Error in re-building vignettes:
  ...
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = "gene"
Joining, by = "gene"
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = "gene"
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = "gene"
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = "gene"
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Joining, by = "gene"
Joining, by = c("group", "gene")
Joining, by = c("group", "gene")
Parsed with column specification:
cols(
  ref = col_double(),
  target = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
You are recommended to install the tinytex package to build PDF.FALSE
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'qpcr_analysis.aux'
   Non-existent destination files:
      'qpcr_analysis.pdf'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -halt-on-error -interaction=batchmode -recorder  "qpcr_analysis.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
Latexmk: List of undefined refs and citations:
  Reference `table1' on page 5 undefined on input line 511
  Reference `table2' on page 5 undefined on input line 512
  Reference `table3' on page 5 undefined on input line 515
  Reference `table4' on page 5 undefined on input line 515
  Reference `table5' on page 5 undefined on input line 518
  Reference `table6' on page 5 undefined on input line 522
Latexmk: Summary of warnings:
  Latex failed to resolve 6 reference(s)
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 256
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs of latex/pdflatex.
Latexmk: Errors, so I did not complete making targets

Latexmk, John Collins, 1 January 2015. Version 4.41
Warning: Your latexmk version seems to be too low. You may need to update the latexmk package or your LaTeX distribution.
! LaTeX Error: \caption outside float.

Error: processing vignette ‘qpcr_analysis.Rmd’ failed with diagnostics:
Failed to compile qpcr_analysis.tex. See qpcr_analysis.log for more info.
Execution halted