Compiling issue - error[E0063]: missing field `gfa_output` in initializer of `GGCATConfig`

[tmtktmtk]

The version 0f8190d cannot be compiled on linux fedora due to these following errors

   Compiling statrs v0.16.1
   Compiling bio v1.6.0
   Compiling genome-graph v9.0.0
   Compiling matchtigs v2.1.8
   Compiling ggcat_assembler v0.1.0 (/home/ktruong/Documents/code/original_fulgor/fulgor/external/ggcat/crates/assembler)
   Compiling ggcat-api v0.1.0 (/home/ktruong/Documents/code/original_fulgor/fulgor/external/ggcat/crates/api)
error[E0063]: missing field `gfa_output` in initializer of `GGCATConfig`
  --> crates/capi/src/lib.rs:19:42
   |
19 |     let instance = GGCATInstance::create(GGCATConfig {
   |                                          ^^^^^^^^^^^ missing `gfa_output`

error[E0061]: this method takes 11 arguments but 10 arguments were supplied
   --> crates/capi/src/lib.rs:93:10
    |
93  |           .build_graph(
    |  __________^^^^^^^^^^^-
94  | |             input_blocks,
95  | |             PathBuf::from(output_file),
96  | |             if color_names.len() > 0 {
...   |
118 | |             },
119 | |         )
    | |_________- argument #11 of type `bool` is missing
    |
note: method defined here
   --> /home/ktruong/Documents/code/original_fulgor/fulgor/external/ggcat/crates/api/src/lib.rs:199:12
    |
199 |     pub fn build_graph(
    |            ^^^^^^^^^^^
help: provide the argument
    |
93  ~         .build_graph(input_blocks, PathBuf::from(output_file), if color_names.len() > 0 {
94  +                 Some(color_names)
95  +             } else {
96  +                 None
97  +             }, kmer_length, threads_count, forward_only, if minimizer_length == usize::MAX {
98  +                 None
99  +             } else {
100 +                 Some(minimizer_length)
101 +             }, colors, min_multiplicity, match extra_elab {
102 +                 EXTRA_ELABORATION_STEP_NONE => ExtraElaboration::None,
103 +                 EXTRA_ELABORATION_STEP_UNITIG_LINKS => ExtraElaboration::UnitigLinks,
104 +                 EXTRA_ELABORATION_STEP_GREEDY_MATCHTIGS => ExtraElaboration::GreedyMatchtigs,
105 +                 EXTRA_ELABORATION_STEP_EULERTIGS => ExtraElaboration::Eulertigs,
106 +                 EXTRA_ELABORATION_STEP_PATHTIGS => ExtraElaboration::Pathtigs,
107 +                 _ => panic!("Invalid extra_elab value: {}", extra_elab),
108 +             }, /* bool */)
    |

Some errors have detailed explanations: E0061, E0063.
For more information about an error, try `rustc --explain E0061`.
error: could not compile `ggcat-cpp-bindings` (lib) due to 2 previous errors
make[3]: *** [Makefile:15: lib/libggcat_cpp_bindings.a] Error 101
make[2]: *** [CMakeFiles/ggcat_cpp_api.dir/build.make:70: CMakeFiles/ggcat_cpp_api] Error 2
make[1]: *** [CMakeFiles/Makefile2:86: CMakeFiles/ggcat_cpp_api.dir/all] Error 2
make: *** [Makefile:91: all] Error 2

[karel-brinda]

One comment – it seems to be potentially related to the CMake part of Fulgor. cargo build finishes without any issue if executed manually.

[Alessio-Campa]

The bug has been fixed by reverting the GGCAT update. If your last pulled commit is 0f8190d, executing the following commands should bring you to the correct commit.

git fetch
git reset HEAD~
git pull
git submodule update --init --recursive

Then run make -j in the build directory

[karel-brinda]

Actually, the previous commit was fixing another GGCAT-related compilation issue on other platforms: #41.

[karel-brinda]

Maybe moving towards (actually backwards :)) the latest official release – v1.1.0 – may fix the things?

[jermp]

ahah I totally forgot about the other GGCAT issue! So whatever we do, GGCAT refuses to compile :(

[luizirber]

It is an upstream error in GGCAT, they updated the C API but didn't test it before merging the change. I hit it in #47 (comment) too...

[jermp]

Guys, I must admit I'm now a bit confused on how we should proceed to solve this issue. The PR @luizirber opened (Thank you so much!) should fix this?

[karel-brinda]

I think the issue is to find with which GGCAT version Fulgor is compilable everywhere. My guess would be that the official release should work https://github.com/algbio/ggcat/releases/tag/v1.1.0 as they likely tested it widely (unlike their progressive individual commits in main).

What I can tell about the current state on my mac:

• the current main doesn't compile (commit a776176)
• if I switch ggcat to v1.1.0, it works

I've created the following PR so that everyone can test it: #48

[jermp]

Let me rephrase a bit: "The issue is to find a version of GGCAT that compiles/works everywhere" :-D

The release you mentioned is the one inducing the latest compilation error reported here in this issue...

[karel-brinda]

I think the version causing this issue was not the release (v1.1.0), but the latest head, no (see your comment #41 (comment))?

[jermp]

Oh @karel-brinda , I think you're right, yes! So, with the commit of the release, does it work correctly on your end?