Fails to build from source

[vedranmiletic]

I am a GROMACS contributor and I am very curious about Lumol. I tried to compile it with Rust 1.75 and 1.76 nightly and I get the following error:

/home/vedran/workspace/lumol/target/debug/build/chemfiles-sys-7ef0e8e38b1e6bbe/out/build/chemfiles/external/xdrfile/src/xdrfile.c:2020:5: error: incompatible function pointer types initializing 'unsigned int (*)(XDR *)' (aka 'unsigned int (*)(struct XDR *)') with an expression of type 'int64_t (XDR *)' (aka 'long (struct XDR *)') [-Wincompatible-function-pointer-types]
xdrstdio_getpos,   /* get offset in the stream */
^~~~~~~~~~~~~~~
/home/vedran/workspace/lumol/target/debug/build/chemfiles-sys-7ef0e8e38b1e6bbe/out/build/chemfiles/external/xdrfile/src/xdrfile.c:2021:5: error: incompatible function pointer types initializing 'int (*)(XDR *, unsigned int)' (aka 'int (*)(struct XDR *, unsigned int)') with an expression of type 'int(XDR *, int64_t, int)' (aka 'int (struct XDR *, long, int)') [-Wincompatible-function-pointer-types]
xdrstdio_setpos,   /* set offset in the stream */
^~~~~~~~~~~~~~~
2 errors generated.
gmake[2]: *** [/home/vedran/workspace/lumol/target/debug/build/chemfiles-sys-7ef0e8e38b1e6bbe/out/build/chemfiles/external/xdrfile/CMakeFiles/xdrfile.dir/build.make:76: /home/vedran/workspace/lumol/target/debug/build/chemfiles-sys-7ef0e8e38b1e6bbe/out/build/chemfiles/external/xdrfile/CMakeFiles/xdrfile.dir/src/xdrfile.c.o] Greška 1
gmake[1]: *** [CMakeFiles/Makefile2:541: chemfiles/external/xdrfile/CMakeFiles/xdrfile.dir/all] Greška 2
gmake[1]: *** Čeka se na nedovršene poslove....
gmake: *** [Makefile:136: all] Greška 2
thread 'main' panicked at /home/vedran/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cmake-0.1.50/src/lib.rs:1098:5:

command did not execute successfully, got: exit status: 2

build script failed, must exit now
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: cmake::fail
3: cmake::run
4: cmake::Config::build
5: build_script_build::build_chemfiles
6: build_script_build::main
7: core::ops::function::FnOnce::call_once
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

This is on FreeBSD 14, but it doesn't seem like a FreeBSD-specific error. Any ideas why would chemfiles be incompatible with its own bundled xdrfile?

[Luthaf]

That might just be an issue with older chemfiles on freebsd. I haven't been able to work on lumol for a long time, and everything here is a bit outdated. I'll try updating chemfiles to the latest release to see if this fixes it!

[Luthaf]

Ok, I've updated chemfiles and other dependencies, it should now hopefully build for you.

[vedranmiletic]

Thanks for a quick response!

Indeed, now it goes a bit further, but still fails with:

error: linking with `cc` failed: exit status: 1
|
= note: LC_ALL="C" PATH="/usr/local/lib/rustlib/x86_64-unknown-freebsd/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/home/vedran/bin" VSLANG="1033" "cc" "-m64" "/tmp/rustcQevRot/symbols.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.130h5kqru05rr8ro.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.1at30heg74g0c2e6.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.1i3t0v8r5eovt8vj.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.1rf7p6t4islwzwf7.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.1u8rl6lsr3p3dpit.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.1xryfs9kll1oodc8.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.2bmpnjz8x0gouyd8.rcgu.o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25.2f8oqycsmsj89qmw.rcgu.o" 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"/home/vedran/workspace/lumol/target/debug/deps/libcolorchoice-e3f0bb0e4c50c0ee.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libanstyle_parse-9939fe0a7485741d.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libutf8parse-f3ccd09581932eb3.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libclap_lex-2c0bf59f3bcaa105.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libanstyle-3c57e224ef964a94.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libchrono-035cb39a84b09ded.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libnum_traits-effd3fcbf008d0c3.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libiana_time_zone-c01ec3fcc96110ef.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libbacktrace-9ea7549e89b3c602.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libminiz_oxide-5b0e45bda437bbc3.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libadler-a905b27adb3df7ae.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libobject-7665aead2a5bc33a.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libmemchr-00caa8612e79ad09.rlib" "/home/vedran/workspace/lumol/target/debug/deps/liblibc-e5c91cb361609993.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libaddr2line-14585abcbd2c6883.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libgimli-f350de4a1c584736.rlib" "/home/vedran/workspace/lumol/target/debug/deps/libcfg_if-b4544ba88038e686.rlib" "/home/vedran/workspace/lumol/target/debug/deps/librustc_demangle-fc0684191aed3f95.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libstd-749fc163998e3b57.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libpanic_unwind-3324aedb7da8df53.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libobject-bc443a8c9b6a5af6.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libmemchr-32aa4d6d2c594b5a.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libaddr2line-ed7601c080312510.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libgimli-0081e03f58ee1da7.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/librustc_demangle-d609ff5272dccaba.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libstd_detect-3a5ac86785f500b3.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libhashbrown-32378335710e5990.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/librustc_std_workspace_alloc-1bdd891611287621.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libminiz_oxide-10783897338a5242.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libadler-a209363d25099528.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libunwind-5df04f060bbbbd80.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libcfg_if-24680301f326b512.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/liblibc-157fec8f38914dc1.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/liballoc-fa2699c8de87ae5a.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/librustc_std_workspace_core-9d191736d9334602.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libcore-5cc782c3786c4249.rlib" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib/libcompiler_builtins-86cbd9faabce4993.rlib" "-Wl,-Bdynamic" "-lc++" "-lm" "-lc" "-lgcc" "-lgcc_s" "-lrt" "-lutil" "-lexecinfo" "-lkvm" "-lmemstat" "-lkvm" "-lutil" "-lprocstat" "-lrt" "-ldevstat" "-lexecinfo" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lrt" "-lutil" "-lexecinfo" "-lkvm" "-lmemstat" "-lkvm" "-lutil" "-lprocstat" "-lrt" "-ldevstat" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/usr/local/lib/rustlib/x86_64-unknown-freebsd/lib" "-o" "/home/vedran/workspace/lumol/target/debug/deps/lumol-ef1b8494ed028c25" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-nodefaultlibs"
= note: ld: error: undefined symbol: lseek64
>>> referenced by gzlib.c
>>>               gzlib.c.o:(gz_open) in archive /home/vedran/workspace/lumol/target/debug/deps/libchemfiles_sys-67207b92ccc9a731.rlib
>>> referenced by gzlib.c
>>>               gzlib.c.o:(gz_open) in archive /home/vedran/workspace/lumol/target/debug/deps/libchemfiles_sys-67207b92ccc9a731.rlib
>>> referenced by gzlib.c
>>>               gzlib.c.o:(gzrewind) in archive /home/vedran/workspace/lumol/target/debug/deps/libchemfiles_sys-67207b92ccc9a731.rlib
>>> referenced 3 more times
cc: error: linker command failed with exit code 1 (use -v to see invocation)

error: could not compile `lumol` (bin "lumol") due to previous error

Any ideas? I completely understand if Lumol is not your focus anymore and don't have time to look into it deeper.

[Luthaf]

Well, these are all chemfiles errors, on which I'm still working =). Let's open an issue over there (https://github.com/chemfiles/chemfiles.rs/issues/46) about this.

[Luthaf]

Ok, now that the chemfiles fix is published, you should be able to build lumol with a cargo update.