |
#0 131.1 798 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:799:21
#0 131.1     |
#0 131.1 799 |                     b'A' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 799 |                     (b'A' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:805:21
#0 131.1     |
#0 131.1 805 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:806:21
#0 131.1     |
#0 131.1 806 |                     b'c' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 806 |                     (b'c' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:812:21
#0 131.1     |
#0 131.1 812 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:813:21
#0 131.1     |
#0 131.1 813 |                     b'C' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 813 |                     (b'C' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:819:21
#0 131.1     |
#0 131.1 819 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:820:21
#0 131.1     |
#0 131.1 820 |                     b's' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 820 |                     (b's' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:826:21
#0 131.1     |
#0 131.1 826 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:827:21
#0 131.1     |
#0 131.1 827 |                     b'S' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 827 |                     (b'S' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:833:21
#0 131.1     |
#0 131.1 833 |                     ctag,
#0 131.1     |                     ^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1     = note: expected raw pointer `*const u8`
#0 131.1                found raw pointer `*mut i8`
#0 131.1 
#0 131.1 error[E0308]: mismatched types
#0 131.1    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:834:21
#0 131.1     |
#0 131.1 834 |                     b'i' as i8,
#0 131.1     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1     |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1     |
#0 131.1 834 |                     (b'i' as i8).try_into().unwrap(),
#0 131.1     |                     +          +++++++++++++++++++++
#0 131.1 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:840:21
#0 131.2     |
#0 131.2 840 |                     ctag,
#0 131.2     |                     ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:841:21
#0 131.2     |
#0 131.2 841 |                     b'I' as i8,
#0 131.2     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2     |
#0 131.2 841 |                     (b'I' as i8).try_into().unwrap(),
#0 131.2     |                     +          +++++++++++++++++++++
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:847:21
#0 131.2     |
#0 131.2 847 |                     ctag,
#0 131.2     |                     ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:848:21
#0 131.2     |
#0 131.2 848 |                     b'f' as i8,
#0 131.2     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2     |
#0 131.2 848 |                     (b'f' as i8).try_into().unwrap(),
#0 131.2     |                     +          +++++++++++++++++++++
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:855:21
#0 131.2     |
#0 131.2 855 |                     ctag,
#0 131.2     |                     ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:856:21
#0 131.2     |
#0 131.2 856 |                     b'd' as i8,
#0 131.2     |                     ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2     |
#0 131.2 856 |                     (b'd' as i8).try_into().unwrap(),
#0 131.2     |                     +          +++++++++++++++++++++
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:864:25
#0 131.2     |
#0 131.2 864 |                         ctag,
#0 131.2     |                         ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:865:25
#0 131.2     |
#0 131.2 865 |                         b'Z' as i8,
#0 131.2     |                         ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2     |
#0 131.2 865 |                         (b'Z' as i8).try_into().unwrap(),
#0 131.2     |                         +          +++++++++++++++++++++
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:874:25
#0 131.2     |
#0 131.2 874 |                         ctag,
#0 131.2     |                         ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:875:25
#0 131.2     |
#0 131.2 875 |                         b'H' as i8,
#0 131.2     |                         ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2     |
#0 131.2 875 |                         (b'H' as i8).try_into().unwrap(),
#0 131.2     |                         +          +++++++++++++++++++++
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:884:25
#0 131.2     |
#0 131.2 884 |                         ctag,
#0 131.2     |                         ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:891:25
#0 131.2     |
#0 131.2 891 |                         ctag,
#0 131.2     |                         ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.2 error[E0308]: mismatched types
#0 131.2    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:900:25
#0 131.2     |
#0 131.2 900 |                         ctag,
#0 131.2     |                         ^^^^ expected `u8`, found `i8`
#0 131.2     |
#0 131.2     = note: expected raw pointer `*const u8`
#0 131.2                found raw pointer `*mut i8`
#0 131.2 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:907:25
#0 131.3     |
#0 131.3 907 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:916:25
#0 131.3     |
#0 131.3 916 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:923:25
#0 131.3     |
#0 131.3 923 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:932:25
#0 131.3     |
#0 131.3 932 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:939:25
#0 131.3     |
#0 131.3 939 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:948:25
#0 131.3     |
#0 131.3 948 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.3 error[E0308]: mismatched types
#0 131.3    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:955:25
#0 131.3     |
#0 131.3 955 |                         ctag,
#0 131.3     |                         ^^^^ expected `u8`, found `i8`
#0 131.3     |
#0 131.3     = note: expected raw pointer `*const u8`
#0 131.3                found raw pointer `*mut i8`
#0 131.3 
#0 131.4 error[E0308]: mismatched types
#0 131.4    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:964:25
#0 131.4     |
#0 131.4 964 |                         ctag,
#0 131.4     |                         ^^^^ expected `u8`, found `i8`
#0 131.4     |
#0 131.4     = note: expected raw pointer `*const u8`
#0 131.4                found raw pointer `*mut i8`
#0 131.4 
#0 131.4 error[E0308]: mismatched types
#0 131.4    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:971:25
#0 131.4     |
#0 131.4 971 |                         ctag,
#0 131.4     |                         ^^^^ expected `u8`, found `i8`
#0 131.4     |
#0 131.4     = note: expected raw pointer `*const u8`
#0 131.4                found raw pointer `*mut i8`
#0 131.4 
#0 131.4 error[E0308]: mismatched types
#0 131.4    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:980:25
#0 131.4     |
#0 131.4 980 |                         ctag,
#0 131.4     |                         ^^^^ expected `u8`, found `i8`
#0 131.4     |
#0 131.4     = note: expected raw pointer `*const u8`
#0 131.4                found raw pointer `*mut i8`
#0 131.4 
#0 131.4 error[E0308]: mismatched types
#0 131.4    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:987:25
#0 131.4     |
#0 131.4 987 |                         ctag,
#0 131.4     |                         ^^^^ expected `u8`, found `i8`
#0 131.4     |
#0 131.4     = note: expected raw pointer `*const u8`
#0 131.4                found raw pointer `*mut i8`
#0 131.4 
#0 131.4 error[E0308]: mismatched types
#0 131.4     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:1009:17
#0 131.4      |
#0 131.4 1009 |                 c_str.as_ptr() as *mut i8,
#0 131.4      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.4      |
#0 131.4      = note: expected raw pointer `*const u8`
#0 131.4                 found raw pointer `*mut i8`
#0 131.4 
#0 131.5 error[E0308]: mismatched types
#0 131.5    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:268:55
#0 131.5     |
#0 131.5 268 |             let _ = htslib::sam_hdr_line_name(header, b"SQ".as_ptr().cast::<i8>(), 0);
#0 131.5     |                                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5     |
#0 131.5     = note: expected raw pointer `*const u8`
#0 131.5                found raw pointer `*const i8`
#0 131.5 
#0 131.5    Compiling bio v0.41.0
#0 131.5 error[E0308]: mismatched types
#0 131.5    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:943:17
#0 131.5     |
#0 131.5 943 |                 text as *const i8,
#0 131.5     |                 ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5     |
#0 131.5     = note: expected raw pointer `*const u8`
#0 131.5                found raw pointer `*const i8`
#0 131.5 
#0 131.5 error[E0308]: mismatched types
#0 131.5    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:946:27
#0 131.5     |
#0 131.5 946 |             (*rec).text = text as *mut i8;
#0 131.5     |             -----------   ^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5     |             |
#0 131.5     |             expected due to the type of this binding
#0 131.5     |
#0 131.5     = note: expected raw pointer `*mut u8`
#0 131.5                found raw pointer `*mut i8`
#0 131.5 
#0 131.5 error[E0308]: mismatched types
#0 131.5     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:1212:66
#0 131.5      |
#0 131.5 1212 |             let rec = htslib::sam_hdr_parse((l_text + 1) as u64, text as *const i8);
#0 131.5      |                                                                  ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5      |
#0 131.5      = note: expected raw pointer `*const u8`
#0 131.5                 found raw pointer `*const i8`
#0 131.5 
#0 131.6 error[E0308]: mismatched types
#0 131.6     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:1213:27
#0 131.6      |
#0 131.6 1213 |             (*rec).text = text as *mut i8;
#0 131.6      |             -----------   ^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6      |             |
#0 131.6      |             expected due to the type of this binding
#0 131.6      |
#0 131.6      = note: expected raw pointer `*mut u8`
#0 131.6                 found raw pointer `*mut i8`
#0 131.6 
#0 131.6 error[E0308]: mismatched types
#0 131.6    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:118:17
#0 131.6     |
#0 131.6 118 |                 name_pointers.as_ptr() as *const *mut i8,
#0 131.6     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6     |
#0 131.6     = note: expected raw pointer `*const *mut u8`
#0 131.6                found raw pointer `*const *mut i8`
#0 131.6 
#0 131.6 error[E0308]: mismatched types
#0 131.6    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:341:17
#0 131.6     |
#0 131.6 341 |                 c_str.as_ptr() as *mut i8,
#0 131.6     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6     |
#0 131.6     = note: expected raw pointer `*const u8`
#0 131.6                found raw pointer `*mut i8`
#0 131.6 
#0 131.6 error[E0308]: mismatched types
#0 131.6    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:366:17
#0 131.6     |
#0 131.6 366 |                 c_str_tag.as_ptr() as *mut i8,
#0 131.6     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6     |
#0 131.6     = note: expected raw pointer `*const u8`
#0 131.6                found raw pointer `*mut i8`
#0 131.6 
#0 131.6 error[E0308]: mismatched types
#0 131.6    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:403:17
#0 131.6     |
#0 131.6 403 |                 c_str.as_ptr() as *const i8,
#0 131.6     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6     |
#0 131.6     = note: expected raw pointer `*const u8`
#0 131.6                found raw pointer `*const i8`
#0 131.6 
#0 131.7 error[E0308]: mismatched types
#0 131.7    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:431:17
#0 131.7     |
#0 131.7 431 |                 c_str.as_ptr() as *const i8,
#0 131.7     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7     |
#0 131.7     = note: expected raw pointer `*const u8`
#0 131.7                found raw pointer `*const i8`
#0 131.7 
#0 131.7 error[E0308]: mismatched types
#0 131.7    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:319:68
#0 131.7     |
#0 131.7 319 |             htslib::bcf_update_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8)
#0 131.7     |                                                                    ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7     |
#0 131.7     = note: expected raw pointer `*const u8`
#0 131.7                found raw pointer `*mut i8`
#0 131.7 
#0 131.7 error[E0308]: mismatched types
#0 131.7    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:332:68
#0 131.7     |
#0 131.7 332 |             htslib::bcf_update_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8)
#0 131.7     |                                                                    ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7     |
#0 131.7     = note: expected raw pointer `*const u8`
#0 131.7                found raw pointer `*mut i8`
#0 131.7 
#0 131.7 error[E0308]: mismatched types
#0 131.7    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:344:73
#0 131.7     |
#0 131.7 344 |         if unsafe { htslib::bcf_add_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8) }
#0 131.7     |                                                                         ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7     |
#0 131.7     = note: expected raw pointer `*const u8`
#0 131.7                found raw pointer `*mut i8`
#0 131.7 
#0 131.7 error[E0308]: mismatched types
#0 131.7    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:591:17
#0 131.7     |
#0 131.7 591 |                 ptrs.as_mut_ptr(),
#0 131.7     |                 ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7     |
#0 131.7     = note: expected raw pointer `*mut *const u8`
#0 131.7                found raw pointer `*mut *const i8`
#0 131.7 
#0 131.8 error[E0308]: mismatched types
#0 131.8    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:825:17
#0 131.8     |
#0 131.8 825 |                 tag_c_str.as_ptr() as *mut i8,
#0 131.8     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8     |
#0 131.8     = note: expected raw pointer `*const u8`
#0 131.8                found raw pointer `*mut i8`
#0 131.8 
#0 131.8 error[E0308]: mismatched types
#0 131.8    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:872:17
#0 131.8     |
#0 131.8 872 |                 tag_c_str.as_ptr() as *mut i8,
#0 131.8     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8     |
#0 131.8     = note: expected raw pointer `*const u8`
#0 131.8                found raw pointer `*mut i8`
#0 131.8 
#0 131.8 error[E0308]: mismatched types
#0 131.8    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:873:17
#0 131.8     |
#0 131.8 873 |                 c_ptrs.as_slice().as_ptr() as *mut *const i8,
#0 131.8     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8     |
#0 131.8     = note: expected raw pointer `*mut *const u8`
#0 131.8                found raw pointer `*mut *const i8`
#0 131.8 
#0 131.9 error[E0308]: mismatched types
#0 131.9    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:918:17
#0 131.9     |
#0 131.9 918 |                 tag_c_str.as_ptr() as *mut i8,
#0 131.9     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9     |
#0 131.9     = note: expected raw pointer `*const u8`
#0 131.9                found raw pointer `*mut i8`
#0 131.9 
#0 131.9 error[E0308]: mismatched types
#0 131.9    --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:973:17
#0 131.9     |
#0 131.9 973 |                 tag_c_str.as_ptr() as *mut i8,
#0 131.9     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9     |
#0 131.9     = note: expected raw pointer `*const u8`
#0 131.9                found raw pointer `*mut i8`
#0 131.9 
#0 131.9 error[E0308]: mismatched types
#0 131.9     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1234:17
#0 131.9      |
#0 131.9 1234 |                 c_str.as_ptr() as *mut i8,
#0 131.9      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9      |
#0 131.9      = note: expected raw pointer `*const u8`
#0 131.9                 found raw pointer `*mut i8`
#0 131.9 
#0 131.9 error[E0308]: mismatched types
#0 131.9     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1349:17
#0 131.9      |
#0 131.9 1349 |                 c_str.as_ptr() as *mut i8,
#0 131.9      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9      |
#0 131.9      = note: expected raw pointer `*const u8`
#0 131.9                 found raw pointer `*mut i8`
#0 131.9 
#0 132.0 error[E0308]: mismatched types
#0 132.0     --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1385:17
#0 132.0      |
#0 132.0 1385 |                 c_str.as_ptr() as *mut i8,
#0 132.0      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 132.0      |
#0 132.0      = note: expected raw pointer `*const u8`
#0 132.0                 found raw pointer `*mut i8`
#0 132.0 
#0 132.1 For more information about this error, try `rustc --explain E0308`.
#0 132.1 error: could not compile `rust-htslib` due to 62 previous errors
#0 132.1 warning: build failed, waiting for other jobs to finish...
#0 137.5 error: build failed

[jdidion]

Note that this Dockerfile builds fine on linux, so it is a MacOS (and perhaps an M1) issue.

[rob-p]

Thanks for the report! These all seem to arise from rust-htslib, so we should link the issue over there as well.

[rob-p]

From the response over on the rust-htslib repo, it looks like this is solved in their main branch and should be fixed in the next point release. We'll keep this issue open as a pointer until we can update the dependency.

[rob-p]

Ok, @jdidion, they have now tagged a release with this! Unfortunately, that release hasn't been pushed to crates.io, so crates can't rely on it. I've made an issue for that https://github.com/rust-bio/rust-htslib/issues/353 if you want to vocalize your support for it.

[rob-p]

Ok, so things are not quite that simple ;P. I will also have to update libradicl upstream since we depend on that and that pulls in quickersort which has been yanked from crates.io (but not for being broken, apparently, just for being deprecated). I've already gotten rid of that upstream in the develop branch of libradicl (in alevin-fry) but haven't pushed that to crates.io yet.

[jdidion]

Thanks for making progress on this!