ld error while building Mercurial with Rust #71

paugier · 2020-12-08T14:55:28Z

I tried to build Mercurial with Rust from conda-forge. I did

conda create -n env_hg_rust setuptools rust -y
conda activate env_hg_rust
wget https://www.mercurial-scm.org/release/mercurial-5.6.1.tar.gz
tar -xvf mercurial-5.6.1.tar.gz
cd mercurial-5.6
python setup.py --rust install

It ends with an error related to the fact that the linker can't find libz:

note: /data0/opt/miniconda3/envs/env_hg_rust/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz

I find it strange that /data0/opt/miniconda3/envs/env_hg_rust/x86_64-conda-linux-gnu/bin/ld can't find /data0/opt/miniconda3/envs/env_hg_rust/lib/libz.so.

I tried simple things with LIBRARY_PATH and LD_LIBRARY_PATH but without success.

I don't know if it is something related with Rust or just a conda bug. Do you see how to solve this problem?

Environment (conda list):

$ conda list
# packages in environment at /data0/opt/miniconda3/envs/env_hg_rust:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
binutils_impl_linux-64    2.35.1               h17ad2fc_0    conda-forge
ca-certificates           2020.11.8            ha878542_0    conda-forge
certifi                   2020.11.8        py39hf3d152e_0    conda-forge
gcc_impl_linux-64         9.3.0               h28f5a38_17    conda-forge
kernel-headers_linux-64   2.6.32              h77966d4_13    conda-forge
ld_impl_linux-64          2.35.1               hed1e6ac_0    conda-forge
libffi                    3.3                  h58526e2_1    conda-forge
libgcc-devel_linux-64     9.3.0               hfd08b2a_17    conda-forge
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1h               h516909a_0    conda-forge
pip                       20.3               pyhd8ed1ab_0    conda-forge
python                    3.9.0           hffdb5ce_5_cpython    conda-forge
python_abi                3.9                      1_cp39    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
rust                      1.48.0               h36c2ea0_0    conda-forge
rust-std-x86_64-unknown-linux-gnu 1.48.0               hc1431ca_0    conda-forge
setuptools                49.6.0           py39h079e4ff_2    conda-forge
sqlite                    3.34.0               h74cdb3f_0    conda-forge
sysroot_linux-64          2.12                h77966d4_13    conda-forge
tk                        8.6.10               hed695b0_1    conda-forge
tzdata                    2020d                h516909a_0    conda-forge
wheel                     0.36.0             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : env_hg_rust
    active env location : /data0/opt/miniconda3/envs/env_hg_rust
            shell level : 1
       user config file : /home/pierre/.condarc
 populated config files : /home/pierre/.condarc
          conda version : 4.9.2
    conda-build version : not installed
         python version : 3.7.4.final.0
       virtual packages : __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /data0/opt/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /data0/opt/miniconda3/pkgs
                          /home/pierre/.conda/pkgs
       envs directories : /data0/opt/miniconda3/envs
                          /home/pierre/.conda/envs
               platform : linux-64
             user-agent : conda/4.9.2 requests/2.24.0 CPython/3.7.4 Linux/5.4.0-56-generic ubuntu/20.04.1 glibc/2.31
                UID:GID : 1000:1000
             netrc file : /home/pierre/.netrc
           offline mode : False

The text was updated successfully, but these errors were encountered:

pkgw · 2020-12-09T03:53:26Z

Hmm, I'm not sure what's going on here. But I think that it's very unlikely that your problem is related to how conda-forge packages the Rust toolchain. The error is occurring at the level of conda-forge's C/binutils toolchain, but that toolchain is extremely well tested for basic operations like this. So, my best guess is that the Mercurial+Rust build system is somehow doing something unusual that triggers this error.

I'm going to close this because I just can't see that this issue would be related to how we're packaging Rust. I think you might have to dig deeper into how the Mercurial+Rust build is working.

isuruf · 2020-12-09T03:55:56Z

Try installing compilers package

paugier · 2020-12-09T10:03:25Z

Installing compilers does not help.

However, I think I understood and that this issue should be reopened and fixed so that cargo installed with conda really works 🙂

The problem is related to the fact that "cargo install does not respect LDFLAGS" rust-lang/cargo#3694 and that in conda, the library path miniconda3/envs/env_hg_rust/lib is only given in this environment variable.

$LDFLAGS                                                                                                                                                      
'-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/data0/opt/miniconda3/envs/env_hg_rust/lib -Wl,-rpath-link,/data0/opt/miniconda3/envs/env_hg_rust/lib -L/data0/opt/miniconda3/envs/env_hg_rust/lib'

Therefore cargo cannot find libraries in miniconda3/envs/env_hg_rust/lib.

I was able to compile Mercurial by setting RUSTFLAGS to -L/data0/opt/miniconda3/envs/env_hg_rust/lib.

https://doc.rust-lang.org/cargo/reference/environment-variables.html#environment-variables-cargo-reads

Adding the other options that are in LDFLAGS in RUSTFLAGS does not work.

pkgw · 2020-12-09T13:54:13Z

Thanks for digging a bit deeper, that helps clarify the discussion.

I'm not sure how we should approach this. I kind of want to say that this sort of default search path stuff is the job of the lower-level toolchain, and if there's any problem here it should be addressed at that level rather than in Rust. But I don't understand the semantics of the default library search paths in the compilers that we ship, and I could see that maybe a default RUSTFLAGS environment setting would be appropriate.

paugier · 2020-12-09T16:32:39Z

I don't understand why rustc doesn't take into account LDFLAGS. I mean it uses the linker (via x86_64-conda-linux-gnu-cc) so it should pass the values in LDFLAGS to x86_64-conda-linux-gnu-cc.

I think for conda, the options -Wl,-rpath,/data0/opt/miniconda3/envs/env_hg_rust/lib -Wl,-rpath-link,/data0/opt/miniconda3/envs/env_hg_rust/lib are important. It seems that it is impossible to use them with cargo.

pkgw · 2020-12-09T17:07:39Z

My guess is that the aim is to encourage reproducibility and explicitness in build processes. We may be accustomed to injecting low-level linker flags from environment variables, but it's really not a great method because it adds invisible statefulness to the build.

But anyway, even if we were all convinced that rustc should obey LDFLAGS, we shouldn't make such a change in our Rust package, I think — that would be a pretty profound behavior change to apply in a vendor patch. For this feedstock, I think the question is whether we should be setting up a default RUSTFLAGS environment variable or something.

isuruf · 2020-12-09T19:59:49Z

@paugier, can you try installing rust_linux-64?

paugier · 2020-12-09T21:08:33Z

I tried with rust_linux-64 => same problem...

paugier · 2020-12-10T21:28:29Z

Note that it works with RUSTFLAGS set to

-C link-arg=-Wl,-rpath-link,/data0/opt/miniconda3/envs/env_hg_rust/lib -C link-arg=-Wl,-rpath,/data0/opt/miniconda3/envs/env_hg_rust/lib -L/data0/opt/miniconda3/envs/env_hg_rust/lib

But it does not seem to work with CARGO_BUILD_RUSTFLAGS (as defined in https://github.com/conda-forge/rust-activation-feedstock/blob/master/recipe/activate.sh).

jinlow · 2022-05-05T01:56:00Z

I'm having this same issue with rust 1.60 installed from conda-forge, on Ubuntu 21.10.

note: /home/jinlow/miniconda3/envs/rust_dev/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz
          collect2: error: ld returned 1 exit status

jinlow · 2022-05-05T02:10:09Z

However, @paugier's fix worked for me, running the following before building.

export RUSTFLAGS="-C link-arg=-Wl,-rpath-link,$CONDA_PREFIX/lib -C link-arg=-Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib"

andronat · 2024-02-21T00:26:21Z

JFYI we recently had to build a wheel package that includes a Rust binary inside a conda environment and we stumbled on this problem. using the RUSTFLAGS from @jinlow made the trick 😄

andronat · 2024-02-21T01:48:11Z

I also noticed that https://github.com/conda-forge/rust-activation-feedstock/blob/main/recipe/activate.sh#L19 adds RUSTFLAGS in the env.

pkgw closed this as completed Dec 9, 2020

pkgw reopened this Dec 9, 2020

pkgw mentioned this issue Jan 3, 2021

tectonic v0.4.1 conda-forge/tectonic-feedstock#39

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pkgw mentioned this issue Mar 16, 2021

Error compiling Rust program #76

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paugier mentioned this issue Jun 7, 2022

Build hg with Rust conda-forge/mercurial-feedstock#57

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ld error while building Mercurial with Rust #71

ld error while building Mercurial with Rust #71

paugier commented Dec 8, 2020

pkgw commented Dec 9, 2020

isuruf commented Dec 9, 2020

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andronat commented Feb 21, 2024

andronat commented Feb 21, 2024

ld error while building Mercurial with Rust #71

ld error while building Mercurial with Rust #71

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paugier commented Dec 8, 2020

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isuruf commented Dec 9, 2020

paugier commented Dec 9, 2020

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