Error in re-building vignettes:
  ...
make[1]: Entering directory `/cygdrive/d/temp/RtmpArlXSD'
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make[1]: Entering directory `/cygdrive/d/temp/RtmpArlXSD'
d:/Compiler/gcc-4.9.3/mingw_64/bin/gfortran -m64   -O2  -mtune=core2 -c  d:/RCompile/CRANpkg/lib/3.3/rodeo/fortran/integrators.f95 -o d:/RCompile/CRANpkg/lib/3.3/rodeo/fortran/integrators.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gfortran -m64   -O2  -mtune=core2 -c  d:/RCompile/CRANpkg/local/3.3/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.f95 -o d:/RCompile/CRANpkg/local/3.3/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gfortran -m64   -O2  -mtune=core2 -c  D:/temp/RtmpArlXSD/file2e3cc241de3.f95 -o D:/temp/RtmpArlXSD/file2e3cc241de3.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gfortran -m64   -O2  -mtune=core2 -c  D:/temp/RtmpArlXSD/file2e3c25b973c2.f95 -o D:/temp/RtmpArlXSD/file2e3c25b973c2.o
d:/Compiler/gcc-4.9.3/mingw_64/bin/gfortran -m64 -shared -s -static-libgcc -o D:/temp/RtmpArlXSD/rk52e3c3452158e.dll tmp.def d:/RCompile/CRANpkg/lib/3.3/rodeo/fortran/integrators.o d:/RCompile/CRANpkg/local/3.3/rodeo.Rcheck/vign_test/rodeo/vignettes/examples/linked/waterSediment/functions.o D:/temp/RtmpArlXSD/file2e3cc241de3.o D:/temp/RtmpArlXSD/file2e3c25b973c2.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R-33~1.3/bin/x64 -lR
make[1]: Leaving directory `/cygdrive/d/temp/RtmpArlXSD'
make[1]: Entering directory `/cygdrive/d/temp/RtmpArlXSD'
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make[1]: Entering directory `/cygdrive/d/temp/RtmpArlXSD'
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Sorry, but pdflatex did not succeed.

You may want to visit the MiKTeX project page, if you need help.

pandoc.exe: Error producing PDF
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS rodeoVignette.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output rodeoVignette.pdf --table-of-contents --toc-depth 3 --template "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmd\latex\default-1.17.0.2.tex" --number-sections --highlight-style tango --latex-engine pdflatex --include-in-header preamble-latex.tex --variable graphics=yes --variable "geometry:margin=1in" --bibliography references.bib --filter pandoc-citeproc' had status 43
Error: processing vignette 'rodeoVignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 43
Execution halted