latexmk version is Latexmk, John Collins, 17 Jan. 2018. Version 4.55, OS is Windows with MiKTeX2.9, console emulator I use cmder, which include perl. The perl version is perl5 (revision 5 version 24 subversion 1)

here is my folder structure:

top_dir
|-main.tex
|-charpter1
  |-chap1.tex
|-charpter2
  |-chap2.tex
|-reference
  |-ref.tex
  |-ref_db.bib

My main.tex looks like:

\documentclass[oneside,a4paper]{book}

\begin{document}

\include{chapter1/chap1}
\include{chapter2/chap2}
\include{reference/ref}

\end{document}

Meanwhile, in ref.tex,:

\clearpage
\bibliographystyle{unsrt}
\bibliography{reference/ref_db}

other files are empty.

I can get every correct by using following command:

latexmk -pdf -bibtex --interaction=nonstopmode -pdflatex="pdflatex %O %S"

However, I want to change all outputs to a output dir, then I change my build command to:

latexmk -pdf -bibtex --interaction=nonstopmode -outdir=build -pdflatex="pdflatex -output-directory=build %O %S"

it do can generate output dir namely build, but it will fail when generate reference, it said:

latexmk -pdf -bibtex -outdir=build --interaction=nonstopmode -pdflatex="pdflatex %O %S"
Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Latexmk: making output directory 'build'
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
Latexmk: I am working around an offset relative to my system time by
   -167 secs for file times in directory 'build/'.
------------
Running 'pdflatex  --interaction=nonstopmode -recorder -output-directory="build"  "main.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit)
entering extended mode
(main.tex
LaTeX2e <2017-04-15>
Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\book.cls"
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\bk10.clo"))
(Y:\Latex\latexmk_test\build\main.aux) (chapter1/chap1.tex) (chapter2/chap2.tex
) (reference/ref.tex
No file main.bbl.
) (Y:\Latex\latexmk_test\build\main.aux
(Y:\Latex\latexmk_test\build\chapter1/chap1.aux)
(Y:\Latex\latexmk_test\build\chapter2/chap2.aux)
(Y:\Latex\latexmk_test\build\reference/ref.aux)) )
No pages of output.
Transcript written on Y:\Latex\latexmk_test\build\main.log.
=== TeX engine is 'pdfTeX'
Latexmk: Non-existent bbl file 'build/main.bbl'
 No file main.bbl.
Latexmk: Log file says no output from latex
Latexmk: For rule 'pdflatex', no output was made
Latexmk: Found bibliography file(s) [reference/ref_db.bib]
Latexmk: applying rule 'bibtex build/main'...
Rule 'bibtex build/main': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'build/main.aux'
   Non-existent destination files:
      'build/main.bbl'
------------
Run number 1 of rule 'bibtex build/main'
------------
For rule 'bibtex build/main', running '&run_bibtex(  )' ...
------------
Running 'bibtex  "main"'
------------
This is BibTeX, Version 0.99d (MiKTeX 2.9.6500 64-bit)
The top-level auxiliary file: main.aux
A level-1 auxiliary file: chapter1/chap1.aux
A level-1 auxiliary file: chapter2/chap2.aux
A level-1 auxiliary file: reference/ref.aux
The style file: unsrt.bst
I couldn't open database file reference/ref_db.bib
---line 3 of file reference/ref.aux
 : \bibdata{reference/ref_db
 :                          }
I'm skipping whatever remains of this command
I found no \citation commands---while reading file main.aux
I found no database files---while reading file main.aux
(There were 3 error messages)
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  bibtex build/main: Bibtex errors: See file 'build/main.blg'
  pdflatex: failed to create output file
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs of latex/pdflatex.

Here is the compile pass result without "build" output folder

 latexmk -pdf -bibtex --interaction=nonstopmode -pdflatex="pdflatex %O %S"
Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
Latexmk: I am working around an offset relative to my system time by
   -166 secs for file times in directory ''.
------------
Running 'pdflatex  --interaction=nonstopmode -recorder  "main.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit)
entering extended mode
(main.tex
LaTeX2e <2017-04-15>
Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\book.cls"
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\bk10.clo")) (main.aux)
(chapter1/chap1.tex) (chapter2/chap2.tex) (reference/ref.tex
No file main.bbl.
) (main.aux (chapter1/chap1.aux) (chapter2/chap2.aux) (reference/ref.aux)) )
No pages of output.
Transcript written on main.log.
=== TeX engine is 'pdfTeX'
Latexmk: Non-existent bbl file 'main.bbl'
 No file main.bbl.
Latexmk: Log file says no output from latex
Latexmk: For rule 'pdflatex', no output was made
Latexmk: Found bibliography file(s) [reference/ref_db.bib]
Latexmk: applying rule 'bibtex main'...
Rule 'bibtex main': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'main.aux'
   Non-existent destination files:
      'main.bbl'
------------
Run number 1 of rule 'bibtex main'
------------
For rule 'bibtex main', running '&run_bibtex(  )' ...
------------
Running 'bibtex  "main"'
------------
This is BibTeX, Version 0.99d (MiKTeX 2.9.6500 64-bit)
The top-level auxiliary file: main.aux
A level-1 auxiliary file: chapter1/chap1.aux
A level-1 auxiliary file: chapter2/chap2.aux
A level-1 auxiliary file: reference/ref.aux
The style file: unsrt.bst
I found no \citation commands---while reading file main.aux
Database file #1: reference/ref_db.bib
(There was 1 error message)
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'chapter1/chap1.aux'
      'chapter2/chap2.aux'
      'main.aux'
      'main.bbl'
      'reference/ref.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --interaction=nonstopmode -recorder  "main.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit)
entering extended mode
(main.tex
LaTeX2e <2017-04-15>
Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\book.cls"
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\bk10.clo")) (main.aux
(chapter1/chap1.aux) (chapter2/chap2.aux) (reference/ref.aux))
(chapter1/chap1.tex) (chapter2/chap2.tex) (reference/ref.tex (main.bbl

LaTeX Warning: Empty `thebibliography' environment on input line 3.

)) [1{C:/Users/haochen/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
(main.aux (chapter1/chap1.aux) (chapter2/chap2.aux) (reference/ref.aux)) )<C:/P
rogram Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmbx12.pfb><C:/Program F
iles/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr10.pfb>
Output written on main.pdf (1 page, 17996 bytes).
Transcript written on main.log.
=== TeX engine is 'pdfTeX'
Latexmk: Found input bbl file 'main.bbl'
Latexmk: Log file says output to 'main.pdf'
Latexmk: Found bibliography file(s) [reference/ref_db.bib]
Latexmk: applying rule 'bibtex main'...
Rule 'bibtex main': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'reference/ref.aux'
------------
Run number 2 of rule 'bibtex main'
------------
For rule 'bibtex main', running '&run_bibtex(  )' ...
------------
Running 'bibtex  "main"'
------------
This is BibTeX, Version 0.99d (MiKTeX 2.9.6500 64-bit)
The top-level auxiliary file: main.aux
A level-1 auxiliary file: chapter1/chap1.aux
A level-1 auxiliary file: chapter2/chap2.aux
A level-1 auxiliary file: reference/ref.aux
The style file: unsrt.bst
I found no \citation commands---while reading file main.aux
Database file #1: reference/ref_db.bib
(There was 1 error message)
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'reference/ref.aux'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  --interaction=nonstopmode -recorder  "main.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6500 64-bit)
entering extended mode
(main.tex
LaTeX2e <2017-04-15>
Babel <3.15> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\book.cls"
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\bk10.clo")) (main.aux
(chapter1/chap1.aux) (chapter2/chap2.aux) (reference/ref.aux))
(chapter1/chap1.tex) (chapter2/chap2.tex) (reference/ref.tex (main.bbl

LaTeX Warning: Empty `thebibliography' environment on input line 3.

)) [1{C:/Users/haochen/AppData/Local/MiKTeX/2.9/pdftex/config/pdftex.map}]
(main.aux (chapter1/chap1.aux) (chapter2/chap2.aux) (reference/ref.aux)) )<C:/P
rogram Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmbx12.pfb><C:/Program F
iles/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr10.pfb>
Output written on main.pdf (1 page, 17996 bytes).
Transcript written on main.log.
=== TeX engine is 'pdfTeX'
Latexmk: Found input bbl file 'main.bbl'
Latexmk: Log file says output to 'main.pdf'
Latexmk: Found bibliography file(s) [reference/ref_db.bib]
Latexmk: All targets (main.pdf) are up-to-date
  • If you really need to use a build directory, I suggest to use github.com/reitzig/ltx2any instead of latexmk – samcarter May 8 at 8:55
  • Your invocation of latexmk needs to be changed. You've specified -auxdir as an option to latexmk, but -output-directory only within the pdflatex command. You need to specify the output directory as an option to latexmk (which then passes it to pdflatex, but after latexmk has adjusted its expectations about directories). The following should work: latexmk -pdf -outdir=build --interaction=nonstopmode -pdflatex="pdflatex %O %S", or even just latexmk -pdf -outdir=build --interaction=nonstopmode (unless you have a configuration file overriding latexmk's defaults). – John Collins May 8 at 12:55
  • 1
    @daleif The problem you mention arose when a user specified \bibliography{../../library} (starting with ../. That's not the case here, given the \bibdata line that the OP reports. The setup that is described is one for which latexmk's invocation of bibtex does work. – John Collins May 8 at 12:59
  • @samcarter Latexmk does work with -output-directory, and I use it all the time, including with bibliographies. The problem here appears to be that the OP has invoked latexmk in the wrong way. – John Collins May 8 at 13:01
up vote 2 down vote accepted

The problem arose because the OP was using msys and its Perl together with a native MS-Windows implementation of bibtex (in MiKTeX).

There are two solutions

  1. Update to latexmk 4.56 (which will be on CTAN as soon as the files propagate to the mirror sites, and will then appear in the standard distributions, TeXLive and MiKTeX). It's also available at http://personal.psu.edu/jcc8/latexmk/

  2. Install a native MS-Windows Perl, and ensure that gets used to run latexmk.

Under the hood details (which may be of use to users with related problems): Msys and MinGW give a Unix emulation layer on top of MS-Windows; from latexmk's point-of-view there's effectively a mixture of operating systems, MS-Windows and Unix, particularly as regards names of files. There's some trickery that latexmk goes through to persuade bibtex to work when there is (a) an output directory, (b) included files in the source document, and (c) a .bib file is in the document directory or a subdirectory. The trickery involves a temporary change of directory with a setting of BIBINPUTS and BSTINPUTS. Msys's Perl provides the name of the current directory in Unix form, but it needs to be translated (quite trivially) to MS-Windows form to be useful for bibtex. It turns out latexmk already had a solution to the same problem for cygwin, so once the diagnosis had been made (off-line), the fix was easy.

  • very appricate for the excellent debug off-line with John! – How Chen May 26 at 9:04

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