Native C (bindgen) dependent crates do not compile? #53
Comments
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@softprops trying to figure out this as I go... After jumping into your container bypassing the entrypoint to interactively try to figure this out: And also installing I'm still having compilation issues right after calling I also wonder how does this container build for musl since I cannot seem to find a compiler in there: So far I have been unable to reproduce my host Any ideas on how to fix this are much appreciated! |
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In a nutshell, after getting into the container I do: Minimal changes to your diff --git a/build.sh b/build.sh
index 39320c3..b72d1f0 100755
--- a/build.sh
+++ b/build.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -x
# build and pack a rust lambda library
# https://aws.amazon.com/blogs/opensource/rust-runtime-for-aws-lambda/
@@ -23,7 +23,7 @@ export CARGO_TARGET_DIR=$PWD/target/lambda
# cargo only supports --release flag for release
# profiles. dev is implicit
if [ "${PROFILE}" == "release" ]; then
- cargo build ${CARGO_FLAGS:-} --${PROFILE}
+ cargo build ${CARGO_FLAGS:-} --${PROFILE} --verbose --target x86_64-unknown-linux-musl
else
cargo build ${CARGO_FLAGS:-}
fiAlso slightly modifying the But still I'm getting the same linker error: What am I doing wrong? :/ |
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Hello @nlhepler! I just noticed your recently merged Also @clux refers to other I'm new to rust-htslib and bindgen and *-sys crates and its packaging intricacies, so any directions/suggestions on how to fix this are very appreciated :) |
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Hi @brainstorm! We did! Exciting times. I'm also very new to these things, but I was also trying to follow the guidelines. My understanding is that the -sys library that links the system library needs to specify links=, and indeed, the hts-sys package does specify links: https://github.com/rust-bio/rust-htslib/blob/master/hts-sys/Cargo.toml#L6. My understanding is that rust-htslib does not need links=, it only needs to depend on an hts-sys. |
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LLVM being required may be part of the linker rust uses. I am not entirely sure, I have seen these errors from time to time myself, but I've always had llvm-config to add to PATH. |
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Thanks @nlhepler for the pointers! Yesterday I managed to fix the I'll try to import the fix to this |
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Aaand, problem solved! I just had to do this inside the container:
Since the installed clang/llvm is 3.6 but htslib seems to require clang 3.9 minimum. Next up is pullrequest and a testcase, thanks everyone! |
Closed
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For me it failed here: Is this the same issue or a other one? |
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@johansmitsnl Check |
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I found that musl-gcc is not installed in the image. Installing makes it build. Why is musl-gcc not available? |
The goal here is to leverage a build environment that aligns as closly with the runtime as possible. We could add |
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I wrongly filed this issue on
rust-htslib: rust-bio/rust-htslib#179After a bit more digging, I now believe it belongs here. I've put together a small reproducer using the serverless-aws-rust-multi template, just adding an additional lambda function called
htslib:https://github.com/brainstorm/serverless-aws-rust-multi-fail-native-crate
There's a full explanation and error log on the README from the repo above, but TL;DR the lamda-rust docker container doesn't seem to compile/link the rust-htslib crate with C bindings well:
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