Thanks Zach!

You had the right intuition - this was not a first build. I had done a git pull and then make install. I followed your instructions, removed the ChimeraX.app folder and did `make build-from-scratch` and everything worked fine.

Perhaps this is a question for Tristan, but is there a way to build a compatible version of ISOLDE?

Cheers,
Alexis

On Mon, Oct 20, 2025 at 11:01 PM Zach Pearson <z.pearson9@gmail.com> wrote:
Hi Alexis,

Was this from your first build, or a second build? Sometimes I encounter this error if I’m building a bundle for a second time without a make clean in between, so I always rm -r ChimeraX.app and use the build-from-scratch make target.

— Zach

> On 20 Oct 2025, at 19:40, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> I'd like to build from source in order to play with (and possibly hack at) the MCP server.
>
> I am on macOS 14.7.6 with Xcode 16.2.
>
> I think the compilation went well, but at link time I get warnings and an error. Below is the end of the output of `make install`. What do you recommend I try?
>
> Cheers,
> Alexis
>
>
> available bundle cache has not been initialized yet
> Executing: devel install . user false exit true  noDeps true
> ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.o) was built for newer 'macOS' version (11.0) than being linked (10.9)
> ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/element_cpp/Element.o) was built for newer 'macOS' version (11.0) than being linked (10.9)
> ar: src/lib/libatomstruct_tmpl.a is a fat file (use libtool(1) or lipo(1) and ar(1) on it)
> ar: src/lib/libatomstruct_tmpl.a: Inappropriate file type or format
> Traceback (most recent call last):
>   File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 87, in spawn
>     subprocess.check_call(cmd, env=_inject_macos_ver(env))
>   File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '['/usr/bin/xcrun', 'ar', 'rcs', 'src/lib/libatomstruct_tmpl.a', 'atomic_cpp/atomstruct_cpp/tmpl/Atom.o', 'atomic_cpp/atomstruct_cpp/tmpl/Bond.o', 'atomic_cpp/atomstruct_cpp/tmpl/CoordSet.o', 'atomic_cpp/atomstruct_cpp/tmpl/Molecule.o', 'atomic_cpp/atomstruct_cpp/tmpl/Residue.o', 'atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.o', 'atomic_cpp/atomstruct_cpp/tmpl/amino.o', 'atomic_cpp/atomstruct_cpp/tmpl/camino.o', 'atomic_cpp/atomstruct_cpp/tmpl/findres.o', 'atomic_cpp/atomstruct_cpp/tmpl/general.o', 'atomic_cpp/atomstruct_cpp/tmpl/ions.o', 'atomic_cpp/atomstruct_cpp/tmpl/namino.o', 'atomic_cpp/atomstruct_cpp/tmpl/nucleic.o']' returned non-zero exit status 1.
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