* citeproc citation not found
@ 2020-11-18 17:45 Andrew Mercer
[not found] ` <c5fad0e6-186d-4e31-8b38-063e12ff5547n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-11-18 17:45 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 2650 bytes --]
The new citeproc is behaving very oddly.
Firstly, the latex template is incorrect, cslreferences needs now to read
CSLReferences
But there are two problems I haven't been able to fix.
The first problem is a little odd,: the first reference gets "10" prepended
to the first author name .
The second problem is really confusing.
At first citeproc would not find references in a bib file. A single
reference in the yaml was found but nothing else. I then converted the
reference in the bib to yaml and added it to the yaml markdown documents
yaml. This works.
What is odd is that I converted the bib to yaml using pandoc without a
problem. I am confused.
*Here is the markdown text with two references in the yaml.*
*---*
*title: Minimum Working Example*
*author: Andrew Mercer*
*date: V.1*
*papersize: a4*
*geometry: margin=2cm*
*font: 11*
*linestretch: 1.2*
*references:*
*- id: auth2020*
* type: article-journal*
* author:*
* - family: Surname*
* given: Firstname*
* - family: Efternamn*
* given: Förnamn*
* issued:*
* - year: 2019*
* title: Title of article*
* container-title: Journal Name*
* page: 1-12*
* volume: '1'*
* issue: '1'*
* abstract: 'The abstract text describing the article '*
*- author:*
* - family: Rees*
* given: William Gareth*
* id: rees2013physical*
* issued: 2013*
* publisher: Cambridge University Press*
* title: Physical principles of remote sensing*
* type: book*
*---*
*# Section heading {#sec:sec1}*
*Here is some text with a reference in the yaml @auth2020*
*Here is a reference to a bib entry @rees2013physical.*
*# References*
*This is the command I used and the message returned:*
*```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
--resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
*WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is being
run through 2.11.1.1. This is not supported. Strange things may (and likely
will) happen silently.*
*[WARNING] Citeproc: citation rees2013physical not found```*
I have no control over the citeproc version as it now is embedded in pandoc
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <c5fad0e6-186d-4e31-8b38-063e12ff5547n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-11-18 19:53 ` Pranesh Prakash
[not found] ` <3e0b4d78-7fa0-49a1-9aec-76f0f35a68dbn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Pranesh Prakash @ 2020-11-18 19:53 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 3703 bytes --]
Hi. I tried to reproduce this without pandoc-crossref, but failed. Perhaps
that is what is causing issues? Could you check if your command works
without pandoc-crossref?
I used your text, and ran:
```
pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
markdown MinWrkEx.md -o MinWrkEx.pdf
```
I'm running Pandoc 2.11.1.1.
Also, I think cslreferences -> CSLReferences in the default LaTeX template
was changed already:
```
$ pandoc -D latex | grep -i cslref
\newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
```
I believe it was changed when citeproc was added to pandoc:
https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30 mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
wrote:
> The new citeproc is behaving very oddly.
>
> Firstly, the latex template is incorrect, cslreferences needs now to read
> CSLReferences
>
> But there are two problems I haven't been able to fix.
> The first problem is a little odd,: the first reference gets "10"
> prepended to the first author name .
>
> The second problem is really confusing.
> At first citeproc would not find references in a bib file. A single
> reference in the yaml was found but nothing else. I then converted the
> reference in the bib to yaml and added it to the yaml markdown documents
> yaml. This works.
> What is odd is that I converted the bib to yaml using pandoc without a
> problem. I am confused.
>
> *Here is the markdown text with two references in the yaml.*
>
> *---*
> *title: Minimum Working Example*
> *author: Andrew Mercer*
> *date: V.1*
> *papersize: a4*
> *geometry: margin=2cm*
> *font: 11*
> *linestretch: 1.2*
> *references:*
> *- id: auth2020*
> * type: article-journal*
> * author:*
> * - family: Surname*
> * given: Firstname*
> * - family: Efternamn*
> * given: Förnamn*
> * issued:*
> * - year: 2019*
> * title: Title of article*
> * container-title: Journal Name*
> * page: 1-12*
> * volume: '1'*
> * issue: '1'*
> * abstract: 'The abstract text describing the article '*
> *- author:*
> * - family: Rees*
> * given: William Gareth*
> * id: rees2013physical*
> * issued: 2013*
> * publisher: Cambridge University Press*
> * title: Physical principles of remote sensing*
> * type: book*
> *---*
>
> *# Section heading {#sec:sec1}*
>
> *Here is some text with a reference in the yaml @auth2020*
> *Here is a reference to a bib entry @rees2013physical.*
>
>
> *# References*
>
>
> *This is the command I used and the message returned:*
>
> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is being
> run through 2.11.1.1. This is not supported. Strange things may (and likely
> will) happen silently.*
> *[WARNING] Citeproc: citation rees2013physical not found```*
>
> I have no control over the citeproc version as it now is embedded in pandoc
>
>
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <3e0b4d78-7fa0-49a1-9aec-76f0f35a68dbn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-01 13:31 ` Andrew Mercer
[not found] ` <b1de277e-6993-49ff-80be-34161ed23c18n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-12-01 13:31 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 4125 bytes --]
Removing pandoc-crossref doesn't help (and means figure refernces don't
work).
I have also tried converting the bib to json and to an external yaml but
neither of these helped
On Wednesday, 18 November 2020 at 20:53:15 UTC+1 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
> Hi. I tried to reproduce this without pandoc-crossref, but failed.
> Perhaps that is what is causing issues? Could you check if your command
> works without pandoc-crossref?
>
> I used your text, and ran:
> ```
> pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
> markdown MinWrkEx.md -o MinWrkEx.pdf
> ```
> I'm running Pandoc 2.11.1.1.
>
> Also, I think cslreferences -> CSLReferences in the default LaTeX
> template was changed already:
>
> ```
> $ pandoc -D latex | grep -i cslref
> \newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
> ```
>
> I believe it was changed when citeproc was added to pandoc:
>
> https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
> On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30
> mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>
>> The new citeproc is behaving very oddly.
>>
>> Firstly, the latex template is incorrect, cslreferences needs now to read
>> CSLReferences
>>
>> But there are two problems I haven't been able to fix.
>> The first problem is a little odd,: the first reference gets "10"
>> prepended to the first author name .
>>
>> The second problem is really confusing.
>> At first citeproc would not find references in a bib file. A single
>> reference in the yaml was found but nothing else. I then converted the
>> reference in the bib to yaml and added it to the yaml markdown documents
>> yaml. This works.
>> What is odd is that I converted the bib to yaml using pandoc without a
>> problem. I am confused.
>>
>> *Here is the markdown text with two references in the yaml.*
>>
>> *---*
>> *title: Minimum Working Example*
>> *author: Andrew Mercer*
>> *date: V.1*
>> *papersize: a4*
>> *geometry: margin=2cm*
>> *font: 11*
>> *linestretch: 1.2*
>> *references:*
>> *- id: auth2020*
>> * type: article-journal*
>> * author:*
>> * - family: Surname*
>> * given: Firstname*
>> * - family: Efternamn*
>> * given: Förnamn*
>> * issued:*
>> * - year: 2019*
>> * title: Title of article*
>> * container-title: Journal Name*
>> * page: 1-12*
>> * volume: '1'*
>> * issue: '1'*
>> * abstract: 'The abstract text describing the article '*
>> *- author:*
>> * - family: Rees*
>> * given: William Gareth*
>> * id: rees2013physical*
>> * issued: 2013*
>> * publisher: Cambridge University Press*
>> * title: Physical principles of remote sensing*
>> * type: book*
>> *---*
>>
>> *# Section heading {#sec:sec1}*
>>
>> *Here is some text with a reference in the yaml @auth2020*
>> *Here is a reference to a bib entry @rees2013physical.*
>>
>>
>> *# References*
>>
>>
>> *This is the command I used and the message returned:*
>>
>> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
>> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
>> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
>> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is being
>> run through 2.11.1.1. This is not supported. Strange things may (and likely
>> will) happen silently.*
>> *[WARNING] Citeproc: citation rees2013physical not found```*
>>
>> I have no control over the citeproc version as it now is embedded in
>> pandoc
>>
>>
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <b1de277e-6993-49ff-80be-34161ed23c18n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-01 14:01 ` Andrew Mercer
[not found] ` <0a64670e-a33d-4f2d-8e79-4e03bda6ffc6n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-12-01 14:01 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 4646 bytes --]
Tried confirming this on Ubuntu only to discover that pandoc doesn't create
a data-dir on Ubuntu. I checked the locations indicated by --version and
neither contained a pandoc directory.
This latest update seems to be full of holes. It would be nice if an older,
functioning version were still available. Some sort of LTR
On Tuesday, 1 December 2020 at 14:31:33 UTC+1 Andrew Mercer wrote:
> Removing pandoc-crossref doesn't help (and means figure refernces don't
> work).
> I have also tried converting the bib to json and to an external yaml but
> neither of these helped
>
>
> On Wednesday, 18 November 2020 at 20:53:15 UTC+1 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
> wrote:
>
>> Hi. I tried to reproduce this without pandoc-crossref, but failed.
>> Perhaps that is what is causing issues? Could you check if your command
>> works without pandoc-crossref?
>>
>> I used your text, and ran:
>> ```
>> pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
>> markdown MinWrkEx.md -o MinWrkEx.pdf
>> ```
>> I'm running Pandoc 2.11.1.1.
>>
>> Also, I think cslreferences -> CSLReferences in the default LaTeX
>> template was changed already:
>>
>> ```
>> $ pandoc -D latex | grep -i cslref
>> \newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
>> ```
>>
>> I believe it was changed when citeproc was added to pandoc:
>>
>> https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
>> On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30
>> mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>>
>>> The new citeproc is behaving very oddly.
>>>
>>> Firstly, the latex template is incorrect, cslreferences needs now to
>>> read CSLReferences
>>>
>>> But there are two problems I haven't been able to fix.
>>> The first problem is a little odd,: the first reference gets "10"
>>> prepended to the first author name .
>>>
>>> The second problem is really confusing.
>>> At first citeproc would not find references in a bib file. A single
>>> reference in the yaml was found but nothing else. I then converted the
>>> reference in the bib to yaml and added it to the yaml markdown documents
>>> yaml. This works.
>>> What is odd is that I converted the bib to yaml using pandoc without a
>>> problem. I am confused.
>>>
>>> *Here is the markdown text with two references in the yaml.*
>>>
>>> *---*
>>> *title: Minimum Working Example*
>>> *author: Andrew Mercer*
>>> *date: V.1*
>>> *papersize: a4*
>>> *geometry: margin=2cm*
>>> *font: 11*
>>> *linestretch: 1.2*
>>> *references:*
>>> *- id: auth2020*
>>> * type: article-journal*
>>> * author:*
>>> * - family: Surname*
>>> * given: Firstname*
>>> * - family: Efternamn*
>>> * given: Förnamn*
>>> * issued:*
>>> * - year: 2019*
>>> * title: Title of article*
>>> * container-title: Journal Name*
>>> * page: 1-12*
>>> * volume: '1'*
>>> * issue: '1'*
>>> * abstract: 'The abstract text describing the article '*
>>> *- author:*
>>> * - family: Rees*
>>> * given: William Gareth*
>>> * id: rees2013physical*
>>> * issued: 2013*
>>> * publisher: Cambridge University Press*
>>> * title: Physical principles of remote sensing*
>>> * type: book*
>>> *---*
>>>
>>> *# Section heading {#sec:sec1}*
>>>
>>> *Here is some text with a reference in the yaml @auth2020*
>>> *Here is a reference to a bib entry @rees2013physical.*
>>>
>>>
>>> *# References*
>>>
>>>
>>> *This is the command I used and the message returned:*
>>>
>>> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
>>> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
>>> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
>>> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is being
>>> run through 2.11.1.1. This is not supported. Strange things may (and likely
>>> will) happen silently.*
>>> *[WARNING] Citeproc: citation rees2013physical not found```*
>>>
>>> I have no control over the citeproc version as it now is embedded in
>>> pandoc
>>>
>>>
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <0a64670e-a33d-4f2d-8e79-4e03bda6ffc6n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-01 15:06 ` Andrew Mercer
[not found] ` <26044863-4227-481e-bf49-598d385ba76fn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 15:09 ` Pranesh Prakash
2020-12-01 18:37 ` John MacFarlane
2 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-12-01 15:06 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 5005 bytes --]
Further update. Adding references to the yaml works but ALL references in
the yaml are then place in the reference list at the end of the compiled
document.
On Tuesday, 1 December 2020 at 15:01:11 UTC+1 Andrew Mercer wrote:
> Tried confirming this on Ubuntu only to discover that pandoc doesn't
> create a data-dir on Ubuntu. I checked the locations indicated by --version
> and neither contained a pandoc directory.
> This latest update seems to be full of holes. It would be nice if an
> older, functioning version were still available. Some sort of LTR
>
> On Tuesday, 1 December 2020 at 14:31:33 UTC+1 Andrew Mercer wrote:
>
>> Removing pandoc-crossref doesn't help (and means figure refernces don't
>> work).
>> I have also tried converting the bib to json and to an external yaml but
>> neither of these helped
>>
>>
>> On Wednesday, 18 November 2020 at 20:53:15 UTC+1 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>> wrote:
>>
>>> Hi. I tried to reproduce this without pandoc-crossref, but failed.
>>> Perhaps that is what is causing issues? Could you check if your command
>>> works without pandoc-crossref?
>>>
>>> I used your text, and ran:
>>> ```
>>> pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
>>> markdown MinWrkEx.md -o MinWrkEx.pdf
>>> ```
>>> I'm running Pandoc 2.11.1.1.
>>>
>>> Also, I think cslreferences -> CSLReferences in the default LaTeX
>>> template was changed already:
>>>
>>> ```
>>> $ pandoc -D latex | grep -i cslref
>>> \newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
>>> ```
>>>
>>> I believe it was changed when citeproc was added to pandoc:
>>>
>>> https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
>>> On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30
>>> mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>>>
>>>> The new citeproc is behaving very oddly.
>>>>
>>>> Firstly, the latex template is incorrect, cslreferences needs now to
>>>> read CSLReferences
>>>>
>>>> But there are two problems I haven't been able to fix.
>>>> The first problem is a little odd,: the first reference gets "10"
>>>> prepended to the first author name .
>>>>
>>>> The second problem is really confusing.
>>>> At first citeproc would not find references in a bib file. A single
>>>> reference in the yaml was found but nothing else. I then converted the
>>>> reference in the bib to yaml and added it to the yaml markdown documents
>>>> yaml. This works.
>>>> What is odd is that I converted the bib to yaml using pandoc without a
>>>> problem. I am confused.
>>>>
>>>> *Here is the markdown text with two references in the yaml.*
>>>>
>>>> *---*
>>>> *title: Minimum Working Example*
>>>> *author: Andrew Mercer*
>>>> *date: V.1*
>>>> *papersize: a4*
>>>> *geometry: margin=2cm*
>>>> *font: 11*
>>>> *linestretch: 1.2*
>>>> *references:*
>>>> *- id: auth2020*
>>>> * type: article-journal*
>>>> * author:*
>>>> * - family: Surname*
>>>> * given: Firstname*
>>>> * - family: Efternamn*
>>>> * given: Förnamn*
>>>> * issued:*
>>>> * - year: 2019*
>>>> * title: Title of article*
>>>> * container-title: Journal Name*
>>>> * page: 1-12*
>>>> * volume: '1'*
>>>> * issue: '1'*
>>>> * abstract: 'The abstract text describing the article '*
>>>> *- author:*
>>>> * - family: Rees*
>>>> * given: William Gareth*
>>>> * id: rees2013physical*
>>>> * issued: 2013*
>>>> * publisher: Cambridge University Press*
>>>> * title: Physical principles of remote sensing*
>>>> * type: book*
>>>> *---*
>>>>
>>>> *# Section heading {#sec:sec1}*
>>>>
>>>> *Here is some text with a reference in the yaml @auth2020*
>>>> *Here is a reference to a bib entry @rees2013physical.*
>>>>
>>>>
>>>> *# References*
>>>>
>>>>
>>>> *This is the command I used and the message returned:*
>>>>
>>>> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
>>>> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
>>>> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
>>>> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is
>>>> being run through 2.11.1.1. This is not supported. Strange things may (and
>>>> likely will) happen silently.*
>>>> *[WARNING] Citeproc: citation rees2013physical not found```*
>>>>
>>>> I have no control over the citeproc version as it now is embedded in
>>>> pandoc
>>>>
>>>>
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <0a64670e-a33d-4f2d-8e79-4e03bda6ffc6n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 15:06 ` Andrew Mercer
@ 2020-12-01 15:09 ` Pranesh Prakash
[not found] ` <d99b3932-8d94-4112-b5eb-3bb04bceeaaen-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 18:37 ` John MacFarlane
2 siblings, 1 reply; 12+ messages in thread
From: Pranesh Prakash @ 2020-12-01 15:09 UTC (permalink / raw)
To: pandoc-discuss
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Dear Andrew,
I am still unable to reproduce the error you're getting on Ubuntu 20.10
using pandoc 2.11.2.
~~~
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.10
Release: 20.10
Codename: groovy
$ pandoc --version
pandoc 2.11.2
Compiled with pandoc-types 1.22, texmath 0.12.0.3, skylighting 0.10.0.3,
citeproc 0.2, ipynb 0.1.0.1
User data directory: /home/sol/.local/share/pandoc or /home/sol/.pandoc
Copyright (C) 2006-2020 John MacFarlane. Web: https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
$ cat MinWrkEx.md
---
title: Minimum Working Example
author: Andrew Mercer
date: V.1
papersize: a4
geometry: margin=2cm
font: 11
linestretch: 1.2
references:
- id: auth2020
type: article-journal
author:
- family: Surname
given: Firstname
- family: Efternamn
given: Förnamn
issued:
- year: 2019
title: Title of article
container-title: Journal Name
page: 1-12
volume: '1'
issue: '1'
abstract: 'The abstract text describing the article '
- author:
- family: Rees
given: William Gareth
id: rees2013physical
issued: 2013
publisher: Cambridge University Press
title: Physical principles of remote sensing
type: book
---
# Section heading {#sec:sec1}
Here is some text with a reference in the yaml @auth2020
Here is a reference to a bib entry @rees2013physical.
# References
$ pandoc -s --toc --citeproc --csl=apa.csl MinWrkEx.md -o MinWrkEx.pdf
~~~
Here's the resultant PDF.
On Tuesday, 1 December, 2020 at 7:31:11 pm UTC+5:30 mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
wrote:
> Tried confirming this on Ubuntu only to discover that pandoc doesn't
> create a data-dir on Ubuntu. I checked the locations indicated by --version
> and neither contained a pandoc directory.
> This latest update seems to be full of holes. It would be nice if an
> older, functioning version were still available. Some sort of LTR
>
> On Tuesday, 1 December 2020 at 14:31:33 UTC+1 Andrew Mercer wrote:
>
>> Removing pandoc-crossref doesn't help (and means figure refernces don't
>> work).
>> I have also tried converting the bib to json and to an external yaml but
>> neither of these helped
>>
>>
>> On Wednesday, 18 November 2020 at 20:53:15 UTC+1 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>> wrote:
>>
>>> Hi. I tried to reproduce this without pandoc-crossref, but failed.
>>> Perhaps that is what is causing issues? Could you check if your command
>>> works without pandoc-crossref?
>>>
>>> I used your text, and ran:
>>> ```
>>> pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
>>> markdown MinWrkEx.md -o MinWrkEx.pdf
>>> ```
>>> I'm running Pandoc 2.11.1.1.
>>>
>>> Also, I think cslreferences -> CSLReferences in the default LaTeX
>>> template was changed already:
>>>
>>> ```
>>> $ pandoc -D latex | grep -i cslref
>>> \newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
>>> ```
>>>
>>> I believe it was changed when citeproc was added to pandoc:
>>>
>>> https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
>>> On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30
>>> mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>>>
>>>> The new citeproc is behaving very oddly.
>>>>
>>>> Firstly, the latex template is incorrect, cslreferences needs now to
>>>> read CSLReferences
>>>>
>>>> But there are two problems I haven't been able to fix.
>>>> The first problem is a little odd,: the first reference gets "10"
>>>> prepended to the first author name .
>>>>
>>>> The second problem is really confusing.
>>>> At first citeproc would not find references in a bib file. A single
>>>> reference in the yaml was found but nothing else. I then converted the
>>>> reference in the bib to yaml and added it to the yaml markdown documents
>>>> yaml. This works.
>>>> What is odd is that I converted the bib to yaml using pandoc without a
>>>> problem. I am confused.
>>>>
>>>> *Here is the markdown text with two references in the yaml.*
>>>>
>>>> *---*
>>>> *title: Minimum Working Example*
>>>> *author: Andrew Mercer*
>>>> *date: V.1*
>>>> *papersize: a4*
>>>> *geometry: margin=2cm*
>>>> *font: 11*
>>>> *linestretch: 1.2*
>>>> *references:*
>>>> *- id: auth2020*
>>>> * type: article-journal*
>>>> * author:*
>>>> * - family: Surname*
>>>> * given: Firstname*
>>>> * - family: Efternamn*
>>>> * given: Förnamn*
>>>> * issued:*
>>>> * - year: 2019*
>>>> * title: Title of article*
>>>> * container-title: Journal Name*
>>>> * page: 1-12*
>>>> * volume: '1'*
>>>> * issue: '1'*
>>>> * abstract: 'The abstract text describing the article '*
>>>> *- author:*
>>>> * - family: Rees*
>>>> * given: William Gareth*
>>>> * id: rees2013physical*
>>>> * issued: 2013*
>>>> * publisher: Cambridge University Press*
>>>> * title: Physical principles of remote sensing*
>>>> * type: book*
>>>> *---*
>>>>
>>>> *# Section heading {#sec:sec1}*
>>>>
>>>> *Here is some text with a reference in the yaml @auth2020*
>>>> *Here is a reference to a bib entry @rees2013physical.*
>>>>
>>>>
>>>> *# References*
>>>>
>>>>
>>>> *This is the command I used and the message returned:*
>>>>
>>>> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
>>>> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
>>>> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
>>>> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is
>>>> being run through 2.11.1.1. This is not supported. Strange things may (and
>>>> likely will) happen silently.*
>>>> *[WARNING] Citeproc: citation rees2013physical not found```*
>>>>
>>>> I have no control over the citeproc version as it now is embedded in
>>>> pandoc
>>>>
>>>>
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <d99b3932-8d94-4112-b5eb-3bb04bceeaaen-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-01 17:22 ` Pranesh Prakash
0 siblings, 0 replies; 12+ messages in thread
From: Pranesh Prakash @ 2020-12-01 17:22 UTC (permalink / raw)
To: pandoc-discuss
[-- Attachment #1.1: Type: text/plain, Size: 6930 bytes --]
Sorry, the attachment didn't go through the last time.
On Tuesday, 1 December, 2020 at 8:39:58 pm UTC+5:30 Pranesh Prakash wrote:
> Dear Andrew,
> I am still unable to reproduce the error you're getting on Ubuntu 20.10
> using pandoc 2.11.2.
>
> ~~~
> $ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: Ubuntu 20.10
> Release: 20.10
> Codename: groovy
>
> $ pandoc --version
> pandoc 2.11.2
> Compiled with pandoc-types 1.22, texmath 0.12.0.3, skylighting 0.10.0.3,
> citeproc 0.2, ipynb 0.1.0.1
> User data directory: /home/sol/.local/share/pandoc or /home/sol/.pandoc
> Copyright (C) 2006-2020 John MacFarlane. Web: https://pandoc.org
> This is free software; see the source for copying conditions. There is no
> warranty, not even for merchantability or fitness for a particular purpose.
>
> $ cat MinWrkEx.md
> ---
> title: Minimum Working Example
> author: Andrew Mercer
> date: V.1
> papersize: a4
> geometry: margin=2cm
> font: 11
> linestretch: 1.2
> references:
> - id: auth2020
> type: article-journal
> author:
> - family: Surname
> given: Firstname
> - family: Efternamn
> given: Förnamn
> issued:
> - year: 2019
> title: Title of article
> container-title: Journal Name
> page: 1-12
> volume: '1'
> issue: '1'
> abstract: 'The abstract text describing the article '
> - author:
> - family: Rees
> given: William Gareth
> id: rees2013physical
> issued: 2013
> publisher: Cambridge University Press
> title: Physical principles of remote sensing
> type: book
> ---
>
> # Section heading {#sec:sec1}
>
> Here is some text with a reference in the yaml @auth2020
> Here is a reference to a bib entry @rees2013physical.
>
>
> # References
>
> $ pandoc -s --toc --citeproc --csl=apa.csl MinWrkEx.md -o MinWrkEx.pdf
> ~~~
>
> Here's the resultant PDF.
>
> On Tuesday, 1 December, 2020 at 7:31:11 pm UTC+5:30 mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
> wrote:
>
>> Tried confirming this on Ubuntu only to discover that pandoc doesn't
>> create a data-dir on Ubuntu. I checked the locations indicated by --version
>> and neither contained a pandoc directory.
>> This latest update seems to be full of holes. It would be nice if an
>> older, functioning version were still available. Some sort of LTR
>>
>> On Tuesday, 1 December 2020 at 14:31:33 UTC+1 Andrew Mercer wrote:
>>
>>> Removing pandoc-crossref doesn't help (and means figure refernces don't
>>> work).
>>> I have also tried converting the bib to json and to an external yaml but
>>> neither of these helped
>>>
>>>
>>> On Wednesday, 18 November 2020 at 20:53:15 UTC+1 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>>> wrote:
>>>
>>>> Hi. I tried to reproduce this without pandoc-crossref, but failed.
>>>> Perhaps that is what is causing issues? Could you check if your command
>>>> works without pandoc-crossref?
>>>>
>>>> I used your text, and ran:
>>>> ```
>>>> pandoc -s --toc --citeproc --csl=apa.csl --bibliography=library.json -f
>>>> markdown MinWrkEx.md -o MinWrkEx.pdf
>>>> ```
>>>> I'm running Pandoc 2.11.1.1.
>>>>
>>>> Also, I think cslreferences -> CSLReferences in the default LaTeX
>>>> template was changed already:
>>>>
>>>> ```
>>>> $ pandoc -D latex | grep -i cslref
>>>> \newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
>>>> ```
>>>>
>>>> I believe it was changed when citeproc was added to pandoc:
>>>>
>>>> https://github.com/jgm/pandoc/commit/e0984a43a99231e72c02a0a716c8d0315de9abdf#diff-64a9e5fa4509dce2699276c9e39993b4474e2446c3e86941a2f78a379f8c4079
>>>> On Wednesday, 18 November, 2020 at 11:15:32 pm UTC+5:30
>>>> mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>>>>
>>>>> The new citeproc is behaving very oddly.
>>>>>
>>>>> Firstly, the latex template is incorrect, cslreferences needs now to
>>>>> read CSLReferences
>>>>>
>>>>> But there are two problems I haven't been able to fix.
>>>>> The first problem is a little odd,: the first reference gets "10"
>>>>> prepended to the first author name .
>>>>>
>>>>> The second problem is really confusing.
>>>>> At first citeproc would not find references in a bib file. A single
>>>>> reference in the yaml was found but nothing else. I then converted the
>>>>> reference in the bib to yaml and added it to the yaml markdown documents
>>>>> yaml. This works.
>>>>> What is odd is that I converted the bib to yaml using pandoc without a
>>>>> problem. I am confused.
>>>>>
>>>>> *Here is the markdown text with two references in the yaml.*
>>>>>
>>>>> *---*
>>>>> *title: Minimum Working Example*
>>>>> *author: Andrew Mercer*
>>>>> *date: V.1*
>>>>> *papersize: a4*
>>>>> *geometry: margin=2cm*
>>>>> *font: 11*
>>>>> *linestretch: 1.2*
>>>>> *references:*
>>>>> *- id: auth2020*
>>>>> * type: article-journal*
>>>>> * author:*
>>>>> * - family: Surname*
>>>>> * given: Firstname*
>>>>> * - family: Efternamn*
>>>>> * given: Förnamn*
>>>>> * issued:*
>>>>> * - year: 2019*
>>>>> * title: Title of article*
>>>>> * container-title: Journal Name*
>>>>> * page: 1-12*
>>>>> * volume: '1'*
>>>>> * issue: '1'*
>>>>> * abstract: 'The abstract text describing the article '*
>>>>> *- author:*
>>>>> * - family: Rees*
>>>>> * given: William Gareth*
>>>>> * id: rees2013physical*
>>>>> * issued: 2013*
>>>>> * publisher: Cambridge University Press*
>>>>> * title: Physical principles of remote sensing*
>>>>> * type: book*
>>>>> *---*
>>>>>
>>>>> *# Section heading {#sec:sec1}*
>>>>>
>>>>> *Here is some text with a reference in the yaml @auth2020*
>>>>> *Here is a reference to a bib entry @rees2013physical.*
>>>>>
>>>>>
>>>>> *# References*
>>>>>
>>>>>
>>>>> *This is the command I used and the message returned:*
>>>>>
>>>>> *```C:\Users\anwmer\Documents\MinWrkEx>pandoc -s --toc --filter
>>>>> pandoc-crossref --citeproc --csl=apa7.csl --bibliography=refs.bib
>>>>> --resource-path=.;figures MinWrkEx.md -o MinWrkEx.pdf*
>>>>> *WARNING: pandoc-crossref was compiled with pandoc 2.11.0.4 but is
>>>>> being run through 2.11.1.1. This is not supported. Strange things may (and
>>>>> likely will) happen silently.*
>>>>> *[WARNING] Citeproc: citation rees2013physical not found```*
>>>>>
>>>>> I have no control over the citeproc version as it now is embedded in
>>>>> pandoc
>>>>>
>>>>>
--
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^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <0a64670e-a33d-4f2d-8e79-4e03bda6ffc6n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 15:06 ` Andrew Mercer
2020-12-01 15:09 ` Pranesh Prakash
@ 2020-12-01 18:37 ` John MacFarlane
2 siblings, 0 replies; 12+ messages in thread
From: John MacFarlane @ 2020-12-01 18:37 UTC (permalink / raw)
To: Andrew Mercer, pandoc-discuss
Andrew Mercer <mercergeoinfo-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> Tried confirming this on Ubuntu only to discover that pandoc doesn't create
> a data-dir on Ubuntu. I checked the locations indicated by --version and
> neither contained a pandoc directory.
Pandoc has never created a data dir. You have to create it
yourself if you want one. (Pandoc generally won't create
any files you don't explicitly ask for, which I think is polite
behavior.)
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <26044863-4227-481e-bf49-598d385ba76fn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-01 18:39 ` John MacFarlane
[not found] ` <m2im9lxtfb.fsf-jF64zX8BO08an7k8zZ43ob9bIa4KchGshsV+eolpW18@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: John MacFarlane @ 2020-12-01 18:39 UTC (permalink / raw)
To: Andrew Mercer, pandoc-discuss
Andrew Mercer <mercergeoinfo-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> Further update. Adding references to the yaml works but ALL references in
> the yaml are then place in the reference list at the end of the compiled
> document.
Do you have `nocite` in your metadata?
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: citeproc citation not found
[not found] ` <m2im9lxtfb.fsf-jF64zX8BO08an7k8zZ43ob9bIa4KchGshsV+eolpW18@public.gmane.org>
@ 2020-12-08 8:47 ` Andrew Mercer
[not found] ` <ac9eac16-5dab-4879-a5d7-03ab39e95953n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-12-08 8:47 UTC (permalink / raw)
To: pandoc-discuss
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Sorry for the late reply, I thought I had replied to this already.
I have not place a nocite anywhere in the md file.
This really seems like a wandering bug. I cant say whether 2.11.1 placed
all references in the reference list as I didn't test that but it certainly
happens when using 2.11.2
What I find very confusing is the fact that pandoc can create a yaml or
json from a bib file but can't use external references when compiling a
document. All of these files are in the same directory, the mad, bib, json
and yaml.
Perhaps the fact that pandoc couldn't find my latex template, which also
resides in the same directory, indicates a common issue. Somehow the path
is corrupted when compiling a markdown file that calls on secondary files.
On Tuesday, 1 December 2020 at 19:39:21 UTC+1 John MacFarlane wrote:
> Andrew Mercer <mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
>
> > Further update. Adding references to the yaml works but ALL references
> in
> > the yaml are then place in the reference list at the end of the compiled
> > document.
>
> Do you have `nocite` in your metadata?
>
>
--
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* Re: citeproc citation not found
[not found] ` <ac9eac16-5dab-4879-a5d7-03ab39e95953n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-15 15:16 ` Andrew Mercer
[not found] ` <aeffb619-6913-4d05-a293-c93656df0fecn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
0 siblings, 1 reply; 12+ messages in thread
From: Andrew Mercer @ 2020-12-15 15:16 UTC (permalink / raw)
To: pandoc-discuss
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Can confirm that this problem occurs when using pandoc 2.11.2 on Ubuntu.
The workaround is the same; use yaml references in header, not in external
file.
On Tuesday, 8 December 2020 at 09:47:09 UTC+1 Andrew Mercer wrote:
> Sorry for the late reply, I thought I had replied to this already.
> I have not place a nocite anywhere in the md file.
> This really seems like a wandering bug. I cant say whether 2.11.1 placed
> all references in the reference list as I didn't test that but it certainly
> happens when using 2.11.2
> What I find very confusing is the fact that pandoc can create a yaml or
> json from a bib file but can't use external references when compiling a
> document. All of these files are in the same directory, the mad, bib, json
> and yaml.
> Perhaps the fact that pandoc couldn't find my latex template, which also
> resides in the same directory, indicates a common issue. Somehow the path
> is corrupted when compiling a markdown file that calls on secondary files.
>
> On Tuesday, 1 December 2020 at 19:39:21 UTC+1 John MacFarlane wrote:
>
>> Andrew Mercer <mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
>>
>> > Further update. Adding references to the yaml works but ALL references
>> in
>> > the yaml are then place in the reference list at the end of the
>> compiled
>> > document.
>>
>> Do you have `nocite` in your metadata?
>>
>>
--
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* Re: citeproc citation not found
[not found] ` <aeffb619-6913-4d05-a293-c93656df0fecn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2020-12-15 16:57 ` John MacFarlane
0 siblings, 0 replies; 12+ messages in thread
From: John MacFarlane @ 2020-12-15 16:57 UTC (permalink / raw)
To: Andrew Mercer, pandoc-discuss
Are you sure there isn't a `nocite` in your external yaml file?
When you use pandoc to produce a YAML bibliography, e.g. from
a bibtex source
pandoc -t markdown -s mybib.bib
it will insert a `nocite: "[@*]"` in the bibliography, which
will cause all items to be cited. Just remove that line.
Andrew Mercer <mercergeoinfo-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> Can confirm that this problem occurs when using pandoc 2.11.2 on Ubuntu.
> The workaround is the same; use yaml references in header, not in external
> file.
>
> On Tuesday, 8 December 2020 at 09:47:09 UTC+1 Andrew Mercer wrote:
>
>> Sorry for the late reply, I thought I had replied to this already.
>> I have not place a nocite anywhere in the md file.
>> This really seems like a wandering bug. I cant say whether 2.11.1 placed
>> all references in the reference list as I didn't test that but it certainly
>> happens when using 2.11.2
>> What I find very confusing is the fact that pandoc can create a yaml or
>> json from a bib file but can't use external references when compiling a
>> document. All of these files are in the same directory, the mad, bib, json
>> and yaml.
>> Perhaps the fact that pandoc couldn't find my latex template, which also
>> resides in the same directory, indicates a common issue. Somehow the path
>> is corrupted when compiling a markdown file that calls on secondary files.
>>
>> On Tuesday, 1 December 2020 at 19:39:21 UTC+1 John MacFarlane wrote:
>>
>>> Andrew Mercer <mercer...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
>>>
>>> > Further update. Adding references to the yaml works but ALL references
>>> in
>>> > the yaml are then place in the reference list at the end of the
>>> compiled
>>> > document.
>>>
>>> Do you have `nocite` in your metadata?
>>>
>>>
>
> --
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> To unsubscribe from this group and stop receiving emails from it, send an email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
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2020-11-18 17:45 citeproc citation not found Andrew Mercer
[not found] ` <c5fad0e6-186d-4e31-8b38-063e12ff5547n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-11-18 19:53 ` Pranesh Prakash
[not found] ` <3e0b4d78-7fa0-49a1-9aec-76f0f35a68dbn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 13:31 ` Andrew Mercer
[not found] ` <b1de277e-6993-49ff-80be-34161ed23c18n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 14:01 ` Andrew Mercer
[not found] ` <0a64670e-a33d-4f2d-8e79-4e03bda6ffc6n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 15:06 ` Andrew Mercer
[not found] ` <26044863-4227-481e-bf49-598d385ba76fn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 18:39 ` John MacFarlane
[not found] ` <m2im9lxtfb.fsf-jF64zX8BO08an7k8zZ43ob9bIa4KchGshsV+eolpW18@public.gmane.org>
2020-12-08 8:47 ` Andrew Mercer
[not found] ` <ac9eac16-5dab-4879-a5d7-03ab39e95953n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-15 15:16 ` Andrew Mercer
[not found] ` <aeffb619-6913-4d05-a293-c93656df0fecn-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-15 16:57 ` John MacFarlane
2020-12-01 15:09 ` Pranesh Prakash
[not found] ` <d99b3932-8d94-4112-b5eb-3bb04bceeaaen-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2020-12-01 17:22 ` Pranesh Prakash
2020-12-01 18:37 ` John MacFarlane
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