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.
❯ quarto render hikmah-testing-default.qmd
processing file: hikmah-testing-default.qmd
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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
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3/5
4/5 [fig-n-lights]
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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)