Release and compile problems

[colindaven]

Hi,

• is this just for short reads or can I analyze long read bams too ?
• I had problems with the released binary complaining about GLIBs on two different systems ( 1 ubuntu 1804 - too old, fair enough), but also one ubuntu 20.04.
• So tried compiling myself - this doesn't look good. Is my rustc/cargo too old ?

rustc -V
rustc 1.64.0 (a55dd71d5 2022-09-19)

git clone ....
cd best
cargo install --path .

   Compiling noodles-fasta v0.13.0
   Compiling noodles-csi v0.9.1
   Compiling noodles-sam v0.18.0
   Compiling rayon v1.6.1
error[E0308]: mismatched types
   --> /home/hpc/davenpor/.cargo/registry/src/github.com-1ecc6299db9ec823/noodles-sam-0.18.0/src/reader/query.rs:70:62
    |
70  | ...                   if let Err(e) = self.reader.seek(chunk.start()) {
    |                                                   ---- ^^^^^^^^^^^^^ expected struct `VirtualPosition`, found struct `noodles_bgzf::virtual_position::VirtualPosition`
    |                                                   |
    |                                                   arguments to this function are incorrect
    |
    = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: associated function defined here
   --> /home/hpc/davenpor/.cargo/registry/src/github.com-1ecc6299db9ec823/noodles-sam-0.18.0/src/reader.rs:263:12
    |
263 |     pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
    |            ^^^^ ---------  --------------------------

error[E0308]: mismatched types
  --> /home/hpc/davenpor/.cargo/registry/src/github.com-1ecc6299db9ec823/noodles-sam-0.18.0/src/reader/query.rs:74:41
   |
74 | ...                   State::Read(chunk.end())
   |                       ----------- ^^^^^^^^^^^ expected struct `VirtualPosition`, found struct `noodles_bgzf::virtual_position::VirtualPosition`
   |                       |
   |                       arguments to this enum variant are incorrect
   |
   = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: tuple variant defined here
  --> /home/hpc/davenpor/.cargo/registry/src/github.com-1ecc6299db9ec823/noodles-sam-0.18.0/src/reader/query.rs:15:5
   |
15 |     Read(bgzf::VirtualPosition),
   |     ^^^^

For more information about this error, try `rustc --explain E0308`.
error: could not compile `noodles-sam` due to 2 previous errors
warning: build failed, waiting for other jobs to finish...
error: failed to compile `best v0.1.0 (/home/hpc/davenpor/programs/best)`, intermediate artifacts can be found at `/home/hpc/davenpor/programs/best/target`

[danielecook]

I am able to compile on Ubuntu 18.04 with rustc=1.65.0.

= note: perhaps two different versions of crate noodles_bgzf are being used?

I wonder if the version of noodles_bgzf could be the issue?

Here are the versions of some of the noodles packages that worked for me:

[[package]]
name = "noodles-csi"
version = "0.9.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ccb4bac55bfc031dd493f974ea1ee12e9b85e33cc17a63e6273b04551ca8d99e"
dependencies = [
 "bit-vec",
 "byteorder",
 "noodles-bgzf",
 "noodles-core",
]

[[package]]
name = "noodles-sam"
version = "0.18.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "aab026833fde10c98fb822bff2bfd3950829e78d446ddb7fb1ad0e11710a4568"
dependencies = [
 "bitflags",
 "indexmap",
 "lexical-core",
 "memchr",
 "noodles-bgzf",
 "noodles-core",
 "noodles-csi",
 "noodles-fasta",
 "rustc-hash",
]

[[package]]
name = "noodles-bgzf"
version = "0.14.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "36ebbec47ff8c1e931f5da61e077a7774bbb2fc43158d72f334a51dae20dcc4b"
dependencies = [
 "byteorder",
 "bytes",
 "crossbeam-channel",
 "flate2",
]

1. Try rustc 1.65.0
2. Try noodles-bgzf=0.14.0?

[colindaven]

Very strange. Tried all sorts of blacklisting, restricting, hunting and deleting individual versions, trying cargo tree - but still can't work out where noodles-bgzf version "0.15.0" is coming from.

Anyway, I upgraded to the latest cargo v1.66.0, still got the same problem.

I'll leave this for now, but thanks.

cargo tree | grep nood

├── noodles v0.26.0
│   ├── noodles-bam v0.21.0
│   │   ├── noodles-bgzf v0.14.0
│   │   ├── noodles-core v0.8.0
│   │   ├── noodles-csi v0.9.0
│   │   │   ├── noodles-bgzf v0.14.0 (*)
│   │   │   └── noodles-core v0.8.0
│   │   ├── noodles-fasta v0.13.0
│   │   │   ├── noodles-bgzf v0.14.0 (*)
│   │   │   └── noodles-core v0.8.0
│   │   └── noodles-sam v0.18.0
│   │       ├── noodles-bgzf v0.14.0 (*)
│   │       ├── noodles-core v0.8.0
│   │       ├── noodles-csi v0.9.0 (*)
│   │       ├── noodles-fasta v0.13.0 (*)
│   ├── noodles-bed v0.4.0
│   │   └── noodles-core v0.8.0
│   ├── noodles-core v0.8.0
│   ├── noodles-fasta v0.13.0 (*)
│   └── noodles-sam v0.18.0 (*)

Tried all sorts of combinations in the Cargo.toml

noodles = { version = "^0.26", features = ["sam", "bam", "fasta", "bed", "core"] }
#noodles-bgzf = "^0.14.0, <0.15.0"
#noodles-sam = "^0.18.0"
#noodles-csi = "^0.9.0"

[Daniel-Liu-c0deb0t]

@colindaven Both short reads and long reads are supported. See our preprint for an example analysis with Illumina, PacBio, and ONT reads.

Have you tried cargo update? Anyways, it's weird that there's an issue with the versions since a Cargo.lock file exists.

[callumparr]

@Daniel-Liu-c0deb0t sorry to hijack this issue. I am having a similar problem and not worked out to solve this. I am new to installing something built with Rust. I am trying to install on our server which is running Debian 11, version rustc --version rustc 1.73.0 (cc66ad468 2023-10-03)

❯ cargo check
   Compiling autocfg v1.1.0
    Checking cfg-if v1.0.0
   Compiling crossbeam-utils v0.8.16
   Compiling crc32fast v1.3.2
    Checking static_assertions v1.1.0
    Checking adler v1.0.2
    Checking byteorder v1.5.0
   Compiling version_check v0.9.4
   Compiling proc-macro2 v1.0.69
    Checking bytes v1.5.0
   Compiling unicode-ident v1.0.12
    Checking noodles-core v0.8.0
    Checking hashbrown v0.12.3
   Compiling syn v1.0.109
    Checking scopeguard v1.2.0
    Checking bitflags v1.3.2
   Compiling libc v0.2.150
    Checking memchr v2.6.4
    Checking bit-vec v0.6.3
    Checking rustc-hash v1.1.0
   Compiling rayon-core v1.12.0
    Checking os_str_bytes v6.6.1
   Compiling heck v0.4.1
    Checking either v1.9.0
    Checking textwrap v0.16.0
    Checking lexical-util v0.8.5
    Checking once_cell v1.18.0
    Checking termcolor v1.3.0
    Checking miniz_oxide v0.7.1
    Checking strsim v0.10.0
    Checking noodles-bed v0.4.0
    Checking fxhash v0.2.1
    Checking clap_lex v0.2.4
   Compiling indexmap v1.9.3
   Compiling memoffset v0.9.0
   Compiling crossbeam-epoch v0.9.15
   Compiling num-traits v0.2.17
   Compiling proc-macro-error-attr v1.0.4
   Compiling proc-macro-error v1.0.4
    Checking flate2 v1.0.28
    Checking lexical-parse-integer v0.8.6
    Checking lexical-write-integer v0.8.5
    Checking crossbeam-channel v0.5.8
    Checking lexical-parse-float v0.8.5
    Checking lexical-write-float v0.8.5
   Compiling quote v1.0.33
    Checking crossbeam-deque v0.8.3
    Checking noodles-bgzf v0.14.0
    Checking noodles-bgzf v0.15.0
    Checking lexical-core v0.8.5
    Checking atty v0.2.14
    Checking noodles-fasta v0.13.0
    Checking noodles-csi v0.9.1
    Checking rayon v1.8.0
    Checking noodles-sam v0.18.0
    Checking rust-lapper v1.1.0
    Checking ordered-float v3.9.2
error[E0308]: mismatched types
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:70:62
    |
70  | ...                   if let Err(e) = self.reader.seek(chunk.start()) {
    |                                                   ---- ^^^^^^^^^^^^^ expected `VirtualPosition`, found a different `VirtualPosition`
    |                                                   |
    |                                                   arguments to this method are incorrect
    |
    = note: `VirtualPosition` and `VirtualPosition` have similar names, but are actually distinct types
note: `VirtualPosition` is defined in crate `noodles_bgzf`
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.15.0/src/virtual_position.rs:37:1
    |
37  | pub struct VirtualPosition(u64);
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
note: `VirtualPosition` is defined in crate `noodles_bgzf`
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.14.0/src/virtual_position.rs:37:1
    |
37  | pub struct VirtualPosition(u64);
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
    = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: method defined here
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader.rs:263:12
    |
263 |     pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
    |            ^^^^            --------------------------

error[E0308]: mismatched types
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:74:41
   |
74 | ...                   State::Read(chunk.end())
   |                       ----------- ^^^^^^^^^^^ expected `VirtualPosition`, found a different `VirtualPosition`
   |                       |
   |                       arguments to this enum variant are incorrect
   |
   = note: `VirtualPosition` and `VirtualPosition` have similar names, but are actually distinct types
note: `VirtualPosition` is defined in crate `noodles_bgzf`
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.15.0/src/virtual_position.rs:37:1
   |
37 | pub struct VirtualPosition(u64);
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^
note: `VirtualPosition` is defined in crate `noodles_bgzf`
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.14.0/src/virtual_position.rs:37:1
   |
37 | pub struct VirtualPosition(u64);
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^
   = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: tuple variant defined here
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:15:5
   |
15 |     Read(bgzf::VirtualPosition),
   |     ^^^^

For more information about this error, try `rustc --explain E0308`.
error: could not compile `noodles-sam` (lib) due to 2 previous errors
warning: build failed, waiting for other jobs to finish...

[callumparr]

@Daniel-Liu-c0deb0t sorry to hijack this issue. I am having a similar problem and not worked out to solve this. I am new to installing something built with Rust. I am trying to install on our server which is running Debian 11, version rustc --version rustc 1.73.0 (cc66ad468 2023-10-03)

❯ cargo check
   Compiling autocfg v1.1.0
    Checking cfg-if v1.0.0
   Compiling crossbeam-utils v0.8.16
   Compiling crc32fast v1.3.2
    Checking static_assertions v1.1.0
    Checking adler v1.0.2
    Checking byteorder v1.5.0
   Compiling version_check v0.9.4
   Compiling proc-macro2 v1.0.69
    Checking bytes v1.5.0
   Compiling unicode-ident v1.0.12
    Checking noodles-core v0.8.0
    Checking hashbrown v0.12.3
   Compiling syn v1.0.109
    Checking scopeguard v1.2.0
    Checking bitflags v1.3.2
   Compiling libc v0.2.150
    Checking memchr v2.6.4
    Checking bit-vec v0.6.3
    Checking rustc-hash v1.1.0
   Compiling rayon-core v1.12.0
    Checking os_str_bytes v6.6.1
   Compiling heck v0.4.1
    Checking either v1.9.0
    Checking textwrap v0.16.0
    Checking lexical-util v0.8.5
    Checking once_cell v1.18.0
    Checking termcolor v1.3.0
    Checking miniz_oxide v0.7.1
    Checking strsim v0.10.0
    Checking noodles-bed v0.4.0
    Checking fxhash v0.2.1
    Checking clap_lex v0.2.4
   Compiling indexmap v1.9.3
   Compiling memoffset v0.9.0
   Compiling crossbeam-epoch v0.9.15
   Compiling num-traits v0.2.17
   Compiling proc-macro-error-attr v1.0.4
   Compiling proc-macro-error v1.0.4
    Checking flate2 v1.0.28
    Checking lexical-parse-integer v0.8.6
    Checking lexical-write-integer v0.8.5
    Checking crossbeam-channel v0.5.8
    Checking lexical-parse-float v0.8.5
    Checking lexical-write-float v0.8.5
   Compiling quote v1.0.33
    Checking crossbeam-deque v0.8.3
    Checking noodles-bgzf v0.14.0
    Checking noodles-bgzf v0.15.0
    Checking lexical-core v0.8.5
    Checking atty v0.2.14
    Checking noodles-fasta v0.13.0
    Checking noodles-csi v0.9.1
    Checking rayon v1.8.0
    Checking noodles-sam v0.18.0
    Checking rust-lapper v1.1.0
    Checking ordered-float v3.9.2
error[E0308]: mismatched types
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:70:62
    |
70  | ...                   if let Err(e) = self.reader.seek(chunk.start()) {
    |                                                   ---- ^^^^^^^^^^^^^ expected `VirtualPosition`, found a different `VirtualPosition`
    |                                                   |
    |                                                   arguments to this method are incorrect
    |
    = note: `VirtualPosition` and `VirtualPosition` have similar names, but are actually distinct types
note: `VirtualPosition` is defined in crate `noodles_bgzf`
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.15.0/src/virtual_position.rs:37:1
    |
37  | pub struct VirtualPosition(u64);
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
note: `VirtualPosition` is defined in crate `noodles_bgzf`
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.14.0/src/virtual_position.rs:37:1
    |
37  | pub struct VirtualPosition(u64);
    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
    = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: method defined here
   --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader.rs:263:12
    |
263 |     pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
    |            ^^^^            --------------------------

error[E0308]: mismatched types
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:74:41
   |
74 | ...                   State::Read(chunk.end())
   |                       ----------- ^^^^^^^^^^^ expected `VirtualPosition`, found a different `VirtualPosition`
   |                       |
   |                       arguments to this enum variant are incorrect
   |
   = note: `VirtualPosition` and `VirtualPosition` have similar names, but are actually distinct types
note: `VirtualPosition` is defined in crate `noodles_bgzf`
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.15.0/src/virtual_position.rs:37:1
   |
37 | pub struct VirtualPosition(u64);
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^
note: `VirtualPosition` is defined in crate `noodles_bgzf`
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bgzf-0.14.0/src/virtual_position.rs:37:1
   |
37 | pub struct VirtualPosition(u64);
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^
   = note: perhaps two different versions of crate `noodles_bgzf` are being used?
note: tuple variant defined here
  --> /home/callum/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-sam-0.18.0/src/reader/query.rs:15:5
   |
15 |     Read(bgzf::VirtualPosition),
   |     ^^^^

For more information about this error, try `rustc --explain E0308`.
error: could not compile `noodles-sam` (lib) due to 2 previous errors
warning: build failed, waiting for other jobs to finish...

I got it to install by firstly uninstalling rust that I set up on debian 11 server and then migrated to another server we have running Ubuntu 22.04 and installing rust again.

I cloned the repo again.

cargo check, raised no issues but

cd best
cargo install --path .

did not work so I added --locked as recommended.

This time it was installed without issue.

[Daniel-Liu-c0deb0t]

I updated the README with the fix.

[colindaven]

Thanks for this @callumparr , --locked now solved the install issue for me as well.