/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS thesis.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output thesis.tex --table-of-contents --toc-depth 2 --template monashthesis.tex --number-sections --highlight-style tango --latex-engine pdflatex --biblatex --top-level-division=chapter --variable tables=yes --standalone 
output file: thesis.knit.md

tlmgr search --file --global '/authoryear-comp.dbx'
Unknown directive ...containerchecksum 400c4de374d02934965b5488f37c1b052ade07c2acfae957c9846390b2b78315c6aed2b533a2271bbacabd77c40536b63973bd42e2686f4c6d25d1f4c5b4709e... , please fix it! at /usr/local/texlive/2015/tlpkg/TeXLive/TLPOBJ.pm line 210, <$retfh> line 6202.
tlmgr search --file --global '/biblatex-dm.cfg'
Unknown directive ...containerchecksum 400c4de374d02934965b5488f37c1b052ade07c2acfae957c9846390b2b78315c6aed2b533a2271bbacabd77c40536b63973bd42e2686f4c6d25d1f4c5b4709e... , please fix it! at /usr/local/texlive/2015/tlpkg/TeXLive/TLPOBJ.pm line 210, <$retfh> line 6202.
! Package keyval Error: giveninits undefined.

Error: Failed to compile thesis.tex. See thesis.log for more info.
In addition: Warning messages:
1: running command ''tlmgr' search --file --global '/authoryear-comp.dbx'' had status 25 
2: running command ''tlmgr' search --file --global '/biblatex-dm.cfg'' had status 25 
Please delete thesis.Rmd after you finish debugging the error.
Execution halted

Family: gaussian 
Link function: identity 
Formula:
pm7_28 ~ s(X, Y, by = DEM) + s(DEM)
Parametric coefficients:
           Estimate   Std. Error   t value   Pr(>|t|)
(Intercept)     0          0          NA         NA
Approximate significance of smooth terms:
               edf    Ref.df      F       P-value    
s(X,Y):DEM  15.819   20.078   314.7    <0.0000002 ***
s(DEM)       1.001    1.001   601.5    <0.0000002 ***
--
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Rank: 39/40
R-sq.(adj) =  0.672   Deviance explained =   76%
-REML = 187.95  Scale est. = 16.214    n = 60

/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS thesis.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output thesis.tex --table-of-contents --toc-depth 2 --template monashthesis.tex --number-sections --highlight-style tango --latex-engine pdflatex --biblatex --chapters --variable tables=yes --standalone 
output file: thesis.knit.md

[pandoc warning] --chapters is deprecated. Use --top-level-division=chapter instead.
Latexmk: applying rule 'biber thesis'...
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.
Rule 'biber thesis': File changes, etc:
   Non-existent destination files:
      'thesis.bbl'
------------
Run number 1 of rule 'biber thesis'
------------
------------
Running 'biber  "thesis"'
------------
INFO - This is Biber 2.9
INFO - Logfile is 'thesis.blg'
INFO - Reading 'thesis.bcf'
INFO - Found 9 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'thesisrefs.bib' for section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source 'thesisrefs.bib'
INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 'nyt' and locale 'en-US'
INFO - No sort tailoring available for locale 'en-US'
INFO - Writing 'thesis.bbl' with encoding 'UTF-8'
INFO - Output to thesis.bbl
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
Latexmk: Found biber source file(s) [thesis.bcf thesisrefs.bib]
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'thesis.aux'
      'thesis.bbl'
   Non-existent destination files:
      'thesis.pdf'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -halt-on-error -interaction=batchmode -recorder  "thesis.tex"'
------------
=== TeX engine is 'pdfTeX'
Latexmk: Errors, so I did not complete making targets
Latexmk: Found input bbl file 'thesis.bbl'
Latexmk: References changed.
Latexmk: Found biber source file(s) [thesis.bcf thesisrefs.bib]
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'thesis.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs of latex/pdflatex.
Latexmk: This is Latexmk, John Collins, 12 Dec. 2017, version: 4.54c.

Output created: _book/thesis.pdf
Error in tools::file_path_as_absolute(output_file) : 
  file '_book/thesis.pdf' does not exist
Calls: <Anonymous> ... render_book -> render_cur_session -> <Anonymous> -> <Anonymous>
In addition: Warning message:
In file.rename(output, output2) :
  cannot rename file 'thesis.pdf' to '_book/thesis.pdf', reason 'No such file or directory'
Please delete thesis.Rmd after you finish debugging the error.
Execution halted

Exited with status 1.

The hydraulics of open channel flow: 


an introduction: basic principles, sediment motion, 


hydraulic modelling, design of


hydraulic structures

The hydraulics of open channel flow: an introduction: basic principles, 
sediment motion, hydraulic modelling, design of hydraulic structures

output file: thesis.knit.md

! Package xkeyval Error: `giveninits' undefined in families `blx@opt@pre'.

Error: Failed to compile thesis.tex. See thesis.log for more info.
Execution halted

Exited with status 1.