Cfrgtkky

Response on StackOverflow suggested this query better here.

I've spent an hour or so searching this topic after another couple of hours trying to find the "bug" in my bibliography. The following Tex file and bibliography are almost minimal examples. Can anyone suggest what is wrong with either of the files? Thanks. JN

junk.tex:

documentclass[11pt,english]{cv}

usepackage{verbatim}

usepackage{url}

usepackage[

     backend=biber,

     style=numeric,

     natbib=true,

     sorting=none,

     url=true, 

     doi=true,

     eprint=false

]{biblatex}



bibliography{test}



begin{document}

title{All publications and works}

maketitle

nocite{*}

printbibliography

end{document}

test.bib:



@Misc{ quietpenguin,

  author  = {Nash, John C.},

  title = {{Quiet Penguin: an open design concept for discussion}},

  year = {2013},

  month = {June},

  note = {JNfile: 130630quietpenguin.pdf}

}



@article{bolkernonlin13,

 author = {Bolker, Benjamin M. and Gardner, Beth and Maunder, Mark 

 and Berg, Casper W. and Brooks, Mollie and Comita, Liza 

 and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor 

 and de Valpine, Perry and Ford, Jessica and Gimenez, Olivier 

 and K'ery, Marc and Kim, Eun Jung and Lennert-Cody, Cleridy 

 and Magnusson, Arni and Martell, Steve and Nash, John 

 and Nielsen, Anders and Regetz, Jim and Skaug, Hans 

 and Zipkin, Elise},

title = {Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS},

journal = {Methods in Ecology and Evolution},

volume = {4},

number = {6},

issn = {2041-210X},

pages = {501--512},

year = {2013},

note = {Report on special 2-session workshop at National Center for 

 Ecological Analysis and Synthesis, Santa Barbara, CA in 2012.

 JNfile: 13-bolker-strategies.pdf}

}

With just

@Misc{ quietpenguin,

  author  = {Nash, John C.},

  title = {{Quiet Penguin: an open design concept for discussion}},

  year = {2013},

  month = {June},

  note = {JNfile: 130630quietpenguin.pdf}

}



@article{bolkernonlin13,

 author = {Bolker, Benjamin M. and Gardner, Beth and Maunder, Mark 

 and Berg, Casper W. and Brooks, Mollie and Comita, Liza 

 and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor 

 and de Valpine, Perry and Ford, Jessica and Gimenez, Olivier 

 and K'ery, Marc and Kim, Eun Jung and Lennert-Cody, Cleridy 

 and Magnusson, Arni and Martell, Steve and Nash, John 

 and Nielsen, Anders and Regetz, Jim and Skaug, Hans 

 and Zipkin, Elise},

title = {Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS},

journal = {Methods in Ecology and Evolution},

volume = {4},

number = {6},

issn = {2041-210X},

pages = {501--512},

year = {2013},

note = {Report on special 2-session workshop at National Center for 

 Ecological Analysis and Synthesis, Santa Barbara, CA in 2012.

 JNfile: 13-bolker-strategies.pdf}

}

in the .bib file, I get two warnings with your MWE (running under biblatex 3.7/Biber 2.7)

WARN - month field 'June' in entry 'quietpenguin' is not an integer - this will probably not sort properly.

WARN - The entry 'bolkernonlin13' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.

Depending on how your encoding is set up you may not get the second warning.

The first warning you should do something about, instead of

year = {2013},

month = {June},

use

date = {2013-06},

or month = {6}, if you must stick to month and year (note that there is no such thing as a day field!).

In particular there are no warnings about junk characters. Sometimes they can be ignored, but sometimes they warn you about a problem in your file.

The warning will look like (not from your example!)

WARN - BibTeX subsystem: C:Users<User>AppDataLocalTempvdumzDAIKojunchhars.bib_7000.utf8, line 2, warning: 22 characters of junk seen at toplevel

just check at and around the indicated line (in this case line 2) for anything unusual.

From my experience, biblatex is quite picky about some characters. But that probably depends on your chracter encoding. For me (Linux, UTF-8), your example works only if I remove the escaped accent and add it directly:

@Misc{ quietpenguin,

  author  = {Nash, John C.},

  title = {{Quiet Penguin: an open design concept for discussion}},

  year = {2013},

  month = {June},

  note = {JNfile: 130630quietpenguin.pdf}

}



@article{bolkernonlin13,

 author = {Bolker, Benjamin M. and Gardner, Beth and Maunder, Mark 

 and Berg, Casper W. and Brooks, Mollie and Comita, Liza 

 and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor 

 and de Valpine, Perry and Ford, Jessica and Gimenez, Olivier 

 and Kéry, Marc and Kim, Eun Jung and Lennert-Cody, Cleridy 

 and Magnusson, Arni and Martell, Steve and Nash, John 

 and Nielsen, Anders and Regetz, Jim and Skaug, Hans 

 and Zipkin, Elise},

title = {Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS},

journal = {Methods in Ecology and Evolution},

volume = {4},

number = {6},

issn = {2041-210X},

pages = {501--512},

year = {2013},

note = {Report on special 2-session workshop at National Center for 

 Ecological Analysis and Synthesis, Santa Barbara, CA in 2012.

 JNfile: 13-bolker-strategies.pdf}

}

I found my "characters of junk" in whitespace!

TLDR; Remove or comment out white space between entries.

The "characters of junk" warning is to alert the user that they have comment text between entries that are not marked with "%". All text outside of entries are ignored as comments, extraneous text inside entries generate syntax errors. But it's nice of biber to let you know that maybe something is not where you wanted it to be. (Of course "characters of junk" is not the most obvious error message.)

It was in .bib file I maintained using JabRef, by importing references from all over the internet. Using JabRef in BibLaTeX mode I believed everything would be in well-behaved UTF-8 encoding. I could readily identify a few instances of encoding issues by examining the .bib file in Notepad++, but one "3 characters of junk seen at toplevel" warning persisted. By commenting out all the possibly offending entries I was forced to the conclusion that the "characters of junk" were actually in the whitespace between BibLaTeX entries. I resorted to removing all the empty lines near the line that triggered the warning, making sure I selected whole lines. My careful attention was rewarded by noticing that one whitespace character took two backspace strokes to be deleted.

I was able to copy and paste the offending lines to the genius Unicode Character Inspector app by Tim Whitlock, which told me that the whitespace I'd copied contained a 'zero width no-break space'. Once I removed this character, my last "characters of junk" warning from biber disappeared.

I was able to introduce this error into your .bin file by copying the offending whitespace into your example .bib file. This is what the biber output has to say:

PS C:Usersfskdmworkspacecharacters-of-junk> biber .document.bcf

INFO - This is Biber 2.12

INFO - Logfile is '.document.blg'

INFO - Reading '.document.bcf'

INFO - Using all citekeys in bib section 0

INFO - Processing section 0

INFO - Looking for bibtex format file 'test.bib' for section 0

INFO - LaTeX decoding ...

INFO - Found BibTeX data source 'test.bib'

WARN - month field 'June' in entry 'quietpenguin' is not an integer - this will probably not sort properly.

WARN - BibTeX subsystem: C:UsersfskdmAppDataLocalTempqA4TaotRo1test.bib_12364.utf8, line 12, warning: 6 characters of junk seen at toplevel

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 'none/global//global/global' of type 'entry' with template 'none' and locale 'en-US'

INFO - No sort tailoring available for locale 'en-US'

INFO - Writing '.document.bbl' with encoding 'UTF-8'

INFO - Output to .document.bbl

INFO - WARNINGS: 2

PS C:Usersfskdmworkspacecharacters-of-junk>

I've tried to copy & paste an example of this "zero-width no-break space" character into this answer, but without success.

Here's the output from the app: there is really a character between the "x" characters.