Cannot compile bibliography

[vasi786]

Hi, I am using vimtex for my paper and having issues when compiling bibliography. Compiling normal text is working fine, but as soon as I introduce a reference, I get an error saying the key is undefined, but clearly the key is defined. I am using neovim with lazy, below is my configuration. Also weird is that none of the completion works. Am I doing something wrong with the configuration?

The error is as follows

Output written on main.pdf (6 pages, 29273250 bytes).
SyncTeX written on main.synctex.gz.
Transcript written on main.log.
Latexmk: ====Undefined refs and citations with line #s in .tex file:
  Citation 'adupaTertiaryStructureConformational2024' on page 1 undefined on input line 34
  Reference `figure1' on page 1 undefined on input line 36
  Citation 'ossatoTwoStepPathInclusion2010' on page 2 undefined on input line 150
  Citation 'adupaTertiaryStructureConformational2024' on page 2 undefined on input line 153
Latexmk: Getting log file 'main.log'
Latexmk: Examining 'main.fls'
Latexmk: Examining 'main.log'
Latexmk: Found input bbl file 'main.bbl'
Latexmk: References changed.
Latexmk: Log file says output to 'main.pdf'
Latexmk: Bibliography file(s) from .bcf file:
  DNAJB6b-PolyQ-Paper.bib
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 1 reference(s)
  Latex failed to resolve 3 citation(s)
Latexmk: Errors, so I did not complete making targets
------------
Running 'echo vimtex_compiler_callback_failure'
------------
vimtex_compiler_callback_failure
Latexmk: Failure to make the files correctly
    ==> You will need to change a source file before I do another run <==

My vimtex.lua file

return {
  "lervag/vimtex",
  lazy = false,     -- we don't want to lazy load VimTeX
  -- tag = "v2.15", -- uncomment to pin to a specific release
  init = function()
    -- VimTeX configuration goes here, e.g.
    vim.g.vimtex_enabled = "1"
    -- vim.g.vimtex_view_method = "mupdf"
    -- vim.g.vimtex_view_mupdf_send_keys = "f"
    -- vim.g.vimtext_view_general_viewer = "qimgv"
    vim.g.vimtex_compiler_method = "latexmk"
    -- vim.g.vimtex_view_general_options = "--unique file:@pdf\#src:@line@tex"
    vim.g.vimtex_complete_close_braces = "1"
    vim.g.vimtex_complete_enabled = "1"
    vim.g.vimtex_syntax_enabled = "1"
    vim.g.vimtex_complete_commands = "1"
    vim.g.vimtex_complete_environments = "1"
    vim.g.vimtex_complete_filenames = "1"
    vim.g.vimtex_quickfix_ignore_filters = 'Marginpar on page'
    vim.g.vimtex_quickfix_open_on_warning = '0'
  end
}

I have this in my document for bibliography and I use \cite command for calling a particular reference.

\bibliographystyle{unsrt}
\bibliography{DNAJB6b-PolyQ-Paper}

and in the bib file one example entry is as follows

@article{adupaTertiaryStructureConformational2024,
  title = {Tertiary Structure and Conformational Dynamics of the Anti-Amyloidogenic Chaperone {{DNAJB6b}} at Atomistic Resolution},
  author = {Adupa, Vasista and Ustyantseva, Elizaveta and Kampinga, Harm H. and Onck, Patrick R.},
  year = {2024},
  month = apr,
  journal = {Nature Communications},
  volume = {15},
  number = {1},
  pages = {3285},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-024-46587-z},
  urldate = {2025-04-23},
  abstract = {xxxxxxxx},
  copyright = {2024 The Author(s)},
  langid = {english},
  keywords = {Atomistic models,Chaperones,Computational biophysics,Computational models,mywork},
}

Neovim version

NVIM v0.10.4
Build type: Release
LuaJIT 2.1.1713484068

   system vimrc file: "$VIM/sysinit.vim"
  fall-back for $VIM: "/usr/local/share/nvim"

Run :checkhealth for more info

[cosmiccoder01]

fixed it, there are several instances in my file with \sim{} and that is causing the citations to not work.

[lervag]

First, glad to see you were able to fix this yourself.

I just wanted to comment your config. I propose to update it to the following equivalent, simplified and slightly fixed version:

return {
  "lervag/vimtex",
  lazy = false,
  init = function()
    vim.g.vimtex_complete_close_braces = true
    vim.g.vimtex_quickfix_ignore_filters = { "Marginpar on page" }
    vim.g.vimtex_quickfix_open_on_warning = false
  end
}

The options I removed were either 1) not valid options, or 2) not option values that were not changed from their default values.

Notice also that you had used a wrong type for the vimtex_quickfix_ignore_filters option (it needs to be a list/table).