# Building PDF with pdflatex and biber

I am trying to build pdf latex out of source with biber and biblatex, but i get `LaTex warning: There were undefined references. Please (re)run Biber on the file : report` during the third pdflatex run. And the reference appears at the end of the document but the citation simply remains `[test]`.

My source tree is the following:

``````root
src/  - .tex files and .bib
junk/ - build files
pdf/  - final .pdf file
Makefile
``````

and my Makefile:

``````SHELL=/bin/sh
TEXFILE=report
SRC=src
FINAL=pdf
OUT=junk

.SUFFIXES:
.SUFFIXES: .bib .pdf .tex
.PHONY: clean

run: \$(FINAL)/\$(TEXFILE).pdf

\$(FINAL)/\$(TEXFILE).pdf: \$(OUT)/\$(TEXFILE).bbl \$(SRC)/\$(TEXFILE).tex
cd \$(SRC) && pdflatex -draftmode -output-directory ../\$(OUT) \$(TEXFILE).tex
cd \$(SRC) && pdflatex -output-directory ../\$(OUT) \$(TEXFILE).tex
cp \$(OUT)/\$(TEXFILE).pdf \$(FINAL)/\$(TEXFILE).pdf

\$(OUT)/\$(TEXFILE).bbl: \$(OUT)/\$(TEXFILE).aux
biber --output-directory \$(OUT) --input-directory \$(SRC) \$(TEXFILE)

\$(OUT)/\$(TEXFILE).aux: \$(SRC)/\$(TEXFILE).bib \$(SRC)/*.tex
cd \$(SRC) && pdflatex -draftmode -output-directory ../\$(OUT) \$(TEXFILE).tex

clean:
rm -rf \$(OUT)/*
``````

Thank You for any help or advice!

• Check the log- and the blg-file for errors. – Ulrike Fischer Oct 28 '16 at 13:29
• The title is very misleading. You want to build a pdf using pdflatex and biber. ou are not trying to build the binaries. – Johannes_B Oct 28 '16 at 13:41
• Biber doesn't use the `.aux` file (BibTeX does) but the `.bcf` file: `biber report.bcf` (where the extension is omissible). If you are using the Makefile, however, what's the advantage of this folder structure? Just run `make clean` when you're done.... – jon Oct 28 '16 at 15:37
• Well biber finds the .bcf files and the .bbl is generated, the reference section is also present. The problem that the citations are not resolved. I use this structure because i don't want to run make clean every time I build latex while i still work on the document, however i would still like to keep my directories clean. – user2153980 Nov 3 '16 at 15:00