[OS X TeX] biber and biblatex
Scot Mcphee
scot.mcphee at gmail.com
Sat Jan 26 07:49:47 EST 2013
I probably have updated through texlive but I can't be sure.
This is the output of running "latexmk" over the file on the command line. I have attached a test bib with a single entry and the test tex file that makes this output in a zip.
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$ latexmk just-testing.tex
Latexmk: This is Latexmk, John Collins, 11 Nov. 2012, version: 4.35.
**** Report bugs etc to John Collins <collins at phys.psu.edu>. ****
Latexmk: applying rule 'latex'...
Rule 'latex': Rules & subrules not known to be previously run:
latex
Rule 'latex': The following rules & subrules became out-of-date:
'latex'
------------
Run number 1 of rule 'latex'
------------
------------
Running 'latex -recorder "just-testing.tex"'
------------
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
restricted \write18 enabled.
entering extended mode
(./just-testing.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/memoir.cls
Document Class: memoir 2011/03/06 v3.6j configurable book, report, article docu
ment class
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/ifetex/ifetex.sty
(/usr/local/texlive/2012/texmf-dist/tex/plain/ifetex/ifetex.tex))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifluatex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/etex-pkg/etex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mem12.clo)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mempatch.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/lmodern.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/dvips.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex2.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-dm.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-compat.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/standard.bbx))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/cbx/authoryear-comp.cbx)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
(./just-testing.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/lm/t1lmr.fd)
No file just-testing.bbl.
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/ot1lmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omllmm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omslmsy.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omxlmex.fd)
LaTeX Warning: Citation 'Levene:2010hob' on page 1 undefined on input line 18.
LaTeX Warning: Empty bibliography on input line 22.
[1] (./just-testing.aux)
LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex) just-testing
(biblatex) and rerun LaTeX afterwards.
)
Output written on just-testing.dvi (1 page, 2852 bytes).
Transcript written on just-testing.log.
Latexmk: Non-existent bbl file 'just-testing.bbl'
No file just-testing.bbl.
Latexmk: Citation 'Levene:2010hob' on page 1 undefined
Latexmk: Log file says output to 'just-testing.dvi'
Latexmk: Summary of warnings:
Latex failed to resolve 1 citation(s)
Latexmk: applying rule 'biber just-testing'...
Rule 'biber just-testing': File changes, etc:
Non-existent destination files:
'just-testing.bbl'
------------
Run number 1 of rule 'biber just-testing'
------------
------------
Running 'biber "just-testing"'
------------
INFO - This is Biber 1.4
INFO - Logfile is 'just-testing.blg'
data source /var/folders/6_/rr7lzhws0t7743tfbt3y8mhh0000gn/T/par-736d6370686565/cache-ddbe3788cd0c7e345094a0ddbf9d9261e8c1a1f1//inc/lib/Biber/LaTeX/recode_data.xml not found in .
Latexmk: Failed to find one or more biber source files:
NONE
Latexmk: applying rule 'latex'...
Rule 'latex': File changes, etc:
Changed files, or newly in use since previous run(s):
'just-testing.aux'
------------
Run number 2 of rule 'latex'
------------
------------
Running 'latex -recorder "just-testing.tex"'
------------
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
restricted \write18 enabled.
entering extended mode
(./just-testing.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/memoir.cls
Document Class: memoir 2011/03/06 v3.6j configurable book, report, article docu
ment class
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/ifetex/ifetex.sty
(/usr/local/texlive/2012/texmf-dist/tex/plain/ifetex/ifetex.tex))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifluatex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/etex-pkg/etex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mem12.clo)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mempatch.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/lmodern.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/dvips.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex2.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-dm.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-compat.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/standard.bbx))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/cbx/authoryear-comp.cbx)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
(./just-testing.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/lm/t1lmr.fd)
No file just-testing.bbl.
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/ot1lmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omllmm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omslmsy.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omxlmex.fd)
LaTeX Warning: Citation 'Levene:2010hob' on page 1 undefined on input line 18.
LaTeX Warning: Empty bibliography on input line 22.
[1] (./just-testing.aux)
LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex) just-testing
(biblatex) and rerun LaTeX afterwards.
)
Output written on just-testing.dvi (1 page, 2852 bytes).
Transcript written on just-testing.log.
Latexmk: Non-existent bbl file 'just-testing.bbl'
No file just-testing.bbl.
Latexmk: Citation 'Levene:2010hob' on page 1 undefined
Latexmk: Log file says output to 'just-testing.dvi'
Latexmk: Found biber source file(s) [just-testing.bcf]
Latexmk: Summary of warnings:
Latex failed to resolve 1 citation(s)
Latexmk: applying rule 'latex'...
Rule 'latex': File changes, etc:
Changed files, or newly in use since previous run(s):
'just-testing.run.xml'
------------
Run number 3 of rule 'latex'
------------
------------
Running 'latex -recorder "just-testing.tex"'
------------
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
restricted \write18 enabled.
entering extended mode
(./just-testing.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/memoir.cls
Document Class: memoir 2011/03/06 v3.6j configurable book, report, article docu
ment class
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/ifetex/ifetex.sty
(/usr/local/texlive/2012/texmf-dist/tex/plain/ifetex/ifetex.tex))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ifluatex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/etex-pkg/etex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mem12.clo)
(/usr/local/texlive/2012/texmf-dist/tex/latex/memoir/mempatch.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/lmodern.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/dvips.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex2.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/logreq/logreq.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-dm.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/blx-compat.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/authoryear.bbx
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/bbx/standard.bbx))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/cbx/authoryear-comp.cbx)
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
(./just-testing.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/lm/t1lmr.fd)
No file just-testing.bbl.
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/ot1lmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omllmm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omslmsy.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/lm/omxlmex.fd)
LaTeX Warning: Citation 'Levene:2010hob' on page 1 undefined on input line 18.
LaTeX Warning: Empty bibliography on input line 22.
[1] (./just-testing.aux)
LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex) just-testing
(biblatex) and rerun LaTeX afterwards.
)
Output written on just-testing.dvi (1 page, 2852 bytes).
Transcript written on just-testing.log.
Latexmk: Non-existent bbl file 'just-testing.bbl'
No file just-testing.bbl.
Latexmk: Citation 'Levene:2010hob' on page 1 undefined
Latexmk: Log file says output to 'just-testing.dvi'
Latexmk: Found biber source file(s) [just-testing.bcf]
Latexmk: Summary of warnings:
Latex failed to resolve 1 citation(s)
Latexmk: All targets (just-testing.dvi) are up-to-date
Collected error summary (may duplicate other messages):
biber just-testing: Could not find all biber source files for 'just-testing'
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs of latex/pdflatex.
On 26/01/2013, at 21:18 , Herbert Schulz <herbs at wideopenwest.com> wrote:
>
> On Jan 26, 2013, at 4:19 AM, Scot Mcphee <scot.mcphee at gmail.com> wrote:
>
>> Hi,
>>
>> Some weeks ago I started using biblatex and biber for the creation of my bibliography in my PhD. Initially my tests for this were on a test file, just to get a feel for the citation and bibliography styles.
>>
>> Now I've applied it to my first actual thesis chapter and I've found that it no longer works.
>>
>> I even went back to the original test file and found it no longer works either.
>>
>> TeXshop reports the following;
>>
>> Latexmk: Failed to find one or more biber source files:
>> NONE
>>
>> Is the problem it cannot find the .bib file? kpsewhich reports
>>
>> $ kpsewhich phd.bib
>> /Users/smcphee/Library/texmf/bibtex/bib/phd.bib
>>
>> In the .BCF file which is generated, there is a 'bibdata' section;
>> <bcf:bibdata section="0">
>> <bcf:datasource type="file" datatype="bibtex">phd.bib</bcf:datasource>
>> </bcf:bibdata>
>>
>> and a collection of the citekeys appears after that.
>>
>> In my header/preamble there is this
>>
>> \usepackage[backend=biber,sorting=nyt,citestyle=authoryear-comp,bibstyle=authoryear]{biblatex}
>> \addbibresource{phd.bib}
>>
>> There is no complaint that phd.bib can't be found in the TexShop console, but if I trash all the aux files and recompile it complains that every single citation is undefined, and that the "bbl" file is missing.
>>
>> What is going on, or how do I narrow the source of the problem down?
>>
>> many thanks
>> scot
>
> Howdy,
>
> The .bib file is in the correct place.
>
> Did you recently update your TeX distribution (using tlmgr or TeX Live Utility)?
>
> Without a sample file and copy of the console output it's hard to figure out.
>
> It is very typical that an initial run of (pdf/xe)latex will produce a series of errors since the citation information isn't available at the time the initial run is made but only after the biber run. So this sounds as though you are not looking at the last run after biber is run.
>
> Could you tell me what version of latexmk you are running? It should be on one of the early lines in TeXShop's Console output. How about the version of biber and the biblatex package?
> Good Luck,
>
> Herb Schulz
> (herbs at wideopenwest dot com)
>
>
>
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