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Issues with rendering the template? #5

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maxdrohde opened this issue Oct 20, 2023 · 0 comments
Open

Issues with rendering the template? #5

maxdrohde opened this issue Oct 20, 2023 · 0 comments

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@maxdrohde
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maxdrohde commented Oct 20, 2023 •
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Thank you for creating this great template!

I cloned the repository and tried to render the template file as a basic check, but it isn't working. It looks like Quarto can't find the generated .tex file from the second pass through XeLaTeX, but I'm not sure what's causing this. I haven't had a similar issue with other templates.

Below is the error message I receive:

Error

❯ quarto render hikmah-testing-default.qmd


processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: latex
  output-file: hikmah-testing-default.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  cite-method: biblatex

metadata
  block-headings: false
  date-format: full
  geometry:
    - top=10pc
    - bottom=10pc
    - left=11pc
    - right=11pc
    - heightrounded
  colorlinks: true
  linkcolor: DarkSlateBlue
  urlcolor: DarkSlateBlue
  citecolor: DarkSlateBlue
  link-citations: true
  biblio-title: References
  biblio-config: false
  biblatex-chicago: false
  biblio-style: apa
  biblatexoptions:
    - backend=biber
  indent: true
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: docx
  output-file: hikmah-testing-default.docx
  default-image-extension: png
  reference-doc: _extensions/hikmah-manuscript/styles/reference.docx

metadata
  date-format: full
  knitr:
    opts_chunk:
      dev: ragg_png
      dpi: 300
      out.width: 80%
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: odt
  output-file: hikmah-testing-default.odt
  template: _extensions/hikmah-manuscript/templates/odt-manuscript.odt
  default-image-extension: png
  reference-doc: _extensions/hikmah-manuscript/styles/reference.odt

metadata
  date-format: full
  knitr:
    opts_chunk:
      dev: ragg_png
      dpi: 300
      out.width: 80%
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib



processing file: hikmah-testing-default.qmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [fig-n-lights]
5/5
output file: hikmah-testing-default.knit.md

pandoc
  to: latex
  output-file: hikmah-testing-default.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  cite-method: biblatex

metadata
  block-headings: false
  date-format: full
  documentclass: article
  papersize: letter
  fontsize: 12pt
  linestretch: 2
  geometry:
    - top=1in
    - bottom=1in
    - left=1in
    - right=1in
  colorlinks: true
  linkcolor: DarkSlateBlue
  urlcolor: DarkSlateBlue
  citecolor: DarkSlateBlue
  link-citations: true
  biblio-title: References
  biblio-config: false
  biblatex-chicago: false
  biblio-style: apa
  biblatexoptions:
    - backend=biber
  indent: true
  title: |-
    On the Surgical Removal of \
    Cardassian Cranial Implants
  subtitle: A case study of a Cardassian patient
  short-title: Cranial Implants
  published: Under review at *Starfleet Medical Journal*
  code-repo: 'Access the code, data, and analysis at <https://git.starfleet.ufp/bashir/cranial-implants>'
  correspondence-prefix: Correspondence concerning this article should be addressed to
  author:
    - name: Julian Bashir
      email: [email protected]
      orcid: 0000-0002-3948-3914
      title: Chief Medical Officer
      affiliations:
        - id: ds9
          name: Starbase Deep Space Nine
          department: Sick Bay
          address: 1234 Main Street
          city: Anytown
          region: NY
          country: USA
          postal-code: 90210
      attributes:
        corresponding: true
    - name: Elim Garak
      email: [email protected]
      title: Shopkeeper and Tailor
      affiliations:
        - id: terok
          name: Terok Nor
          department: Promenade
        - ref: ds9
  abstract: |
    Space: the final frontier. These are the voyages of the starship *Enterprise*. Its continuing mission: to explore strange new worlds. To seek out new life and new civilizations. To boldly go where no one has gone before!
  thanks: 'Placeholder text generated at <https://vlad-saling.github.io/star-trek-ipsum/>.'
  additional-info: We have no known conflict of interest to disclose.
  keywords:
    - surgery
    - espionage
    - brains
  date: 'August 24, 2022'
  epigraph:
    - text: War is good for business.
      source: Ferengi Rule of Acquisition 34
    - text: Peace is good for business.
      source: Ferengi Rule of Acquisition 35
  bibliography:
    - references.bib

running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode

generating bibliography
  INFO - This is Biber 2.19
  INFO - Logfile is 'hikmah-testing-default.blg'
  INFO - Reading 'hikmah-testing-default.bcf'
  INFO - Found 3 citekeys in bib section 0
  INFO - Processing section 0
  INFO - Looking for bibtex file 'references.bib' for section 0
  INFO - LaTeX decoding ...
  INFO - Found BibTeX data source 'references.bib'
  INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
  INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
  INFO - Sorting list 'apa/apasortcite//global/global' of type 'entry' with template 'apa' and locale 'en-US'
  INFO - No sort tailoring available for locale 'en-US'
  INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
  INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
  INFO - Sorting list 'apa/global//global/global' of type 'entry' with template 'apa' and locale 'en-US'
  INFO - No sort tailoring available for locale 'en-US'
  INFO - Writing 'hikmah-testing-default.bbl' with encoding 'UTF-8'
  INFO - Output to hikmah-testing-default.bbl

running xelatex - 2
  This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode


ERROR: NotFound: No such file or directory (os error 2), open '/Users/max/hikmah-academic-quarto/hikmah-testing-default.tex'

NotFound: No such file or directory (os error 2), open '/Users/max/hikmah-academic-quarto/hikmah-testing-default.tex'
    at async Object.open (deno:runtime/js/40_files.js:55:17)
    at async processLines (file:///Applications/quarto/bin/quarto.js:81521:18)
    at async file:///Applications/quarto/bin/quarto.js:81500:9
    at async Object.complete (file:///Applications/quarto/bin/quarto.js:81077:21)
    at async Object.onPostProcess (file:///Applications/quarto/bin/quarto.js:86678:36)
    at async renderFiles (file:///Applications/quarto/bin/quarto.js:86649:13)
    at async renderProject (file:///Applications/quarto/bin/quarto.js:86800:25)
    at async Command.fn (file:///Applications/quarto/bin/quarto.js:90856:32)
    at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13)
    at async quarto (file:///Applications/quarto/bin/quarto.js:127545:5)
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