citeproc citation not found

citeproc citation not found

[Andrew Mercer]

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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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Re: citeproc citation not found

[Pranesh Prakash]

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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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Re: citeproc citation not found

[Andrew Mercer]

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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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Re: citeproc citation not found

[Andrew Mercer]

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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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Re: citeproc citation not found

[Andrew Mercer]

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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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Re: citeproc citation not found

[Pranesh Prakash]

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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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Re: citeproc citation not found

[Pranesh Prakash]

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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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Re: citeproc citation not found

[John MacFarlane]

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.)

Re: citeproc citation not found

[John MacFarlane]

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?

Re: citeproc citation not found

[Andrew Mercer]

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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

[Andrew Mercer]

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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

[John MacFarlane]

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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