“Stack 3.7.1: linker (-lgmp) failure & wrong toolchain when building vpf-class project”

[tabby678]

Please follow the steps below for reporting a bug in Stack:

Make sure that you are using the latest release (currently Stack 3.7.1). See the
upgrade instructions
to upgrade.

Please use the following schema for your bug report:

General summary/comments (optional)

Trying to build and run the vpf-tools project (exec target vpf-class) on a shared HPC host. I upgraded to Stack 3.7.1 in my home (~/.local/bin/stack), but I’m seeing a few rough edges:
GHC setup/build fails when a conda toolchain is present: the link step uses x86_64-conda-linux-gnu-cc and errors with cannot find -lgmp. Even after providing GMP via conda, Stack/GHC still prefer the conda toolchain unless I scrub env vars.
GHC sanity check and setup produce confusing failures if libtinfo.so.5/GMP are missing.
If STACK_ROOT isn’t exported in the shell, Stack quietly falls back to ~/.stack and tries to unpack GHC there (low-space home), leading to tar Jxf … failures.
In Stack 3.x, --work-dir no longer accepts absolute paths; the error is correct but took a while to discover (docs/UI hint could be clearer).
When a non-ASCII space sneaks into exec --, Stack treats it like runghc and the “Invalid argument vpf-class” message is non-obvious; a more explicit hint would help.
Not all of these are “bugs” per se, but #1 (toolchain contamination) and #5 (diagnostic clarity) might be actionable.

Steps to reproduce

Ensure a conda environment is active (e.g., base), so x86_64-conda-linux-gnu-cc is on PATH/CC.
Clone project and cd:
git clone https://github.com/biocom-uib/vpf-tools
cd vpf-tools

Use user-local Stack:
export PATH=$HOME/.local/bin:$PATH # stack 3.7.1
export STACK_ROOT=/mnt/nas/vol2/fiza/stackroot
Build:
stack --allow-different-user --stack-root "$STACK_ROOT" --work-dir .stack-work-fiza build
Observe link failure using conda toolchain:
/usr/local/miniconda3/.../ld: cannot find -lgmp
x86_64-conda-linux-gnu-cc' failed in phase Linker'. (Exit code: 1)
(If STACK_ROOT is not set) Stack falls back to ~/.stack and GHC unpack fails in a low-space home:
Error: [S-7441]
Raw command: /usr/bin/tar Jxf /home//.stack/programs/x86_64-linux/ghc-8.10.2.tar.xz
Using an absolute --work-dir:
stack --work-dir /mnt/nas/vol2/fiza/vpf-stack-work build
yields:
option --work-dir: ... Stack will not accept an absolute path.
If a non-ASCII space is copied before --, e.g. exec -- vpf-class:
stack: WARNING! Using runghc ...
Invalid argument `exec --'
Error executing interpreter command: stack exec -- vpf-class ...

Include any .yaml configuration, if relevant.
Project stack.yaml is the one in biocom-uib/vpf-tools (resolver targets GHC 8.10.x).

Expected

What you expected to see and happen.
Stack/GHC should ignore conda’s compiler/toolchain by default (or provide a clear hint) and use a system toolchain, or error with a message pointing to GMP/ncurses requirements and how to avoid conda toolchain contamination.

Clearer diagnostics when --work-dir is absolute (e.g., print “use a relative path like .stack-work-user”).

If a non-ASCII space appears in exec --, emit a specific message (“non-ASCII whitespace detected near --; please retype with ASCII space”).

Actual

What actually happened.
Link step fails with:

/usr/local/miniconda3/.../ld: cannot find -lgmp
x86_64-conda-linux-gnu-cc' failed in phase Linker'. (Exit code: 1)
GHC sanity check complains about:
/lib64/libtinfo.so.5: no version information available ...
and then fails to link if GMP/ncurses-compat are missing.
If STACK_ROOT is not exported, Stack tries to unpack GHC into ~/.stack and fails (tar Jxf ... ExitFailure 2) due to space/corruption.
Absolute --work-dir is rejected (as designed) but the error took time to interpret.
Non-ASCII space in exec -- produces runghc invocation and “Invalid argument exec --”, which is confusing.

If you suspect that a Stack command misbehaved, please include the output of
that command in --verbose mode. If the output is larger than a page please
paste the output in a Gist.

conda active; toolchain visible; missing system gmp/libtinfo

stack --allow-different-user --stack-root "$STACK_ROOT" --work-dir .stack-work-fiza build --verbose

stack <your command here> <args> --verbose
<output>

Stack version

stack --version
Version 3.7.1, Git revision cfae313 x86_64 hpack-0.38.1

stack --version
Version 3.7.1, Git revision cfae313a06ea9f7278e0ac55a58341fa0440f1aa x86_64 hpack-0.38.1

Method of installation

Official binary via stack upgrade (placed at ~/.local/bin/stack).
A legacy system-wide 2.7.3 exists in /usr/local/bin (cannot be overwritten; no sudo).

• Official binary, downloaded via haskellstack.org or from Stack's repository
• Via GHCup
• Via Cabal (the tool)
• An unofficial package repository (please specify which)
• Other (please specify)

Platform

x86_64 Linux on an HPC node (RHEL/CentOS/Rocky family; no sudo).
Conda is commonly used on the cluster; envs expose x86_64-conda-linux-gnu-cc.
Your platform (machine architecture and operating system)