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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!

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    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
  • 1
    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

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