[OS X TeX] Latexmk errors that I can't diagnose

Herbert Schulz herbs at wideopenwest.com
Sun Jul 7 15:45:34 EDT 2013 

On Jul 7, 2013, at 2:32 PM, "Nathan A. Paxton" <napaxton at gmail.com> wrote:

> 	I replaced the Texshop bin files as well. The latexmk that's in v4.35 is the one at
> 
>> Macintosh:~ user$ which latexmk/usr/texbin/latexmk
>> Macintosh:~ user$ latexmk -v
>> Latexmk, John Collins, 11 Nov. 2012. Version 4.35
>> Macintosh:~ user$ 

Howdy,

This is NOT the latexmk that is used by the TeXShop engines. I use a local copy of latexmk, in ~/Library/TeXShop/bin/tslatexmk, to ensure that the engines continue to work properly if something radically wrong happens with the latexmk in the TeX Live distribution. My engines have been tested (well, I can't foresee every possibility) with the local version.

>> 
> 	I went to typesetting a (mostly) minimal file, and here's what I get for the log output :
> 
>> Latexmk: This is Latexmk, John Collins, 2 July 2013, version: 4.37.
>> **** Report bugs etc to John Collins <collins at phys.psu.edu>. ****
>> Rule 'biber minimalcites': File changes, etc:
>>   Non-existent destination files:
>>      'minimalcites.bbl'
>> ------------
>> Run number 1 of rule 'biber minimalcites'
>> ------------
>> ------------
>> Running 'biber  "minimalcites"'
>> ------------
>> Latexmk: applying rule 'biber minimalcites'...
>> data source /var/folders/wp/xq1g9lt13m16gjnd3z8wfl4w0000gn/T/par-6e617468616e706178746f6e/cache-ef42c8d5d44e40bdd24828b0ae70de275e379c88//inc/lib/Biber/LaTeX/recode_data.xml not found in .
>> INFO - This is Biber 1.5
>> INFO - Logfile is 'minimalcites.blg'
>> Latexmk: Failed to find one or more biber source files:
>>  NONE
>> Rule 'pdflatex': File changes, etc:
>>   Changed files, or newly in use since previous run(s):
>>      'minimalcites.tex'

Huh! Did you really clean up your files? I've NEVER seen a run of bibtex/biber without a run of pdflatex first!!!

>> ------------
>> Run number 1 of rule 'pdflatex'
>> ------------
>> ------------
>> Running 'pdflatex --shell-escape --synctex=1 --file-line-error  -recorder  "minimalcites.tex"'
>> ------------
>> Latexmk: applying rule 'pdflatex'...
>> This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
>> \write18 enabled.
>> entering extended mode
>> (./minimalcites.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,
>> piedmontese, polish, portuguese, romanian, romansh, russian, sanskrit, serbian
>> , serbianc, slovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, u
>> ppersorbian, welsh, loaded.
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/article.cls
>> Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/size11.clo))
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
>> 
>> Package biblatex Warning: No "backend" specified, using Biber backend.
>> (biblatex)                To use BibTeX, load biblatex with 
>> (biblatex)                the "backend=bibtex" option.
>> 
>> (/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/etex-pkg/etex.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/generic/oberdiek/ifluatex.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/blx-natbib.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.cbx)
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
>> (./minimalcites.aux)
>> No file minimalcites.bbl.
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/omscmr.fd)
>> 
>> LaTeX Warning: Citation 'collier2007a' on page 1 undefined on input line 10.
>> 
>> 
>> LaTeX Warning: Citation 'frieden2006a' on page 1 undefined on input line 11.
>> 
>> 
>> LaTeX Warning: Citation 'haslamschaferbeaudet2009a' on page 1 undefined on inpu
>> t line 12.
>> 
>> 
>> LaTeX Warning: Citation 'sen1999a' on page 1 undefined on input line 13.
>> 
>> [1{/Users/nathanpaxton/Library/texlive/2012/texmf-var/fonts/map/pdftex/updmap/p
>> dftex.map}] (./minimalcites.aux)
>> 
>> LaTeX Warning: There were undefined references.
>> 
>> 
>> Package biblatex Warning: Please (re)run Biber on the file:
>> (biblatex)                minimalcites
>> (biblatex)                and rerun LaTeX afterwards.
>> 
>> )</usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb
>>> </usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
>> /usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
>> Output written on minimalcites.pdf (1 page, 33913 bytes).
>> SyncTeX written on minimalcites.synctex.gz.
>> Transcript written on minimalcites.log.
>> Latexmk: Non-existent bbl file 'minimalcites.bbl'
>> No file minimalcites.bbl.
>> Latexmk: Citation 'collier2007a' on page 1 undefined 
>> Latexmk: Citation 'frieden2006a' on page 1 undefined 
>> Latexmk: Citation 'haslamschaferbeaudet2009a' on page 1 undefined 
>> Latexmk: Citation 'haslamschaferbeaudet2009a' on page 1 undefined 
>> Latexmk: Citation 'sen1999a' on page 1 undefined 
>> Latexmk: Log file says output to 'minimalcites.pdf'
>> Latexmk: Found biber source file(s) [minimalcites.bcf]
>> Latexmk: Summary of warnings:
>>  Latex failed to resolve 5 citation(s)
>> Rule 'pdflatex': File changes, etc:
>>   Changed files, or newly in use since previous run(s):
>>      'minimalcites.aux'
>> ------------
>> Run number 2 of rule 'pdflatex'
>> ------------
>> ------------
>> Running 'pdflatex --shell-escape --synctex=1 --file-line-error  -recorder  "minimalcites.tex"'
>> ------------
>> Latexmk: applying rule 'pdflatex'...
>> This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
>> \write18 enabled.
>> entering extended mode
>> (./minimalcites.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,
>> piedmontese, polish, portuguese, romanian, romansh, russian, sanskrit, serbian
>> , serbianc, slovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, u
>> ppersorbian, welsh, loaded.
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/article.cls
>> Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/size11.clo))
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.sty
>> 
>> Package biblatex Warning: No "backend" specified, using Biber backend.
>> (biblatex)                To use BibTeX, load biblatex with 
>> (biblatex)                the "backend=bibtex" option.
>> 
>> (/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/etex-pkg/etex.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/generic/oberdiek/ifluatex.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/blx-natbib.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.cbx)
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/biblatex.cfg)))
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
>> (./minimalcites.aux)
>> No file minimalcites.bbl.
>> (/usr/local/texlive/2012/texmf-dist/tex/latex/base/omscmr.fd)
>> 
>> LaTeX Warning: Citation 'collier2007a' on page 1 undefined on input line 10.
>> 
>> 
>> LaTeX Warning: Citation 'frieden2006a' on page 1 undefined on input line 11.
>> 
>> 
>> LaTeX Warning: Citation 'haslamschaferbeaudet2009a' on page 1 undefined on inpu
>> t line 12.
>> 
>> 
>> LaTeX Warning: Citation 'sen1999a' on page 1 undefined on input line 13.
>> 
>> [1{/Users/nathanpaxton/Library/texlive/2012/texmf-var/fonts/map/pdftex/updmap/p
>> dftex.map}] (./minimalcites.aux)
>> 
>> LaTeX Warning: There were undefined references.
>> 
>> 
>> Package biblatex Warning: Please (re)run Biber on the file:
>> (biblatex)                minimalcites
>> (biblatex)                and rerun LaTeX afterwards.
>> 
>> )</usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb
>>> </usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb><
>> /usr/local/texlive/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
>> Output written on minimalcites.pdf (1 page, 33913 bytes).
>> SyncTeX written on minimalcites.synctex.gz.
>> Transcript written on minimalcites.log.
>> Latexmk: Non-existent bbl file 'minimalcites.bbl'
>> No file minimalcites.bbl.
>> Latexmk: Citation 'collier2007a' on page 1 undefined 
>> Latexmk: Citation 'frieden2006a' on page 1 undefined 
>> Latexmk: Citation 'haslamschaferbeaudet2009a' on page 1 undefined 
>> Latexmk: Citation 'haslamschaferbeaudet2009a' on page 1 undefined 
>> Latexmk: Citation 'sen1999a' on page 1 undefined 
>> Latexmk: Log file says output to 'minimalcites.pdf'
>> Latexmk: Found biber source file(s) [minimalcites.bcf]
>> Latexmk: Summary of warnings:
>>  Latex failed to resolve 5 citation(s)
>> Collected error summary (may duplicate other messages):
>>  biber minimalcites: Could not find all biber source files for 'minimalcites'
>> Latexmk: Use the -f option to force complete processing,
>> unless error was exceeding maximum runs of latex/pdflatex.
>> Latexmk: All targets (minimalcites.pdf) are up-to-date
>> 
> 
> 
> -----
> Nathan Paxton
> napaxton at gmail.com
> 
> If every professor who backed a lunatic politician were to be sacked, half the interesting minds in academia would be lost.
> 	- The Economist, 5 Jan 2002
> 
> A morning without coffee is like something without something else.
> 
> On 7 Jul 2013, at 12:47 PM, Herbert Schulz wrote:
> 
>> 
>> On Jul 7, 2013, at 11:29 AM, "Nathan A. Paxton" <napaxton at gmail.com> wrote:
>> 
>>> 	Hi all,
>>> 
>>> 	I'm trying to diagnose a pdflatexmk error.
>>> 
>>> 	I'm using Texshop 3.18 on Lion (10.7.5), with latexmk 4.35 and the latest engines from Herbert Schulz (4.37, I think), pn TL 2012.  In the last couple of days, when I try to compile a syllabus with a bunch of references, the file no longer compiles, and it generates the following errors.
>>> 
>>> - Could this be the result of using latexmk4.35 and the engines for 4.37? How can I update latexmk (without going to 2013, which I'm not ready to do quite yet) or downgrade the Schulz engines?
>>> - What else do we need to know to make this work?
>>> 
>>> 
>>> Latexmk: Non-existent bbl file 'syllabus.bbl'
>>> No file syllabus.bbl.
>>> Latexmk: Citation 'collier2007a' on page 4 undefined 
>>> Latexmk: Citation 'frieden2006a' on page 4 undefined 
>>> 
>>> [snip 34 more similar errors]
>>> 
>>> Latexmk: Citation 'chang2011a' on page 9 undefined 
>>> Latexmk: Log file says output to 'syllabus.pdf'
>>> Latexmk: Found biber source file(s) [syllabus.bcf]
>>> Latexmk: Summary of warnings:
>>> Latex failed to resolve 36 citation(s)
>>> Collected error summary (may duplicate other messages):
>>> biber syllabus: Could not find all biber source files for 'syllabus'
>>> Latexmk: Use the -f option to force complete processing,
>>> unless error was exceeding maximum runs of latex/pdflatex.
>>> -----
>>> Nathan Paxton
>>> napaxton at gmail.com
>> Howdy,
>> 
>> First (minor) question: why are you using the 4.37 engines with 4.35? If you downloaded the Latexmk4.37TeXShop.zip there was another folder with a tslatexmk folder containing the update to latexmk 4.37. In any case those engines should work fine with 4.35.
>> 
>> Could you try to clean up all the files from the previous run. Is there, in fact a syllabus.bbl file present? Does the Console show that biber has been run? 
>> 
>> Good Luck,
>> 
>> Herb Schulz
>> (herbs at wideopenwest dot com)


Please send me your minimalcites.tex, the associated .bib file (unless it's embedded in the .tex file) and any other associated files.

Good Luck,

Herb Schulz
(herbs at wideopenwest dot com)

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